Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases.

Science.gov (United States)

Lohman, Jeremy R; Ma, Ming; Osipiuk, Jerzy; Nocek, Boguslaw; Kim, Youngchang; Chang, Changsoo; Cuff, Marianne; Mack, Jamey; Bigelow, Lance; Li, Hui; Endres, Michael; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George N; Shen, Ben

2015-10-13

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.

Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases

Energy Technology Data Exchange (ETDEWEB)

Lohman, Jeremy; Ma, Ming; Osipiuk, Jerzy; Nocek, Boguslaw; Kim, Youngchang; Chang, Changsoo; Cuff, Marianne E.; Mack, Jamey; Bigelow, Lance; Li, Hui; Endres, Michael; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George N.; Shen, B G

2015-10-13

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.

Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases

Science.gov (United States)

Lohman, Jeremy R.; Ma, Ming; Osipiuk, Jerzy; Nocek, Boguslaw; Kim, Youngchang; Chang, Changsoo; Cuff, Marianne; Mack, Jamey; Bigelow, Lance; Li, Hui; Endres, Michael; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George N.; Shen, Ben

2015-01-01

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs. PMID:26420866

Identification and functional characterization of three type III polyketide synthases from Aquilaria sinensis calli

International Nuclear Information System (INIS)

Wang, Xiaohui; Zhang, Zhongxiu; Dong, Xianjuan; Feng, Yingying; Liu, Xiao; Gao, Bowen; Wang, Jinling; Zhang, Le; Wang, Juan; Shi, Shepo; Tu, Pengfei

2017-01-01

Type III polyketide synthases (PKSs) play an important role in biosynthesis of various plant secondary metabolites and plant adaptation to environmental stresses. Aquilaria sinensis (A. sinensis) is the main plant species for production of agarwood, little is known about its PKS family. In this study, AsCHS1 and two new type III PKSs, AsPKS1 and AsPKS2, were isolated and characterized in A. sinensis calli. The comparative sequence and phylogenetic analysis indicated that AsPKS1 and AsPKS2 belonged to non-CHS group different from AsCHS1. The recombinant AsPKS1 and AsPKS2 produced the lactone-type products, suggesting their different enzyme activities from AsCHS1. Three PKS genes had a tissues-specific pattern in A. sinensis. Moreover, we examined the expression profiles of three PKS genes in calli under different abiotic stresses and hormone treatments. AsCHS1 transcript was most significantly induced by salt stress, AsPKS1 abundance was most remarkably enhanced by CdCl 2 treatment, while AsPKS2 expression was most significantly induced by mannitol treatment. Furthermore, AsCHS1, AsPKS1 and AsPKS2 expression was enhanced upon gibberellins (GA3), methyl jasmonate (MeJA), or salicylic acid (SA) treatment, while three PKS genes displayed low transcript levels at the early stage under abscisic acid (ABA) treatment. In addition, three GFP:PKSs fusion proteins were localized in the cytoplasm and cell wall in Nicotiana benthamiana cells. These results indicated the multifunctional role of three type III PKSs in polyketide biosynthesis, plant resistance to abiotic stresses and signal transduction. - Highlights: • Two new PKS genes (AsPKS1 and AsPKS2) were isolated and characterized from A. sinensis. • The recombinant AsPKS1 and AsPKS2 catalyzed lactone-type products in vitro. • AsCHS1, AsPKS1 and AsPKS2 were involved in plant responses to abiotic stresses and hormone stimuli. • Our results also indicated that AsCHS1, AsPKS1 and AsPKS2 were predominantly localized

First discovery of two polyketide synthase genes for mitorubrinic acid and mitorubrinol yellow pigment biosynthesis and implications in virulence of Penicillium marneffei.

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Patrick C Y Woo

Full Text Available BACKGROUND: The genome of P. marneffei, the most important thermal dimorphic fungus causing respiratory, skin and systemic mycosis in China and Southeast Asia, possesses 23 polyketide synthase (PKS genes and 2 polyketide synthase nonribosomal peptide synthase hybrid (PKS-NRPS genes, which is of high diversity compared to other thermal dimorphic pathogenic fungi. We hypothesized that the yellow pigment in the mold form of P. marneffei could also be synthesized by one or more PKS genes. METHODOLOGY/PRINCIPAL FINDINGS: All 23 PKS and 2 PKS-NRPS genes of P. marneffei were systematically knocked down. A loss of the yellow pigment was observed in the mold form of the pks11 knockdown, pks12 knockdown and pks11pks12 double knockdown mutants. Sequence analysis showed that PKS11 and PKS12 are fungal non-reducing PKSs. Ultra high performance liquid chromatography-photodiode array detector/electrospray ionization-quadruple time of flight-mass spectrometry (MS and MS/MS analysis of the culture filtrates of wild type P. marneffei and the pks11 knockdown, pks12 knockdown and pks11pks12 double knockdown mutants showed that the yellow pigment is composed of mitorubrinic acid and mitorubrinol. The survival of mice challenged with the pks11 knockdown, pks12 knockdown and pks11pks12 double knockdown mutants was significantly better than those challenged with wild type P. marneffei (P<0.05. There was also statistically significant decrease in survival of pks11 knockdown, pks12 knockdown and pks11pks12 double knockdown mutants compared to wild type P. marneffei in both J774 and THP1 macrophages (P<0.05. CONCLUSIONS/SIGNIFICANCE: The yellow pigment of the mold form of P. marneffei is composed of mitorubrinol and mitorubrinic acid. This represents the first discovery of PKS genes responsible for mitorubrinol and mitorubrinic acid biosynthesis. pks12 and pks11 are probably responsible for sequential use in the biosynthesis of mitorubrinol and mitorubrinic acid

Nonribosomal biosynthesis of backbone-modified peptides

Science.gov (United States)

Niquille, David L.; Hansen, Douglas A.; Mori, Takahiro; Fercher, David; Kries, Hajo; Hilvert, Donald

2018-03-01

Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l-1), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.

Engineering a Polyketide Synthase for In Vitro Production of Adipic Acid

Energy Technology Data Exchange (ETDEWEB)

Hagen, A; Poust, S; De Rond, T; Fortman, JL; Katz, L; Petzold, CJ; Keasling, JD

2015-10-26

Polyketides have enormous structural diversity, yet polyketide synthases (PKSs) have thus far been engineered to produce only drug candidates or derivatives thereof. Thousands of other molecules, including commodity and specialty chemicals, could be synthesized using PKSs if composing hybrid PKSs from well-characterized parts derived from natural PKSs was more efficient. Here, using modern mass spectrometry techniques as an essential part of the design–build–test cycle, we engineered a chimeric PKS to enable production one of the most widely used commodity chemicals, adipic acid. To accomplish this, we introduced heterologous reductive domains from various PKS clusters into the borrelidin PKS’ first extension module, which we previously showed produces a 3-hydroxy-adipoyl intermediate when coincubated with the loading module and a succinyl-CoA starter unit. Acyl-ACP intermediate analysis revealed an unexpected bottleneck at the dehydration step, which was overcome by introduction of a carboxyacyl-processing dehydratase domain. Appending a thioesterase to the hybrid PKS enabled the production of free adipic acid. Using acyl-intermediate based techniques to “debug” PKSs as described here, it should one day be possible to engineer chimeric PKSs to produce a variety of existing commodity and specialty chemicals, as well as thousands of chemicals that are difficult to produce from petroleum feedstocks using traditional synthetic chemistry.

Molecular characterization of two alkylresorcylic acid synthases from Sordariomycetes fungi

DEFF Research Database (Denmark)

Ramakrishnan, Dhivya; Tiwari, Manish Kumar; Manoharan, Gomathi

2018-01-01

Two putative type III polyketide synthase genes (PKS) were identified from Sordariomycetes fungi. These two type III PKS genes from Sordaria macrospora (SmPKS) and Chaetomium thermophilum (CtPKS), shared 59.8% sequence identity. Both, full-length and truncated versions of type III PKSs were...

Towards Precision Engineering of Canonical Polyketide Synthase Domains: Recent Advances and Future Prospects

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Carmen L. Bayly

2017-02-01

Full Text Available Modular polyketide synthases (mPKSs build functionalized polymeric chains, some of which have become blockbuster therapeutics. Organized into repeating clusters (modules of independently-folding domains, these assembly-line-like megasynthases can be engineered by introducing non-native components. However, poor introduction points and incompatible domain combinations can cause both unintended products and dramatically reduced activity. This limits the engineering and combinatorial potential of mPKSs, precluding access to further potential therapeutics. Different regions on a given mPKS domain determine how it interacts both with its substrate and with other domains. Within the assembly line, these interactions are crucial to the proper ordering of reactions and efficient polyketide construction. Achieving control over these domain functions, through precision engineering at key regions, would greatly expand our catalogue of accessible polyketide products. Canonical mPKS domains, given that they are among the most well-characterized, are excellent candidates for such fine-tuning. The current minireview summarizes recent advances in the mechanistic understanding and subsequent precision engineering of canonical mPKS domains, focusing largely on developments in the past year.

Role of the phosphopantetheinyltransferase enzyme, PswP, in the biosynthesis of antimicrobial secondary metabolites by Serratia marcescens Db10.

Science.gov (United States)

Gerc, Amy J; Stanley-Wall, Nicola R; Coulthurst, Sarah J

2014-08-01

Phosphopantetheinyltransferase (PPTase) enzymes fulfil essential roles in primary and secondary metabolism in prokaryotes, archaea and eukaryotes. PPTase enzymes catalyse the essential modification of the carrier protein domain of fatty acid synthases, polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs). In bacteria and fungi, NRPS and PKS enzymes are often responsible for the biosynthesis of secondary metabolites with clinically relevant properties; these secondary metabolites include a variety of antimicrobial peptides. We have previously shown that in the Gram-negative bacterium Serratia marcescens Db10, the PPTase enzyme PswP is essential for the biosynthesis of an NRPS-PKS dependent antibiotic called althiomycin. In this work we utilize bioinformatic analyses to classify PswP as belonging to the F/KES subfamily of Sfp type PPTases and to putatively identify additional NRPS substrates of PswP, in addition to the althiomycin NRPS-PKS, in Ser. marcescens Db10. We show that PswP is required for the production of three diffusible metabolites by this organism, each possessing antimicrobial activity against Staphylococcus aureus. Genetic analyses identify the three metabolites as althiomycin, serrawettin W2 and an as-yet-uncharacterized siderophore, which may be related to enterobactin. Our results highlight the use of an individual PPTase enzyme in multiple biosynthetic pathways, each contributing to the ability of Ser. marcescens to inhibit competitor bacteria by the production of antimicrobial secondary metabolites. © 2014 The Authors.

Insights into natural products biosynthesis from analysis of 490 polyketide synthases from Fusarium.

Science.gov (United States)

Brown, Daren W; Proctor, Robert H

2016-04-01

Species of the fungus Fusarium collectively cause disease on almost all crop plants and produce numerous natural products (NPs), including some of the mycotoxins of greatest concern to agriculture. Many Fusarium NPs are derived from polyketide synthases (PKSs), large multi-domain enzymes that catalyze sequential condensation of simple carboxylic acids to form polyketides. To gain insight into the biosynthesis of polyketide-derived NPs in Fusarium, we retrieved 488 PKS gene sequences from genome sequences of 31 species of the fungus. In addition to these apparently functional PKS genes, the genomes collectively included 81 pseudogenized PKS genes. Phylogenetic analysis resolved the PKS genes into 67 clades, and based on multiple lines of evidence, we propose that homologs in each clade are responsible for synthesis of a polyketide that is distinct from those synthesized by PKSs in other clades. The presence and absence of PKS genes among the species examined indicated marked differences in distribution of PKS homologs. Comparisons of Fusarium PKS genes and genes flanking them to those from other Ascomycetes provided evidence that Fusarium has the genetic potential to synthesize multiple NPs that are the same or similar to those reported in other fungi, but that have not yet been reported in Fusarium. The results also highlight ways in which such analyses can help guide identification of novel Fusarium NPs and differences in NP biosynthetic capabilities that exist among fungi. Published by Elsevier Inc.

Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production

Energy Technology Data Exchange (ETDEWEB)

Yuzawa, Satoshi [Univ. of California, Berkeley, CA (United States); Deng, Kai [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States); Wang, George [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Baidoo, Edward E. K. [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Northen, Trent R. [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Adams, Paul D. [Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Katz, Leonard [Univ. of California, Berkeley, CA (United States); Synthetic Biology Research Center, Emeryville, CA (United States); Keasling, Jay D. [Univ. of California, Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Synthetic Biology Research Center, Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2016-08-22

Type I modular polyketide synthases (PKSs) are polymerases that utilize acyl-CoAs as substrates. Each polyketide elongation reaction is catalyzed by a set of protein domains called a module. Each module usually contains an acyltransferase (AT) domain, which determines the specific acyl-CoA incorporated into each condensation reaction. Although a successful exchange of individual AT domains can lead to the biosynthesis of a large variety of novel compounds, hybrid PKS modules often show significantly decreased activities. Using monomodular PKSs as models, we have systematically analyzed in this paper the segments of AT domains and associated linkers in AT exchanges in vitro and have identified the boundaries within a module that can be used to exchange AT domains while maintaining protein stability and enzyme activity. Importantly, the optimized domain boundary is highly conserved, which facilitates AT domain replacements in most type I PKS modules. To further demonstrate the utility of the optimized AT domain boundary, we have constructed hybrid PKSs to produce industrially important short-chain ketones. Our in vitro and in vivo analysis demonstrated production of predicted ketones without significant loss of activities of the hybrid enzymes. Finally, these results greatly enhance the mechanistic understanding of PKS modules and prove the benefit of using engineered PKSs as a synthetic biology tool for chemical production.

Engineered biosynthesis of regioselectively modified aromatic polyketides using bimodular polyketide synthases.

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Yi Tang

2004-02-01

Full Text Available Bacterial aromatic polyketides such as tetracycline and doxorubicin are a medicinally important class of natural products produced as secondary metabolites by actinomyces bacteria. Their backbones are derived from malonyl-CoA units by polyketide synthases (PKSs. The nascent polyketide chain is synthesized by the minimal PKS, a module consisting of four dissociated enzymes. Although the biosynthesis of most aromatic polyketide backbones is initiated through decarboxylation of a malonyl building block (which results in an acetate group, some polyketides, such as the estrogen receptor antagonist R1128, are derived from nonacetate primers. Understanding the mechanism of nonacetate priming can lead to biosynthesis of novel polyketides that have improved pharmacological properties. Recent biochemical analysis has shown that nonacetate priming is the result of stepwise activity of two dissociated PKS modules with orthogonal molecular recognition features. In these PKSs, an initiation module that synthesizes a starter unit is present in addition to the minimal PKS module. Here we describe a general method for the engineered biosynthesis of regioselectively modified aromatic polyketides. When coexpressed with the R1128 initiation module, the actinorhodin minimal PKS produced novel hexaketides with propionyl and isobutyryl primer units. Analogous octaketides could be synthesized by combining the tetracenomycin minimal PKS with the R1128 initiation module. Tailoring enzymes such as ketoreductases and cyclases were able to process the unnatural polyketides efficiently. Based upon these findings, hybrid PKSs were engineered to synthesize new anthraquinone antibiotics with predictable functional group modifications. Our results demonstrate that (i bimodular aromatic PKSs present a general mechanism for priming aromatic polyketide backbones with nonacetate precursors; (ii the minimal PKS controls polyketide chain length by counting the number of atoms

Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species.

Science.gov (United States)

Komaki, Hisayuki; Ichikawa, Natsuko; Hosoyama, Akira; Takahashi-Nakaguchi, Azusa; Matsuzawa, Tetsuhiro; Suzuki, Ken-ichiro; Fujita, Nobuyuki; Gonoi, Tohru

2014-04-30

Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they also opportunistically infect the respiratory system, skin, and other organs of humans and animals. Primarily because of the clinical importance of the strains, some Nocardia genomes have been sequenced, and genome sequences have accumulated. Genome sizes of Nocardia strains are similar to those of Streptomyces strains, the producers of most antibiotics. In the present work, we compared secondary metabolite biosynthesis gene clusters of type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) among genomes of representative Nocardia species/strains based on domain organization and amino acid sequence homology. Draft genome sequences of Nocardia asteroides NBRC 15531(T), Nocardia otitidiscaviarum IFM 11049, Nocardia brasiliensis NBRC 14402(T), and N. brasiliensis IFM 10847 were read and compared with published complete genome sequences of Nocardia farcinica IFM 10152, Nocardia cyriacigeorgica GUH-2, and N. brasiliensis HUJEG-1. Genome sizes are as follows: N. farcinica, 6.0 Mb; N. cyriacigeorgica, 6.2 Mb; N. asteroides, 7.0 Mb; N. otitidiscaviarum, 7.8 Mb; and N. brasiliensis, 8.9 - 9.4 Mb. Predicted numbers of PKS-I, NRPS, and PKS-I/NRPS hybrid clusters ranged between 4-11, 7-13, and 1-6, respectively, depending on strains, and tended to increase with increasing genome size. Domain and module structures of representative or unique clusters are discussed in the text. We conclude the following: 1) genomes of Nocardia strains carry as many PKS-I and NRPS gene clusters as those of Streptomyces strains, 2) the number of PKS-I and NRPS gene clusters in Nocardia strains varies substantially depending on species, and N. brasiliensis strains carry the largest numbers of clusters among the species studied, 3) the seven Nocardia strains studied in the present work have seven common PKS-I and/or NRPS clusters, some of whose products are yet to be studied

Towards prediction of metabolic products of polyketide synthases: an in silico analysis.

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Gitanjali Yadav

2009-04-01

Full Text Available Sequence data arising from an increasing number of partial and complete genome projects is revealing the presence of the polyketide synthase (PKS family of genes not only in microbes and fungi but also in plants and other eukaryotes. PKSs are huge multifunctional megasynthases that use a variety of biosynthetic paradigms to generate enormously diverse arrays of polyketide products that posses several pharmaceutically important properties. The remarkable conservation of these gene clusters across organisms offers abundant scope for obtaining novel insights into PKS biosynthetic code by computational analysis. We have carried out a comprehensive in silico analysis of modular and iterative gene clusters to test whether chemical structures of the secondary metabolites can be predicted from PKS protein sequences. Here, we report the success of our method and demonstrate the feasibility of deciphering the putative metabolic products of uncharacterized PKS clusters found in newly sequenced genomes. Profile Hidden Markov Model analysis has revealed distinct sequence features that can distinguish modular PKS proteins from their iterative counterparts. For iterative PKS proteins, structural models of iterative ketosynthase (KS domains have revealed novel correlations between the size of the polyketide products and volume of the active site pocket. Furthermore, we have identified key residues in the substrate binding pocket that control the number of chain extensions in iterative PKSs. For modular PKS proteins, we describe for the first time an automated method based on crucial intermolecular contacts that can distinguish the correct biosynthetic order of substrate channeling from a large number of non-cognate combinatorial possibilities. Taken together, our in silico analysis provides valuable clues for formulating rules for predicting polyketide products of iterative as well as modular PKS clusters. These results have promising potential for discovery of

Biological effects of paenilamicin, a secondary metabolite antibiotic produced by the honey bee pathogenic bacterium Paenibacillus larvae.

Science.gov (United States)

Garcia-Gonzalez, Eva; Müller, Sebastian; Hertlein, Gillian; Heid, Nina; Süssmuth, Roderich D; Genersch, Elke

2014-10-01

Paenibacillus larvae is the etiological agent of American Foulbrood (AFB) a world-wide distributed devastating disease of the honey bee brood. Previous comparative genome analysis and more recently, the elucidation of the bacterial genome, provided evidence that this bacterium harbors putative functional nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) and therefore, might produce nonribosomal peptides (NRPs) and polyketides (PKs). Such biosynthesis products have been shown to display a wide-range of biological activities such as antibacterial, antifungal or cytotoxic activity. Herein we present an in silico analysis of the first NRPS/PKS hybrid of P. larvae and we show the involvement of this cluster in the production of a compound named paenilamicin (Pam). For the characterization of its in vitro and in vivo bioactivity, a knock-out mutant strain lacking the production of Pam was constructed and subsequently compared to wild-type species. This led to the identification of Pam by mass spectrometry. Purified Pam-fractions showed not only antibacterial but also antifungal and cytotoxic activities. The latter suggested a direct effect of Pam on honey bee larval death which could, however, not be corroborated in laboratory infection assays. Bee larvae infected with the non-producing Pam strain showed no decrease in larval mortality, but a delay in the onset of larval death. We propose that Pam, although not essential for larval mortality, is a virulence factor of P. larvae influencing the time course of disease. These findings are not only of significance in elucidating and understanding host-pathogen interactions but also within the context of the quest for new compounds with antibiotic activity for drug development. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

An Sfp-type PPTase and associated polyketide and nonribosomal peptide synthases in Agrobacterium vitis are essential for induction of tobacco hypersensitive response and grape necrosis.

Science.gov (United States)

Zheng, Desen; Burr, Thomas J

2013-07-01

An Sfp-type phosphopantetheinyl transferase (PPTase) encoding gene F-avi5813 in Agrobacterium vitis F2/5 was found to be required for the induction of a tobacco hypersensitive response (HR) and grape necrosis. Sfp-type PPTases are post-translation modification enzymes that activate acyl-carry protein (ACP) domains in polyketide synthases (PKS) and peptidyl-carrier protein (PCP) domains of nonribosomal peptide synthases (NRPS). Mutagenesis of PKS and NRPS genes in A. vitis led to the identification of a PKS gene (F-avi4330) and NRPS gene (F-avi3342) that are both required for HR and necrosis. The gene immediately downstream of F-avi4330 (F-avi4329) encoding a predicted aminotransferase was also found to be required for HR and necrosis. Regulation of F-avi4330 and F-avi3342 by quorum-sensing genes avhR, aviR, and avsR and by a lysR-type regulator, lhnR, was investigated. It was determined that F-avi4330 expression is positively regulated by avhR, aviR, and lhnR and negatively regulated by avsR. F-avi3342 was found to be positively regulated by avhR, aviR, and avsR and negatively regulated by lhnR. Our results suggest that a putative hybrid peptide-polyketide metabolite synthesized by F-avi4330 and F-avi3342 is associated with induction of tobacco HR and grape necrosis. This is the first report that demonstrates that NRPS and PKS play essential roles in conferring the unique ability of A. vitis to elicit a non-host-specific HR and host-specific necrosis.

Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges.

Science.gov (United States)

Yuzawa, Satoshi; Keasling, Jay D; Katz, Leonard

2017-04-01

Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containing discrete enzymatic domains organized into modules. The modular nature of PKSs has enabled a multitude of efforts to engineer the PKS genes to produce novel polyketides of predicted structure. We have repurposed PKSs to produce a number of short-chain mono- and di-carboxylic acids and ketones that could have applications as fuels or industrial chemicals.

Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges

Energy Technology Data Exchange (ETDEWEB)

Yuzawa, Satoshi [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; Keasling, Jay D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; Univ. of California, Berkeley, CA (United States). QB3 Inst.; Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering; Technical Univ. of Denmark, Horsholm (Denmark). Novo Nordisk Foundation Center for Biosustainability; Katz, Leonard [Univ. of California, Berkeley, CA (United States). QB3 Inst.

2016-11-16

Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containing discrete enzymatic domains organized into modules. The modular nature of PKSs has enabled a multitude of efforts to engineer the PKS genes to produce novel polyketides of predicted structure. Finally, we have repurposed PKSs to produce a number of short-chain mono- and di-carboxylic acids and ketones that could have applications as fuels or industrial chemicals.

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) present in bacteria and fungi are themajor multi-modular enzyme complexes which synthesize secondary metabolites like the pharmacologically importantantibiotics and siderophores. Each of the multiple modules of an NRPS activates a ...

Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin-Producing Gambierdiscus polynesiensis and G. excentricus (Dinophyceae).

Science.gov (United States)

Kohli, Gurjeet S; Campbell, Katrina; John, Uwe; Smith, Kirsty F; Fraga, Santiago; Rhodes, Lesley L; Murray, Shauna A

2017-09-01

Gambierdiscus, a benthic dinoflagellate, produces ciguatoxins that cause the human illness Ciguatera. Ciguatoxins are polyether ladder compounds that have a polyketide origin, indicating that polyketide synthases (PKS) are involved in their production. We sequenced transcriptomes of Gambierdiscus excentricus and Gambierdiscus polynesiensis and found 264 contigs encoding single domain ketoacyl synthases (KS; G. excentricus: 106, G. polynesiensis: 143) and ketoreductases (KR; G. excentricus: 7, G. polynesiensis: 8) with sequence similarity to type I PKSs, as reported in other dinoflagellates. In addition, 24 contigs (G. excentricus: 3, G. polynesiensis: 21) encoding multiple PKS domains (forming typical type I PKSs modules) were found. The proposed structure produced by one of these megasynthases resembles a partial carbon backbone of a polyether ladder compound. Seventeen contigs encoding single domain KS, KR, s-malonyltransacylase, dehydratase and enoyl reductase with sequence similarity to type II fatty acid synthases (FAS) in plants were found. Type I PKS and type II FAS genes were distinguished based on the arrangement of domains on the contigs and their sequence similarity and phylogenetic clustering with known PKS/FAS genes in other organisms. This differentiation of PKS and FAS pathways in Gambierdiscus is important, as it will facilitate approaches to investigating toxin biosynthesis pathways in dinoflagellates. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.

Discriminating the reaction types of plant type III polyketide synthases.

Science.gov (United States)

Shimizu, Yugo; Ogata, Hiroyuki; Goto, Susumu

2017-07-01

Functional prediction of paralogs is challenging in bioinformatics because of rapid functional diversification after gene duplication events combined with parallel acquisitions of similar functions by different paralogs. Plant type III polyketide synthases (PKSs), producing various secondary metabolites, represent a paralogous family that has undergone gene duplication and functional alteration. Currently, there is no computational method available for the functional prediction of type III PKSs. We developed a plant type III PKS reaction predictor, pPAP, based on the recently proposed classification of type III PKSs. pPAP combines two kinds of similarity measures: one calculated by profile hidden Markov models (pHMMs) built from functionally and structurally important partial sequence regions, and the other based on mutual information between residue positions. pPAP targets PKSs acting on ring-type starter substrates, and classifies their functions into four reaction types. The pHMM approach discriminated two reaction types with high accuracy (97.5%, 39/40), but its accuracy decreased when discriminating three reaction types (87.8%, 43/49). When combined with a correlation-based approach, all 49 PKSs were correctly discriminated, and pPAP was still highly accurate (91.4%, 64/70) even after adding other reaction types. These results suggest pPAP, which is based on linear discriminant analyses of similarity measures, is effective for plant type III PKS function prediction. pPAP is freely available at ftp://ftp.genome.jp/pub/tools/ppap/. goto@kuicr.kyoto-u.ac.jp. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases

DEFF Research Database (Denmark)

Knudsen, Michael; Søndergaard, Dan Ariel; Tofting-Olesen, Claus

2016-01-01

Motivation: By using a class of large modular enzymes known as Non-Ribosomal Peptide Synthetases (NRPS), bacteria and fungi are capable of synthesizing a large variety of secondary metabolites, many of which are bioactive and have potential, pharmaceutical applications as e.g.~antibiotics. There ...

The Post-polyketide Synthase Steps in iso-Migrastatin Biosynthesis Featuring Tailoring Enzymes with Broad Substrate Specificity

Science.gov (United States)

Ma, Ming; Kwong, Thomas; Lim, Si-Kyu; Ju, Jianhua; Lohman, Jeremy R.; Shen, Ben

2013-01-01

The iso-migrastatin (iso-MGS) biosynthetic gene cluster from Streptomyces platensis NRRL 18993 consists of 11 genes, featuring an acyltransferase (AT)-less type I polyketide synthase (PKS) and three tailoring enzymes MgsIJK. Systematic inactivation of mgsIJK in S. platensis enabled us to (i) identify two nascent products (10 and 13) of the iso-MGS AT-less type I PKS, establishing an unprecedented novel feature for AT-less type I PKSs, and (ii) account for the formation of all known post-PKS biosynthetic intermediates (10-17) generated by the three tailoring enzymes MgsIJK, which possessed significant substrate promiscuities. PMID:23394593

Partai Islam Se-Malaysia (PAS) dan Partai Keadilan Sejahtera (PKS) sebagai Partai Islam Pendukung Demokrasi PKS Pada Pemilu

OpenAIRE

Ahmad Ali Nurdin

2015-01-01

The article compares the achievement of Partai Islam se-Malaysia (PAS) and Partai Keadilan Sejahtera (PKS) in the latest general election held in 2013 in Malaysia and in 2014 in Indonesia. The writer finds that the political performance of PAS and PKS has indicated differently contrast results. While political electability of PAS in the 2013 Malaysia’s general election has disappointed this party, PKS has successfully proved that surveys held by a number of survey institutes—predicting that t...

Partai Islam Se-Malaysia (PAS dan Partai Keadilan Sejahtera (PKS sebagai Partai Islam Pendukung Demokrasi PKS Pada Pemilu

Directory of Open Access Journals (Sweden)

Ahmad Ali Nurdin

2015-11-01

Full Text Available The article compares the achievement of Partai Islam se-Malaysia (PAS and Partai Keadilan Sejahtera (PKS in the latest general election held in 2013 in Malaysia and in 2014 in Indonesia. The writer finds that the political performance of PAS and PKS has indicated differently contrast results. While political electability of PAS in the 2013 Malaysia’s general election has disappointed this party, PKS has successfully proved that surveys held by a number of survey institutes—predicting that the party would cease within the 2014 Indonesia’s national election—were totally false. Many political figures of PAS have failed to gain positions in the legislative assembly. Meanwhile, in viewing PKS’s political performance during the 2014 national election, one may assume that this party was luckily survive. This is because, a number of surveys conducted before the election had predicted that PKS could be considered lucky when it was able to gain five percent of vote, as its former president has been suspected of being corrupt for his involvement in cows import. However, the fact shows that PKS has not only magnificently survived but it was even able to gain almost seven percent of voters’ vote. Unfortunately, PKS was unsuccessful to achieve its political target to be the biggest three of national vote.

Amplification and diversity analysis of keto synthase domains of putative polyketide synthase genes in Aspergillus ochraceus and Aspergillus carbonarius producers of ochratoxin A

International Nuclear Information System (INIS)

Atoui, A.; Phong Dao, H.; Mathieu, F.; Lebrihi, A.

2006-01-01

The diversity of polyketide synthase (PKS) genes in Aspergillus ochraceus NRRL 3174 and Aspergil- lus carbonarius 2Mu134 has been investigated using different primer pairs previously developed for the ketosynthase (KS) domain of fungal PKSs. Nine different KS domain sequences in A. ochraceus NRRL 3174 as well as five different KS domain sequences in A. carbonarius 2Mu134 have been identified. The identified KS fragments were distributed in five different clusters on the phylogenetic tree, indicating that they most probably represent PKSs responsible for different functions. (author)

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria

NARCIS (Netherlands)

Chevrette, Marc G.; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R.; Medema, M.H.

2017-01-01

Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables

Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production

DEFF Research Database (Denmark)

Yuzawa, Satoshi; Deng, Kai; Wang, George

2017-01-01

AT domain replacements in most type I PKS modules. To further demonstrate the utility of the optimized AT domain boundary, we have constructed hybrid PKSs to produce industrially important short-chain ketones. Our in vitro and in vivo analysis demonstrated production of predicted ketones without significant...

Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius

Energy Technology Data Exchange (ETDEWEB)

Gallo, Antonia; Knox, Benjamin P.; Bruno, Kenneth S.; Solfrizzo, Michele; Baker, Scott E.; Perrone, Giancarlo

2014-06-02

Ochratoxin A (OTA) is a potent mycotoxin produced by Aspergillus and Penicillium species and is a common contaminant of a wide variety of food commodities, with Aspergillus carbonarius being the main producer of OTA contamination in grapes and wine. The molecular structure of OTA is composed of a dihydroisocoumarin ring linked to phenylalanine and, as shown in different producing fungal species, a polyketide synthase (PKS) is a component of the OTA biosynthetic pathway. Similar to observations in other filamentous ascomycetes, the genome sequence of A. carbonarius contains a large number of genes predicted to encode PKSs. In this work a pks gene identified within the putative OTA cluster of A. carbonarius, designated as AcOTApks, was inactivated and the resulting mutant strain was unable to produce OTA, confirming the role of AcOTApks in this biosynthetic pathway. AcOTApks protein is characteristic of the highly reduced (HR)-PKS family, and also contains a putative methyltransferase domain likely responsible for the addition of the methyl group to the OTA polyketide structure. AcOTApks is different from the ACpks protein that we previously described which showed an expression profile compatible with OTA production. We performed phylogenetic analyses of the β-ketosynthase and acyl-transferase domains of the OTA PKSs which had been identified and characterized in different OTA producing fungal species. The phylogenetic results were similar for both the two domains analyzed and showed that OTA PKS of A. carbonarius, Aspergillus niger, and Aspergillus ochraceus clustered in a monophyletic group with 100% bootstrap support suggesting a common origin, while the other OTA PKSs analyzed were phylogenetically distant. A qRT-PCR assay monitored AcOTApks expression during fungal growth and concomitant production of OTA by A. carbonarius in synthetic grape medium. A clear correlation between the expression profile of AcOTApks and kinetics of OTA production was observed with

Interactions between Melanin Enzymes and Their Atypical Recruitment to the Secretory Pathway by Palmitoylation

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Srijana Upadhyay

2016-11-01

Full Text Available Melanins are biopolymers that confer coloration and protection to the host organism against biotic or abiotic insults. The level of protection offered by melanin depends on its biosynthesis and its subcellular localization. Previously, we discovered that Aspergillus fumigatus compartmentalizes melanization in endosomes by recruiting all melanin enzymes to the secretory pathway. Surprisingly, although two laccases involved in the late steps of melanization are conventional secretory proteins, the four enzymes involved in the early steps of melanization lack a signal peptide or a transmembrane domain and are thus considered “atypical” secretory proteins. In this work, we found interactions among melanin enzymes and all melanin enzymes formed protein complexes. Surprisingly, the formation of protein complexes by melanin enzymes was not critical for their trafficking to the endosomal system. By palmitoylation profiling and biochemical analyses, we discovered that all four early melanin enzymes were strongly palmitoylated during conidiation. However, only the polyketide synthase (PKS Alb1 was strongly palmitoylated during both vegetative hyphal growth and conidiation when constitutively expressed alone. This posttranslational lipid modification correlates the endosomal localization of all early melanin enzymes. Intriguingly, bioinformatic analyses predict that palmitoylation is a common mechanism for potential membrane association of polyketide synthases (PKSs and nonribosomal peptide synthetases (NRPSs in A. fumigatus. Our findings indicate that protein-protein interactions facilitate melanization by metabolic channeling, while posttranslational lipid modifications help recruit the atypical enzymes to the secretory pathway, which is critical for compartmentalization of secondary metabolism.

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Energy Technology Data Exchange (ETDEWEB)

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

2013-01-24

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

The Catalytic Diversity of Multimodular Polyketide Synthases: Natural Product Biosynthesis Beyond Textbook Assembly Rules.

Science.gov (United States)

Gulder, Tobias A M; Freeman, Michael F; Piel, Jörn

2011-03-01

Bacterial multimodular polyketide synthases (PKSs) are responsible for the biosynthesis of a wide range of pharmacologically active natural products. These megaenzymes contain numerous catalytic and structural domains and act as biochemical templates to generate complex polyketides in an assembly line-like fashion. While the prototypical PKS is composed of only a few different domain types that are fused together in a combinatorial fashion, an increasing number of enzymes is being found that contain additional components. These domains can introduce remarkably diverse modifications into polyketides. This review discusses our current understanding of such noncanonical domains and their role in expanding the biosynthetic versatility of bacterial PKSs.

Toblerols: Cyclopropanol-Containing Polyketide Modulators of Antibiosis in Methylobacteria.

Science.gov (United States)

Ueoka, Reiko; Bortfeld-Miller, Miriam; Morinaka, Brandon I; Vorholt, Julia A; Piel, Jörn

2018-01-22

Trans-AT polyketide synthases (PKSs) are a family of biosynthetically versatile modular type I PKSs that generate bioactive polyketides of impressive structural diversity. In this study, we detected, in the genome of several bacteria a cryptic, architecturally unusual trans-AT PKS gene cluster which eluded automated PKS prediction. Genomic mining of one of these strains, the model methylotroph Methylobacterium extorquens AM1, revealed unique epoxide- and cyclopropanol-containing polyketides named toblerols. Relative and absolute stereochemistry were determined by NMR experiments, chemical derivatization, and the comparison of CD data between the derivatized natural product and a synthesized model compound. Biosynthetic data suggest that the cyclopropanol moiety is generated by carbon-carbon shortening of a more extended precursor. Surprisingly, a knock-out strain impaired in polyketide production showed strong inhibitory activity against other methylobacteria in contrast to the wild-type producer. The activity was inhibited by complementation with toblerols, thus suggesting that these compounds modulate an as-yet unknown methylobacterial antibiotic. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The BL Lac objects PKS 1144-379

International Nuclear Information System (INIS)

Nicolson, G.D.; Glass, I.S.; Feast, M.W.; Andrews, P.J.

1979-01-01

The highly variable radio source PKS 1144-379 has been monitored at 13 cm and 6 cm over a period of 3 years. It has been identified with an object whose photographic image is star-like. From infrared photometry, UBVRsub(KC)Isub(KC) photometry and spectroscopy, it is concluded that PKS 1144-379 is a BL Lac object with msub(v) approximately = 16.2. (author)

Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

Energy Technology Data Exchange (ETDEWEB)

Brown, Daren W.; Butchko, Robert A.; Baker, Scott E.; Proctor, Robert H.

2012-02-01

Fusarium species are ubiquitous in nature, cause a range of plant diseases, and produce a variety of chemicals often referred to as secondary metabolites. Although some fungal secondary metabolites affect plant growth or protect plants from other fungi and bacteria, their presence in grain based food and feed is more often associated with a variety of diseases in plants and in animals. Many of these structurally diverse metabolites are derived from a family of related enzymes called polyketide synthases (PKSs). A search of genomic sequence of Fusarium verticillioides, F. graminearum, F. oxysporum and Nectria haematococca (anamorph F. solani) identified a total of 58 PKS genes. To gain insight into how this gene family evolved and to guide future studies, we conducted a phylogenomic and functional domain analysis. The resulting genealogy suggested that Fusarium PKSs represent 34 different groups responsible for synthesis of different core metabolites. The analyses indicate that variation in the Fusarium PKS gene family is due to gene duplication and loss events as well as enzyme gain-of-function due to the acquisition of new domains or of loss-of-function due to nucleotide mutations. Transcriptional analysis indicate that the 16 F. verticillioides PKS genes are expressed under a range of conditions, further evidence that they are functional genes that confer the ability to produce secondary metabolites.

Structure of PKS 1148-001

International Nuclear Information System (INIS)

Venugopal, V.R.; Ananthakrishnan, S.; Swarup, G.; Pynzar, A.V.; Udaltsov, V.A.

1985-01-01

Interplanetary scintillation (IPS) observations of PKS1148-001 at 326.5 and 102.5 MHz are described. The results from these are combined with published VLBI results at various frequencies to derive a three-component model for the source. The three components have sizes 0.0015, 0.01 and 0.1 arcsec and synchrotron self-absorption below frequencies about 1.5, 0.4 and 0.05 GHz respectively. This model is consistent with the total flux density spectrum. It is suggested that the results of the earlier two IPS surveys made at 327 and 408 MHz at Ooty and Arecibo need to be revised, since PKS 1148-001 is more compact than IPS calibrators used in those surveys. (author)

The Varied Variability of PKS 0736+017

Science.gov (United States)

Clements, S. D.; Cubides, L. A.; Greiwe, C. L.; Habermas, K. S.; Jenks, A. K.; Long, A. M.; Patel, J. A.; Torres, Y. V.

2003-05-01

The flat spectrum radio quasar PKS 0736+017 has been an exciting observing target, exhibiting diverse optical variability behaviors and even sharing its field one evening with a minor planet. The behavior of PKS 0736+017 has included persistently faint and quiescent periods, episodes of quasi-periodic microvariability, dramatic flaring events, and periods of unusual oscillations. These assorted behaviors are examined, with particular emphasis on the quasi-periodic variations and unusual oscillations that accompanied a dramatic flare.

Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

DEFF Research Database (Denmark)

Leclère, Valérie; Weber, Tilmann; Jacques, Philippe

2016-01-01

-dimensional structure of the peptides can be compared with the structural patterns of all known NRPs. The presented workflow leads to an efficient and rapid screening of genomic data generated by high throughput technologies. The exploration of such sequenced genomes may lead to the discovery of new drugs (i......This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes...... and the deciphering of the domain architecture of the nonribosomal peptide synthetases (NRPSs). In the next step, candidate peptides synthesized by these NRPSs are predicted in silico, considering the specificity of incorporated monomers together with their isomery. To assess their novelty, the two...

Heterologous gene expression and functional analysis of a type III polyketide synthase from Aspergillus niger NRRL 328

Energy Technology Data Exchange (ETDEWEB)

Kirimura, Kohtaro, E-mail: kkohtaro@waseda.jp; Watanabe, Shotaro; Kobayashi, Keiichi

2016-05-13

Type III polyketide synthases (PKSs) catalyze the formation of pyrone- and resorcinol-types aromatic polyketides. The genomic analysis of the filamentous fungus Aspergillus niger NRRL 328 revealed that this strain has a putative gene (chr-8-2: 2978617–2979847) encoding a type III PKS, although its functions are unknown. In this study, for functional analysis of this putative type III PKS designated as An-CsyA, cloning and heterologous expression of the An-CsyA gene (An-csyA) in Escherichia coli were performed. Recombinant His-tagged An-CsyA was successfully expressed in E. coli BL21 (DE3), purified by Ni{sup 2+}-affinity chromatography, and used for in vitro assay. Tests on the substrate specificity of the His-tagged An-CsyA with myriad acyl-CoAs as starter substrates and malonyl-CoA as extender substrate showed that His-tagged An-CsyA accepted fatty acyl-CoAs (C2-C14) and produced triketide pyrones (C2-C14), tetraketide pyrones (C2-C10), and pentaketide resorcinols (C10-C14). Furthermore, acetoacetyl-CoA, malonyl-CoA, isobutyryl-CoA, and benzoyl-CoA were also accepted as starter substrates, and both of triketide pyrones and tetraketide pyrones were produced. It is noteworthy that the His-tagged An-CsyA produced polyketides from malonyl-CoA as starter and extender substrates and produced tetraketide pyrones from short-chain fatty acyl-CoAs as starter substrates. Therefore, this is the first report showing the functional properties of An-CsyA different from those of other fungal type III PKSs. -- Highlights: •Type III PKS from Aspergillus niger NRRL 328, An-CsyA, was cloned and characterized. •An-CsyA produced triketide pyrones, tetraketide pyrones and pentaketide resorcinols. •Functional properties of An-CsyA differs from those of other fungal type III PKSs.

Heterologous gene expression and functional analysis of a type III polyketide synthase from Aspergillus niger NRRL 328

International Nuclear Information System (INIS)

Kirimura, Kohtaro; Watanabe, Shotaro; Kobayashi, Keiichi

2016-01-01

Type III polyketide synthases (PKSs) catalyze the formation of pyrone- and resorcinol-types aromatic polyketides. The genomic analysis of the filamentous fungus Aspergillus niger NRRL 328 revealed that this strain has a putative gene (chr-8-2: 2978617–2979847) encoding a type III PKS, although its functions are unknown. In this study, for functional analysis of this putative type III PKS designated as An-CsyA, cloning and heterologous expression of the An-CsyA gene (An-csyA) in Escherichia coli were performed. Recombinant His-tagged An-CsyA was successfully expressed in E. coli BL21 (DE3), purified by Ni"2"+-affinity chromatography, and used for in vitro assay. Tests on the substrate specificity of the His-tagged An-CsyA with myriad acyl-CoAs as starter substrates and malonyl-CoA as extender substrate showed that His-tagged An-CsyA accepted fatty acyl-CoAs (C2-C14) and produced triketide pyrones (C2-C14), tetraketide pyrones (C2-C10), and pentaketide resorcinols (C10-C14). Furthermore, acetoacetyl-CoA, malonyl-CoA, isobutyryl-CoA, and benzoyl-CoA were also accepted as starter substrates, and both of triketide pyrones and tetraketide pyrones were produced. It is noteworthy that the His-tagged An-CsyA produced polyketides from malonyl-CoA as starter and extender substrates and produced tetraketide pyrones from short-chain fatty acyl-CoAs as starter substrates. Therefore, this is the first report showing the functional properties of An-CsyA different from those of other fungal type III PKSs. -- Highlights: •Type III PKS from Aspergillus niger NRRL 328, An-CsyA, was cloned and characterized. •An-CsyA produced triketide pyrones, tetraketide pyrones and pentaketide resorcinols. •Functional properties of An-CsyA differs from those of other fungal type III PKSs.

Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton

Directory of Open Access Journals (Sweden)

Xueqiang Su

2017-10-01

Full Text Available Plant type III polyketide synthase (PKS can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I–IV. The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber.

Implementation of communication-mediating domains for non-ribosomal peptide production in Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Siewers, Verena; San-Bento, Rita; Nielsen, Jens

2010-01-01

Saccharomyces cerevisiae has in several cases been proven to be a suitable host for the production of natural products and was recently exploited for the production of non-ribosomal peptides. Synthesis of non-ribosomal peptides (NRPs) is mediated by NRP synthetases (NRPSs), modular enzymes, which...... are often organized in enzyme complexes. In these complexes, partner NRPSs interact via communication-mediating domains (COM domains). In order to test whether functional interaction between separate NRPS modules is possible in yeast we constructed a yeast strain expressing two modules with compatible COM...

Nonribosomal Peptide Synthetase Genes pesL and pes1 Are Essential for Fumigaclavine C Production in Aspergillus fumigatus

DEFF Research Database (Denmark)

O'Hanlon, Karen A.; Gallagher, Lorna; Schrettl, Markus

2012-01-01

The identity of metabolites encoded by the majority of nonribosomal peptide synthetases in the opportunistic pathogen, Aspergillus fumigatus, remains outstanding. We found that the nonribosomal peptide (NRP) synthetases PesL and Pes1 were essential for fumigaclavine C biosynthesis, the end produc...

Fusarium graminearum PKS14 is involved in orsellinic acid and orcinol synthesis

DEFF Research Database (Denmark)

Jørgensen, Simon Hartung; Frandsen, Rasmus John Normand; Nielsen, Kristian Fog

2014-01-01

and cultivated two of the resulting mutants on RM medium. This led to the production of two compounds, which were only detected in the PKS14 overexpressing mutants and not in the wild type or PKS14 deletion mutants. The two compounds were tentatively identified as orsellinic acid and orcinol by comparing...... spectroscopic data (mass spectroscopy and chromatography) to authentic standards. NMR analysis of putative orcinol isolated from the PKS14 overexpressing mutant supported our identification. Orcinol and orsellinic acid, not previously detected in Fusarium, have primarily been detected in lichen fungi...

De novo design and engineering of non-ribosomal peptide synthetases

Science.gov (United States)

Bozhüyük, Kenan A. J.; Fleischhacker, Florian; Linck, Annabell; Wesche, Frank; Tietze, Andreas; Niesert, Claus-Peter; Bode, Helge B.

2018-03-01

Peptides derived from non-ribosomal peptide synthetases (NRPSs) represent an important class of pharmaceutically relevant drugs. Methods to generate novel non-ribosomal peptides or to modify peptide natural products in an easy and predictable way are therefore of great interest. However, although the overall modular structure of NRPSs suggests the possibility of adjusting domain specificity and selectivity, only a few examples have been reported and these usually show a severe drop in production titre. Here we report a new strategy for the modification of NRPSs that uses defined exchange units (XUs) and not modules as functional units. XUs are fused at specific positions that connect the condensation and adenylation domains and respect the original specificity of the downstream module to enable the production of the desired peptides. We also present the use of internal condensation domains as an alternative to other peptide-chain-releasing domains for the production of cyclic peptides.

Ability of secondary metabolites from trichoderma virens to mediate communication during mutualistic or pathogenic interactions

Science.gov (United States)

A bioinformatic study was conducted to identify the putative genes in the biocontrol agent Trichoderma virens that encode for non-ribosomal peptide synthetases (NRPS). Gene expression analysis of 22 putative NRPSs and 4 NRPS/PKS (polyketide synthase) hybrid enzymes was conducted in the presence and...

Filling the Gaps in the Kirromycin Biosynthesis: Deciphering the Role of Genes Involved in Ethylmalonyl-CoA Supply and Tailoring Reactions

DEFF Research Database (Denmark)

Robertsen, Helene L.; Musiol-Kroll, Ewa M.; Ding, Ling

2018-01-01

Kirromycin is the main product of the soil-dwelling Streptomyces collinus Tü 365. The elucidation of the biosynthetic pathway revealed that the antibiotic is synthesised via a unique combination of trans-/cis-AT type I polyketide synthases and non-ribosomal peptide synthetases (PKS I/NRPS). This ...

Structural basis of nonribosomal peptide macrocyclization in fungi.

Science.gov (United States)

Zhang, Jinru; Liu, Nicholas; Cacho, Ralph A; Gong, Zhou; Liu, Zhu; Qin, Wenming; Tang, Chun; Tang, Yi; Zhou, Jiahai

2016-12-01

Nonribosomal peptide synthetases (NRPSs) in fungi biosynthesize important pharmaceutical compounds, including penicillin, cyclosporine and echinocandin. To understand the fungal strategy of forging the macrocyclic peptide linkage, we determined the crystal structures of the terminal condensation-like (C T ) domain and the holo thiolation (T)-C T complex of Penicillium aethiopicum TqaA. The first, to our knowledge, structural depiction of the terminal module in a fungal NRPS provides a molecular blueprint for generating new macrocyclic peptide natural products.

A nonribosomal peptide synthetase (Pes1) confers protection against oxidative stress in Aspergillus fumigatus.

Science.gov (United States)

Reeves, Emer P; Reiber, Kathrin; Neville, Claire; Scheibner, Olaf; Kavanagh, Kevin; Doyle, Sean

2006-07-01

Aspergillus fumigatus is an important human fungal pathogen. The Aspergillus fumigatus genome contains 14 nonribosomal peptide synthetase genes, potentially responsible for generating metabolites that contribute to organismal virulence. Differential expression of the nonribosomal peptide synthetase gene, pes1, in four strains of Aspergillus fumigatus was observed. The pattern of pes1 expression differed from that of a putative siderophore synthetase gene, sidD, and so is unlikely to be involved in iron acquisition. The Pes1 protein (expected molecular mass 698 kDa) was partially purified and identified by immunoreactivity, peptide mass fingerprinting (36% sequence coverage) and MALDI LIFT-TOF/TOF MS (four internal peptides sequenced). A pes1 disruption mutant (delta pes1) of Aspergillus fumigatus strain 293.1 was generated and confirmed by Southern and western analysis, in addition to RT-PCR. The delta pes1 mutant also showed significantly reduced virulence in the Galleria mellonella model system (P < 0.001) and increased sensitivity to oxidative stress (P = 0.002) in culture and during neutrophil-mediated phagocytosis. In addition, the mutant exhibited altered conidial surface morphology and hydrophilicity, compared to Aspergillus fumigatus 293.1. It is concluded that pes1 contributes to improved fungal tolerance against oxidative stress, mediated by the conidial phenotype, during the infection process.

Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia.

Science.gov (United States)

Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Eng, Shu-Kee; Goh, Bey-Hing; Yin, Wai-Fong; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan

2014-01-01

The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135(T) that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.

Investigation of biotechnological potential of sponge-associated bacteria collected in Brazilian coast.

Science.gov (United States)

Santos, O C S; Soares, A R; Machado, F L S; Romanos, M T V; Muricy, G; Giambiagi-deMarval, M; Laport, M S

2015-02-01

Marine bacteria are a rich source of structurally unique natural compounds, several of which have shown a wide variety of biological activities. In this study, the metabolites present in the culture supernatants of the eight sponge-associated bacteria were extracted using ethyl acetate, and all extracts showed activity against Staphylococcus aureus. Subsequently, the extracts of the Pseudomonas fluorescens H40 and H41, and Pseudomonas aeruginosa H51 were subjected to solvent partitioning, and the active fractions were submitted to chromatographic separation. Three different active fractions were obtained, one of which was identified as diketopiperazine cyclo-(L-Leu-L-Pro). This substance was bactericidal for Staph. aureus and Ps. aeruginosa and showed cytotoxic activity against HEp-2 tumour cells. Putative gene fragments coding for the type I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) domains were PCR-amplified from five and three strains, respectively. The results suggest that sponge-associated bacteria analysed in this study may represent a potential source for production of antimicrobial substances against bacterial pathogens of medical importance. © 2014 The Society for Applied Microbiology.

Bioactivities by a crude extract from the Greenlandic Pseudomonas sp. In5 involves the nonribosomal peptides, nunamycin and nunapeptin

DEFF Research Database (Denmark)

Frydenlund Michelsen, Charlotte; Jensen, Helle; Venditto, Vincent J.

2015-01-01

Bioactive microbial metabolites provide a successful source of novel compounds with pharmaceutical potentials. The bacterium Pseudomonas sp. In5 is a biocontrol strain isolated from a plant disease suppressive soil in Greenland, which produces two antimicrobial nonribosomal peptides (NRPs), nunap......), nunapeptin and nunamycin. In this study, we used in vitro antimicrobial and anticancer bioassays to evaluate the potential bioactivities of both a crude extract derived from Pseudomonas sp. In5 and NRPs purified from the crude extract....

Genetic diversity, phylogroup distribution and virulence gene profile of pks positive Escherichia coli colonizing human intestinal polyps.

Science.gov (United States)

Sarshar, Meysam; Scribano, Daniela; Marazzato, Massimiliano; Ambrosi, Cecilia; Aprea, Maria Rita; Aleandri, Marta; Pronio, Annamaria; Longhi, Catia; Nicoletti, Mauro; Zagaglia, Carlo; Palamara, Anna Teresa; Conte, Maria Pia

2017-11-01

Some Escherichia coli strains of phylogroup B2 harbor a (pks) pathogenicity island that encodes a polyketide-peptide genotoxin called colibactin. It causes DNA double-strand breaks and megalocytosis in eukaryotic cells and it may contribute to cancer development. Study of bacterial community that colonizes the adenomatous polyp lesion, defined as precancerous lesions, could be helpful to assess if such pathogenic bacteria possess a role in the polyp progression to cancer. In this cross-sectional study, a total of 1500 E. coli isolates were obtained from biopsies of patients presenting adenomatous colon polyps, the normal tissues adjacent to the polyp lesion and patients presenting normal mucosa. pks island frequency, phylogenetic grouping, fingerprint genotyping, and virulence gene features of pks positive (pks + ) E. coli isolates were performed. We found pks + E. coli strongly colonize two patients presenting polypoid lesions and none were identified in patients presenting normal mucosa. Predominant phylogroups among pks + E. coli isolates were B2, followed by D. Clustering based on fragment profiles of composite analysis, typed the pks + isolates into 5 major clusters (I-V) and 17 sub-clusters, demonstrating a high level of genetic diversity among them. The most prevalent virulence genes were fimH and fyuA (100%), followed by vat (92%), hra and papA (69%), ibeA (28%), and hlyA (25%). Our results revealed that pks + E. coli can colonize the precancerous lesions, with a high distribution in both the polyp lesions and in normal tissues adjacent to the lesion. The high differences in fingerprinting patterns obtained indicate that pks + E. coli strains were genetically diverse, possibly allowing them to more easily adapt to environmental variations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Polyketide Synthases in the Microbiome of the Marine Sponge Plakortis halichondrioides: A Metagenomic Update

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Gerardo Della Sala

2014-11-01

Full Text Available Sponge-associated microorganisms are able to assemble the complex machinery for the production of secondary metabolites such as polyketides, the most important class of marine natural products from a drug discovery perspective. A comprehensive overview of polyketide biosynthetic genes of the sponge Plakortis halichondrioides and its symbionts was obtained in the present study by massively parallel 454 pyrosequencing of complex and heterogeneous PCR (Polymerase Chain Reaction products amplified from the metagenomic DNA of a specimen of P. halichondrioides collected in the Caribbean Sea. This was accompanied by a survey of the bacterial diversity within the sponge. In line with previous studies, sequences belonging to supA and swfA, two widespread sponge-specific groups of polyketide synthase (PKS genes were dominant. While they have been previously reported as belonging to Poribacteria (a novel bacterial phylum found exclusively in sponges, re-examination of current genomic sequencing data showed supA and swfA not to be present in the poribacterial genome. Several non-supA, non-swfA type-I PKS fragments were also identified. A significant portion of these fragments resembled type-I PKSs from protists, suggesting that bacteria may not be the only source of polyketides from P. halichondrioides, and that protistan PKSs should receive further investigation as a source of novel polyketides.

GERAKAN REVIVALISME ISLAM DAN WACANA PENERAPAN SYARIAH DI INDONESIA: Telaah Pengalaman PKS dan Salafi

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Moh. Nurhakim

2013-09-01

Full Text Available This essay tries to critically evaluate a way of thinking developed among Salafi leader dan PKS as a movement of Islamic revivalism which related to the implementation of Islamic law (syari’ah into the Indonesian democracy context. There are a number of critical notes was discovered from literary researches and interviews with several leader of the movement. Firstly, basicly both PKS and Salafi leader longing for the implementation of Islamic law in the Indonesian democracy context. Despite the fact that PKS tend to act disparagingly toward democracy, while Salafi clearly repudiate democracy system, however, both of this group agree to “manipulate” this system to strugle for the embodiment of Islamic law with different strategies and substance. Secondly, PKS enters this system while trying to “objectify” Islamic values through preaching dan politics (structurally and culturally. In the same vein, Salafi manipulates democracy to strenghthen their ideological basis and their Islamic puritans awareness through preaching. Regarding politics, Salafi tends to be “pasive”.  Lastly, there are indications that the idea of the Islamic law implementation among PKS leader has dynamically changed following the politics dynamics. This often percieved as an inconsistency by the society. Meanwhile, the idea and efforts to implement Islamic law among Salafi leader is limited to the area of family rule and rarely about public rules. The result of this critical evaluation upon the implementation of Islamic law done by PKS and Salafi leaders, up to this point, have not provide a viable  recomendation as an ideal model of strengthening democracy system and implementing Islamic law in Indonesia.

Identification of the Biosynthetic Gene Clusters for the Lipopeptides Fusaristatin A and W493 B in Fusarium graminearum and F. pseudograminearum

DEFF Research Database (Denmark)

Sørensen, Jens Laurids; Sondergaard, Teis Esben; Covarelli, Lorenzo

2014-01-01

The closely related species Fusarium graminearum and Fusarium pseudograminearum differ in that each contains a gene cluster with a polyketide synthase (PKS) and a nonribosomal peptide synthetase (NRPS) that is not present in the other species. To identify their products, we deleted PKS6 and NRPS7...... Fusarium species. On the basis of genes in the putative gene clusters we propose a model for biosynthesis where the polyketide product is shuttled to the NPRS via a CoA ligase and a thioesterase in F. pseudograminearum. In F. graminearum the polyketide is proposed to be directly assimilated by the NRPS....

[Diversity of cultivable actinobacteria in Xinghu wetland sediments].

Science.gov (United States)

Xue, Dong; Zhao, Guozhen; Yao, Qing; Zhao, Haiquan; Zhu, Honghui

2015-11-04

To study the diversity of cultivable actinobacteria in Xinghu wetland and screen actinobacteria with a pharmaceutical potential for producing biologically active secondary metabolites. We studied the diversity of actinobacteria isolated from Xinghu wetland by using different selective isolation media and methods. The high bioactive actinobacteria were identified and further investigated for the presence of polyketide synthases (PKS-I, PKS-II), nonribosomal peptide synthetases (NRPS), 3-amino-5-hydroxybenzoic acid synthases (AHBA) and 3-hydroxy-3-methylglutaryl Coenzyme A (HMG CoA) sequences by specific amplification. More than 300 actinobacteria were isolated, and 135 isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The isolates belonged to 7 orders, 10 families, 13 genera, Streptomyces was the most frequently isolated genus, followed by the genera Micromonospora and Nocardia. Twenty-four isolates showed high activity against Staphylococcus aureus and Escherichia coli, but there no strain displaying antagonistic activity against Salmonella sp. High frequencies of positive PCR amplification were obtained for PKS-I (16.7%, 4/24), PKS-II (62.5%,15/24), NRPS (16.7%, 4/24), HMG CoA (29.2%, 7/24) and AHBA (12.5%, 3/24) biosynthetic systems. High Performance Liquid Chromatography showed that strain XD7, XD114, XD128 produce lots of secondary metabolites. This study indicated that actinobacteria isolated from Xinghu wetland are abundant and have potentially beneficial and diverse bioactivities which should be pursued for their biotechnical promise.

Diversity and Antimicrobial Activities of Actinobacteria Isolated from Tropical Mangrove Sediments in Malaysia

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Learn-Han Lee

2014-01-01

Full Text Available The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135T that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS and nonribosomal polyketide synthetase (NRPS genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%, PKS-II (42.5%, and NRPS (5.7% genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.

Prediction of monomer isomery in Florine: a workflow dedicated to nonribosomal peptide discovery.

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Thibault Caradec

Full Text Available Nonribosomal peptides represent a large variety of natural active compounds produced by microorganisms. Due to their specific biosynthesis pathway through large assembly lines called NonRibosomal Peptide Synthetases (NRPSs, they often display complex structures with cycles and branches. Moreover they often contain non proteogenic or modified monomers, such as the D-monomers produced by epimerization. We investigate here some sequence specificities of the condensation (C and epimerization (E domains of NRPS that can be used to predict the possible isomeric state (D or L of each monomer in a putative peptide. We show that C- and E- domains can be divided into 2 sub-regions called Up-Seq and Down-Seq. The Up-Seq region corresponds to an InterPro domain (IPR001242 and is shared by C- and E-domains. The Down-Seq region is specific to the enzymatic activity of the domain. Amino-acid signatures (represented as sequence logos previously described for complete C-and E-domains have been restricted to the Down-Seq region and amplified thanks to additional sequences. Moreover a new Down-Seq signature has been found for Ct-domains found in fungi and responsible for terminal cyclization of the peptides. The identification of these signatures has been included in a workflow named Florine, aimed to predict nonribosomal peptides from NRPS sequence analyses. In some cases, the prediction of isomery is guided by genus-specific rules. Florine was used on a Pseudomonas genome to allow the determination of the type of pyoverdin produced, the update of syringafactin structure and the identification of novel putative products.

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

KAUST Repository

Othoum, Ghofran K

2018-05-22

BackgroundThe increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions.ResultsWe report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species.ConclusionsB. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.

Mapping of polyketide biosynthesis pathways in Aspergillus nidulans using a genome wide PKS gene deletion library

DEFF Research Database (Denmark)

Larsen, Thomas Ostenfeld; Rank, Christian; Klejnstrup, Marie Louise

In order to map new links between PKS genes and their products in Aspergillus nidulans we have systematically deleted all thirty-two individual genes predicted to encode polyketide synthases in this model organism. This number greatly exceeds the number of currently known PKs calling for new appr...

Characterisation of pks15/1 in clinical isolates of Mycobacterium tuberculosis from Mexico

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Roberto Zenteno-Cuevas

2013-09-01

Full Text Available Tuberculosis (TB is an infectocontagious respiratory disease caused by members of the Mycobacterium tuberculosis complex. A 7 base pair (bp deletion in the locus polyketide synthase (pks15/1 is described as polymorphic among members of the M. tuberculosis complex, enabling the identification of Euro-American, Indo-Oceanic and Asian lineages. The aim of this study was to characterise this locus in TB isolates from Mexico. One hundred twenty clinical isolates were recovered from the states of Veracruz and Estado de Mexico. We determined the nucleotide sequence of a ± 400 bp fragment of the locus pks15/1, while genotypic characterisation was performed by spoligotyping. One hundred and fifty isolates contained the 7 bp deletion, while five had the wild type locus. Lineages X (22%, LAM (18% and T (17% were the most frequent; only three (2% of the isolates were identified as Beijing and two (1% EAI-Manila. The wild type pks15/1 locus was observed in all Asian lineage isolates tested. Our results confirm the utility of locus pks15/1 as a molecular marker for identifying Asian lineages of the M. tuberculosis complex. This marker could be of great value in the epidemiological surveillance of TB, especially in countries like Mexico, where the prevalence of such lineages is unknown.

Rapid interstellar scintillation of quasar PKS 1257-326

NARCIS (Netherlands)

Bignall, Hayley E.; Jauncey, David L.; Lovell, James E. J.; Tzioumis, Anastasios K.; Macquart, Jean-Pierre; Kedziora-Chudczer, Lucyna; Engvold, O

2005-01-01

PKS 1257-326 is one of three quasars known to show unusually large and rapid, intra-hour intensity variations, as a result of scintillation in the turbulent Galactic interstellar medium. We have measured time delays in the variability pattern arrival times at the VLA and the ATCA, as well as an

Structural basis for phosphopantetheinyl carrier domain interactions in the terminal module of nonribosomal peptide synthetases

Science.gov (United States)

Liu, Ye; Zheng, Tengfei; Bruner, Steven D.

2011-01-01

Summary Phosphopantetheine-modified carrier domains play a central role in the template-directed, biosynthesis of several classes of primary and secondary metabolites. Fatty acids, polyketides and nonribosomal peptides are constructed on multidomain enzyme assemblies using phosphopantetheinyl thioester-linked carrier domains to traffic and activate building blocks. The carrier domain is a dynamic component of the process, shuttling pathway intermediates to sequential enzyme active sites. Here we report an approach to structurally fix carrier domain/enzyme constructs suitable for X-ray crystallographic analysis. The structure of a two-domain construct of E. coli EntF was determined with a conjugated phosphopantetheinyl-based inhibitor. The didomain structure is locked in an active orientation relevant to the chemistry of nonribosomal peptide biosynthesis. This structure provides details into the interaction of phosphopantetheine arm with the carrier domain and the active site of the thioesterase domain. PMID:22118682

A test of unification towards the radio source PKS1413+135

International Nuclear Information System (INIS)

Ferreira, M.C.; Julião, M.D.; Martins, C.J.A.P.; Monteiro, A.M.R.V.L.

2013-01-01

We point out that existing astrophysical measurements of combinations of the fine-structure constant α, the proton-to-electron mass ratio μ and the proton gyromagnetic ratio g p towards the radio source PKS1413+135 can be used to individually constrain each of these fundamental couplings. While the accuracy of the available measurements is not yet sufficient to test the spatial dipole scenario, our analysis serves as a proof of concept as new observational facilities will soon allow significantly more robust tests. Moreover, these measurements can also be used to obtain constraints on certain classes of unification scenarios, and we compare the constraints obtained for PKS1413+135 with those previously obtained from local atomic clock measurements

A test of unification towards the radio source PKS1413+135

Energy Technology Data Exchange (ETDEWEB)

Ferreira, M.C., E-mail: up200802537@fc.up.pt [Centro de Astrofísica, Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4150-007 Porto (Portugal); Julião, M.D., E-mail: meinf12013@fe.up.pt [Centro de Astrofísica, Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Faculdade de Engenharia, Universidade do Porto, Rua Dr Roberto Frias, 4200-465 Porto (Portugal); Martins, C.J.A.P., E-mail: Carlos.Martins@astro.up.pt [Centro de Astrofísica, Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Monteiro, A.M.R.V.L., E-mail: mmonteiro@fc.up.pt [Centro de Astrofísica, Universidade do Porto, Rua das Estrelas, 4150-762 Porto (Portugal); Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4150-007 Porto (Portugal); Department of Applied Physics, Delft University of Technology, P.O. Box 5046, 2600 GA Delft (Netherlands)

2013-07-09

We point out that existing astrophysical measurements of combinations of the fine-structure constant α, the proton-to-electron mass ratio μ and the proton gyromagnetic ratio g{sub p} towards the radio source PKS1413+135 can be used to individually constrain each of these fundamental couplings. While the accuracy of the available measurements is not yet sufficient to test the spatial dipole scenario, our analysis serves as a proof of concept as new observational facilities will soon allow significantly more robust tests. Moreover, these measurements can also be used to obtain constraints on certain classes of unification scenarios, and we compare the constraints obtained for PKS1413+135 with those previously obtained from local atomic clock measurements.

Both a PKS and a PPTase are involved in melanin biosynthesis and regulation of Aureobasidium melanogenum XJ5-1 isolated from the Taklimakan desert.

Science.gov (United States)

Jiang, Hong; Liu, Guang-Lei; Chi, Zhe; Wang, Jian-Ming; Zhang, Ly-Ly; Chi, Zhen-Ming

2017-02-20

A PKS1 gene responsible for the melanin biosynthesis and a NPG1 gene in Aureobasidium melanogenum XJ5-1 were cloned and characterized. An ORF of the PKS1 gene encoding a protein with 2165 amino acids contained 6495bp while an ORF of the NPG1 gene encoding a protein with 340 amino acids had 1076bp. After analysis of their promoters, it was found that expression of both the PKS1 gene and the NPG1 gene was repressed by nitrogen sources and glucose, respectively. The PKS deduced from the cloned gene consisted of one ketosynthase, one acyl transferase, two acyl carrier proteins, one thioesterase and one cyclase while the PPTase belonged to the family Sfp-type. After disruption of the PKS1 gene and the NPG1 gene, expression of the PKS1 gene and the NPG1 gene and the melanin biosynthesis in the disruptants K5 and DP107 disappeared and expression of the PKS1 gene in the disruptant DP107 was also negatively influenced. However, after the NPG1 gene was complemented in the disruptant DP107, the melanin biosynthesis in the complementary strain BP17 was restored and expression of the PKS1 gene and the NPG1 gene was greatly enhanced, suggesting that the PKS was indeed activated and regulated by the PPTase and expression of the PKS1 gene and the NPG1 gene had a coordinate regulation. Copyright © 2016 Elsevier B.V. All rights reserved.

Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis.

Science.gov (United States)

Noar, Roslyn D; Daub, Margaret E

2016-01-01

Mycosphaerella fijiensis, causal agent of black Sigatoka disease of banana, is a Dothideomycete fungus closely related to fungi that produce polyketides important for plant pathogenicity. We utilized the M. fijiensis genome sequence to predict PKS genes and their gene clusters and make bioinformatics predictions about the types of compounds produced by these clusters. Eight PKS gene clusters were identified in the M. fijiensis genome, placing M. fijiensis into the 23rd percentile for the number of PKS genes compared to other Dothideomycetes. Analysis of the PKS domains identified three of the PKS enzymes as non-reducing and two as highly reducing. Gene clusters contained types of genes frequently found in PKS clusters including genes encoding transporters, oxidoreductases, methyltransferases, and non-ribosomal peptide synthases. Phylogenetic analysis identified a putative PKS cluster encoding melanin biosynthesis. None of the other clusters were closely aligned with genes encoding known polyketides, however three of the PKS genes fell into clades with clusters encoding alternapyrone, fumonisin, and solanapyrone produced by Alternaria and Fusarium species. A search for homologs among available genomic sequences from 103 Dothideomycetes identified close homologs (>80% similarity) for six of the PKS sequences. One of the PKS sequences was not similar (< 60% similarity) to sequences in any of the 103 genomes, suggesting that it encodes a unique compound. Comparison of the M. fijiensis PKS sequences with those of two other banana pathogens, M. musicola and M. eumusae, showed that these two species have close homologs to five of the M. fijiensis PKS sequences, but three others were not found in either species. RT-PCR and RNA-Seq analysis showed that the melanin PKS cluster was down-regulated in infected banana as compared to growth in culture. Three other clusters, however were strongly upregulated during disease development in banana, suggesting that they may encode

Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis.

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Roslyn D Noar

Full Text Available Mycosphaerella fijiensis, causal agent of black Sigatoka disease of banana, is a Dothideomycete fungus closely related to fungi that produce polyketides important for plant pathogenicity. We utilized the M. fijiensis genome sequence to predict PKS genes and their gene clusters and make bioinformatics predictions about the types of compounds produced by these clusters. Eight PKS gene clusters were identified in the M. fijiensis genome, placing M. fijiensis into the 23rd percentile for the number of PKS genes compared to other Dothideomycetes. Analysis of the PKS domains identified three of the PKS enzymes as non-reducing and two as highly reducing. Gene clusters contained types of genes frequently found in PKS clusters including genes encoding transporters, oxidoreductases, methyltransferases, and non-ribosomal peptide synthases. Phylogenetic analysis identified a putative PKS cluster encoding melanin biosynthesis. None of the other clusters were closely aligned with genes encoding known polyketides, however three of the PKS genes fell into clades with clusters encoding alternapyrone, fumonisin, and solanapyrone produced by Alternaria and Fusarium species. A search for homologs among available genomic sequences from 103 Dothideomycetes identified close homologs (>80% similarity for six of the PKS sequences. One of the PKS sequences was not similar (< 60% similarity to sequences in any of the 103 genomes, suggesting that it encodes a unique compound. Comparison of the M. fijiensis PKS sequences with those of two other banana pathogens, M. musicola and M. eumusae, showed that these two species have close homologs to five of the M. fijiensis PKS sequences, but three others were not found in either species. RT-PCR and RNA-Seq analysis showed that the melanin PKS cluster was down-regulated in infected banana as compared to growth in culture. Three other clusters, however were strongly upregulated during disease development in banana, suggesting that

POLA REKRUTMEN CALONLEGISLATIF DAPIL 1 PROVINSI ACEH YANG DILAKUKAN OLEH PARTAI KEADILAN SEJAHTERA (PKS DAN PARTAI NASIONAL DEMOKRAT (NASDEM

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Ruslan Ruslan

2016-12-01

Full Text Available Political recruitment is the process of filling positions in political institutions, including political parties. While the Political Party is a vehicle to bring a particular party political interests in the throne of power in order to achieve what is expected. The purpose of this research is to see how the pattern of recruiting candidates for legislative constituency 1 Aceh province conducted by PKS and NasDem Party, criteria to be used in recruiting candidates for legislative constituency 1 Aceh province conducted by PKS and NasDem Party and what the opportunities and challenges in recruiting candidates one electoral district conducted by PKS and NasDem Party. The method used is descriptive method with qualitative approach. The data collection was done by interview and documentation. The result showed that the pattern of recruiting candidates for the electoral district legilatif 1 Aceh province conducted by the PKS and NasDem show that much different. In connection with this, it is an opportunity and a challenge PKS namely the legislative elections of 2014 more challenges than opportunities obtained by the PKS because of money politics so were experienced by the Party NasDem money politics becomes the greatest challenge in the legislative election first times followed by the Party NasDem   DOI : http://dx.doi.org/10.17977/um019v1i22016p111

Far UV observations of PKS2155-304

International Nuclear Information System (INIS)

Maraschi, L.; Tanzi, E.G.; Treves, A.; Tarenghi, M.

1980-01-01

Several spectra of the BL Lac object PKS2155 - 304 are reported in the 1,150 - 3,200 A band taken with the IUE when the object was in a bright phase. The UV flux connects smoothly with the optical and IR observations of the source in its brightest state and its extrapolation matches the soft X-ray flux, implying a change in spectral slope around 10 15 Hz. (UK)

Islamisme dan Politisasi Agama Model PKS dalam Pilpres 2009

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Akh. Muzakki

2014-01-01

Full Text Available In the past decade or so, Islamism as a political concept and perhaps as an ideology has gained strong momentum in Indonesia. The fall of Soeharto after more than three decades in power has helped this ideology to emerge and exert itself particularly in the form of religion oriented political party. This paper is interested in exploring the expression and actualization of Islamism by scrutinizing the political behavior of Justice and Welfare Party (Partai Keadilan Sejahtera / PKS during the 2009 presidential election. We are particularly interested in looking at the use of religious symbols and rites by the party for clear political purposes. We argue that Islamism has been manipulated by PKS during that election as a vehicle to gain power. Hence, the main problem that this paper deals with is actually the idea of the politization of religion by a political party claiming to have represented Islam and its noble teaching.

The Insect Pathogen Serratia marcescens Db10 Uses a Hybrid Non-Ribosomal Peptide Synthetase-Polyketide Synthase to Produce the Antibiotic Althiomycin

Science.gov (United States)

Challis, Gregory L.; Stanley-Wall, Nicola R.; Coulthurst, Sarah J.

2012-01-01

There is a continuing need to discover new bioactive natural products, such as antibiotics, in genetically-amenable micro-organisms. We observed that the enteric insect pathogen, Serratia marcescens Db10, produced a diffusible compound that inhibited the growth of Bacillis subtilis and Staphyloccocus aureus. Mapping the genetic locus required for this activity revealed a putative natural product biosynthetic gene cluster, further defined to a six-gene operon named alb1–alb6. Bioinformatic analysis of the proteins encoded by alb1–6 predicted a hybrid non-ribosomal peptide synthetase-polyketide synthase (NRPS-PKS) assembly line (Alb4/5/6), tailoring enzymes (Alb2/3) and an export/resistance protein (Alb1), and suggested that the machinery assembled althiomycin or a related molecule. Althiomycin is a ribosome-inhibiting antibiotic whose biosynthetic machinery had been elusive for decades. Chromatographic and spectroscopic analyses confirmed that wild type S. marcescens produced althiomycin and that production was eliminated on disruption of the alb gene cluster. Construction of mutants with in-frame deletions of specific alb genes demonstrated that Alb2–Alb5 were essential for althiomycin production, whereas Alb6 was required for maximal production of the antibiotic. A phosphopantetheinyl transferase enzyme required for althiomycin biosynthesis was also identified. Expression of Alb1, a predicted major facilitator superfamily efflux pump, conferred althiomycin resistance on another, sensitive, strain of S. marcescens. This is the first report of althiomycin production outside of the Myxobacteria or Streptomyces and paves the way for future exploitation of the biosynthetic machinery, since S. marcescens represents a convenient and tractable producing organism. PMID:23028578

Antimicrobial assay and genetic screening of selected freshwater Cyanobacteria and identification of a biomolecule dihydro-2H-pyran-2-one derivative.

Science.gov (United States)

Srivastava, A; Singh, V K; Patnaik, S; Tripathi, J; Singh, P; Nath, G; Asthana, R K

2017-04-01

Explorations of freshwater Cyanobacteria as antimicrobial (bacteria, fungi and methicillin-resistant Staphylococcus aureus (MRSA) strains) drug resource using bioassay, NRPS (non-ribosomal polypeptide synthetase) and PKS (polyketide synthase) genes, as well as in silico approach. We have bioassayed the extracts of Phormidium CCC727, Geitlerinema CCC728, Arthrospira CCC729, Leptolyngbya CCC732, Phormidium CCC730, Phormidium CCC731 against six pathogenic bacteria comprising Gram (+ve): S. aureus including seven clinical MRSA and Enterococcus faecalis, Gram (-ve): Escherichia coli, Salmonella Typhimurium, Klebsiella pneumoniae and Shigella boydii along with non-pathogenic Enterobacter aerogenes as well as fungal strains (Cryptococcus neoformans and Candida albicans, C. krusei, C. tropicalis and Aspergillus niger) exhibiting antimicrobial potential. The NRPS and PKS genes of the target strains were also amplified and sequenced. The putative protein structures were predicted using bioinformatics approach. PKS gene expression indicated β keto-acyl synthase as one of the important active domains in the biomolecules related to antitumour and antifungal group. The simultaneous identification of the biomolecule (dihydro-2H-pyran-2-one derivative) was also inferred spectroscopically. Freshwater Cyanobacteria are prolific producers of secondary metabolite(s) that may act as the antimicrobial drug resource in addition to their much explored marine counterpart. © 2016 The Society for Applied Microbiology.

Is the GeV-TeV emission of PKS 0447-439 from the proton synchrotron radiation?

Science.gov (United States)

Gao, Quan-Gui; Lu, Fang-Wu; Ma, Ju; Ren, Ji-Yang; Li, Huai-Zhen

2018-06-01

We study the multi-wavelength emission features of PKS 0447-439 in the frame of the one-zone homogeneous lepto-hadronic model. In this model, we assumed that the steady power-laws with exponential cut-offs distributions of protons and electrons are injected into the source. The non-linear time-dependent kinematic equations, describing the evolution of protons, electrons and photons, are defined; these equations self-consistently involve synchrotron radiation of protons, photon-photon interaction, synchrotron radiation of electron/positron pairs, inverse Compton scattering and synchrotron self-absorption. The model is applied to reproduce the multi-wavelength spectrum of PKS 0447-439. Our results indicate that the spectral energy distribution (SED) of PKS 0447-439 can be reproduced well by the model. In particular, the GeV-TeV emission is produced by the synchrotron radiation of relativistic protons. The physically plausible solutions require the magnetic strength 10 G≲ B ≲ 100 G. We found that the observed spectrum of PKS 0447-439 can be reproduced well by the model whether z = 0.16 or z = 0.2, and the acceptable upper limit of redshift is z=0.343.

PROFIL PEMBELAJARAN SAINS BERBASIS KELASS SEBAGAI UPAYA MENGEMBANGKAN KPS DAN MENINGKATKAN PKS SISWA (STUDI KASUS DI SMPN 1 KOTA JAMBI

Directory of Open Access Journals (Sweden)

Sukarno Sukarno

2014-10-01

Full Text Available Kegiatan Belajar Mengajar (KBM sains di tingkat SMP bertujuan untuk mengembangkan Keterampilan Proses Sains (KPS dan menanamkan Penguasaan Konsep Sains (PKS. Oleh karena itu, KBM sains harus memberikan peluang untuk mengembangkan KPS dan PKS secara bersama-sama dan tidak terpisahkan. KBM sains berbasis Kegiatan Eksplorasi Lingkungan Alam di Sekitar Sekolah (KELASS dianggap mampu memberikan ruang yang luas untuk mengembangkan KPS siswa dan PKS. Oleh karena itu, penelitian kualitatif ini dilakukan dengan tujuan untuk mengetahui apa saja faktor pendukung dan faktor penghambat pelaksanaan KBM sains berbasis KELASS dan implikasinya terhadap KPS dan PKS siswa. Data hasil wawancara, observasi dan tes menunjukkan bahwa faktor pendukung KBM sains berbasis KELASS adalah sarana dan prasarana (indoor dan outdoor yang memadai. Sedangkan kendala utama bagi para guru sains adalah tidak adanya bahan ajar sains yang berorientasi pada eksplorasi lingkungan alam sekitar sekolah untuk mengembangkan mahasiswa KPS dan PKS. Oleh karena itu, perlu dikembangkan bahan ajar sains yang dapat mempermudah guru sains dalam melakukan KBM sains berbasis KELASS.   Kata kunci:    eksplorasi lingkungan alam di sekitar sekolah, keterampilan proses sains, penguasaan konsep sains

Optical features associated with the quasar PKS 2135-14

International Nuclear Information System (INIS)

Hawkins, M.R.S.

1978-01-01

The field surrounding the quasar PKS 2135-14 has been investigated from B and R photographs taken with the 3.8-m Anglo-Australian telescope. Isophotal plots of the plates, produced with the COSMOS measuring machine, have revealed a number of faint optical features apparently associated with the radio source. (author)

CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

Czech Academy of Sciences Publication Activity Database

Novák, Jiří; Lemr, Karel; Schug, K. A.; Havlíček, Vladimír

2015-01-01

Roč. 26, č. 10 (2015), s. 1780-1786 ISSN 1044-0305 R&D Projects: GA ČR(CZ) GAP206/12/1150 Grant - others:OPPC(XE) CZ.2.16/3.1.00/24023 Institutional support: RVO:61388971 Keywords : De novo sequencing * Nonribosomal peptides * Linear Subject RIV: CE - Biochemistry Impact factor: 3.031, year: 2015

Arabidopsis protein kinase PKS5 inhibits the plasma membrane H+ -ATPase by preventing interaction with 14-3-3 protein

DEFF Research Database (Denmark)

Fuglsang, Anja Thoe; Guo, Yan; Cuin, Tracey A.

2007-01-01

Regulation of the trans-plasma membrane pH gradient is an important part of plant responses to several hormonal and environmental cues, including auxin, blue light, and fungal elicitors. However, little is known about the signaling components that mediate this regulation. Here, we report...... that an Arabidopsis thaliana Ser/Thr protein kinase, PKS5, is a negative regulator of the plasma membrane proton pump (PM Hþ-ATPase). Loss-of-function pks5 mutant plants are more tolerant of high external pH due to extrusion of protons to the extracellular space. PKS5 phosphorylates the PM Hþ-ATPase AHA2 at a novel...

Terminal Alkene Formation by the Thioesterase of Curacin A Biosynthesis: Structure of a Decarboxylating Thioesterase

Energy Technology Data Exchange (ETDEWEB)

Gehret, Jennifer J.; Gu, Liangcai; Gerwick, William H.; Wipf, Peter; Sherman, David H.; Smith, Janet L. (Pitt); (Michigan); (UCSD)

2011-11-07

Curacin A is a polyketide synthase (PKS)-non-ribosomal peptide synthetase-derived natural product with potent anticancer properties generated by the marine cyanobacterium Lyngbya majuscula. Type I modular PKS assembly lines typically employ a thioesterase (TE) domain to off-load carboxylic acid or macrolactone products from an adjacent acyl carrier protein (ACP) domain. In a striking departure from this scheme the curacin A PKS employs tandem sulfotransferase and TE domains to form a terminal alkene moiety. Sulfotransferase sulfonation of {beta}-hydroxy-acyl-ACP is followed by TE hydrolysis, decarboxylation, and sulfate elimination (Gu, L., Wang, B., Kulkarni, A., Gehret, J. J., Lloyd, K. R., Gerwick, L., Gerwick, W. H., Wipf, P., Hakansson, K., Smith, J. L., and Sherman, D. H. (2009) J. Am. Chem. Soc. 131, 16033-16035). With low sequence identity to other PKS TEs (<15%), the curacin TE represents a new thioesterase subfamily. The 1.7-{angstrom} curacin TE crystal structure reveals how the familiar {alpha}/{beta}-hydrolase architecture is adapted to specificity for {beta}-sulfated substrates. A Ser-His-Glu catalytic triad is centered in an open active site cleft between the core domain and a lid subdomain. Unlike TEs from other PKSs, the lid is fixed in an open conformation on one side by dimer contacts of a protruding helix and on the other side by an arginine anchor from the lid into the core. Adjacent to the catalytic triad, another arginine residue is positioned to recognize the substrate {beta}-sulfate group. The essential features of the curacin TE are conserved in sequences of five other putative bacterial ACP-ST-TE tridomains. Formation of a sulfate leaving group as a biosynthetic strategy to facilitate acyl chain decarboxylation is of potential value as a route to hydrocarbon biofuels.

Actinomycetes from red sea sponges: Sources for chemical and phylogenetic diversity

KAUST Repository

Abdelmohsen, Usama Ramadan

2014-05-12

The diversity of actinomycetes associated with marine sponges collected off Fsar Reef (Saudi Arabia) was investigated in the present study. Forty-seven actinomycetes were cultivated and phylogenetically identified based on 16S rRNA gene sequencing and were assigned to 10 different actinomycete genera. Eight putatively novel species belonging to genera Kocuria, Mycobacterium, Nocardia, and Rhodococcus were identified based on sequence similarity values below 98.2% to other 16S rRNA gene sequences available in the NCBI database. PCR-based screening for biosynthetic genes including type I and type II polyketide synthases (PKS-I, PKS-II) as well as nonribosomal peptide synthetases (NRPS) showed that 20 actinomycete isolates encoded each at least one type of biosynthetic gene. The organic extracts of nine isolates displayed bioactivity against at least one of the test pathogens, which were Gram-positive and Gram-negative bacteria, fungi, human parasites, as well as in a West Nile Virus protease enzymatic assay. These results emphasize that marine sponges are a prolific resource for novel bioactive actinomycetes with potential for drug discovery. 2014 by the authors; licensee MDPI.

Actinomycetes from red sea sponges: Sources for chemical and phylogenetic diversity

KAUST Repository

Abdelmohsen, Usama Ramadan; Yang, Chen; Horn, Hannes; Hajjar, Dina A.; Ravasi, Timothy; Hentschel, Ute

2014-01-01

The diversity of actinomycetes associated with marine sponges collected off Fsar Reef (Saudi Arabia) was investigated in the present study. Forty-seven actinomycetes were cultivated and phylogenetically identified based on 16S rRNA gene sequencing and were assigned to 10 different actinomycete genera. Eight putatively novel species belonging to genera Kocuria, Mycobacterium, Nocardia, and Rhodococcus were identified based on sequence similarity values below 98.2% to other 16S rRNA gene sequences available in the NCBI database. PCR-based screening for biosynthetic genes including type I and type II polyketide synthases (PKS-I, PKS-II) as well as nonribosomal peptide synthetases (NRPS) showed that 20 actinomycete isolates encoded each at least one type of biosynthetic gene. The organic extracts of nine isolates displayed bioactivity against at least one of the test pathogens, which were Gram-positive and Gram-negative bacteria, fungi, human parasites, as well as in a West Nile Virus protease enzymatic assay. These results emphasize that marine sponges are a prolific resource for novel bioactive actinomycetes with potential for drug discovery. 2014 by the authors; licensee MDPI.

Dinamika Islam Politik Pasca Orde baru: Kajian Psikoanalisi Lacanian atas Hubungan KAMMI dan PKS

Directory of Open Access Journals (Sweden)

Ahmad Rizky Mardhatillah Umar

2014-07-01

Full Text Available This article aims at analyzing the relations between student movement andpolitical party in post-reform era of Indonesia. KAMMI, a prominent Islamiststudent movement in Indonesia, often associated with PKS (Prosperous JusticeParty in terms of identity and political practices. It has created ‘independencedilemma’ for KAMMI because since its first Congress in 1998, this studentorganization has declared ‘independent from all political forces’. This article,using Lacanian psychoanalytical tradition, exposes the forms of KAMMI’ssubjectivity and PKS interpellation that enable this political party to dominateKAMMI’s articulatory practices. The interpellation process is supported withthe projection of fantacy, emotion, and mirror in the development of KAMMIsince 1998 until present. It leads to PKS creating the KAMMI identity andthus made KAMMI’s articulatory practices identical with this party. However,there were several attempts to dislocate the hegemony through several internalreform movements. These attempts, although made contribution to internaldynamics within KAMMI, were unable to create alternative discourse dueto several limits of those movements. The case of KAMMI can be a model toexplain how other student movements develop and relate to political parties inIndonesian post-reform.

PERAN BUDAYA ORGANISASI DALAM MEWUJUDKAN VISI MISI PARTAI KEADILAN SEJAHTERA (PKS

Directory of Open Access Journals (Sweden)

Much. Yulianto

2016-11-01

The results showed: (1 organizational culture play a role in shaping the identity and character of party members; (2 The organizational culture also plays a role in encouraging loyalty and solidity of party members; (3 the organizational culture at PKS played role in strengthening the confidence of individual members.

A 4'-phosphopantetheinyl transferase mediates non-ribosomal peptide synthetase activation in Aspergillus fumigatus.

Science.gov (United States)

Neville, Claire; Murphy, Alan; Kavanagh, Kevin; Doyle, Sean

2005-04-01

Aspergillus fumigatus is a significant human pathogen. Non-ribosomal peptide (NRP) synthesis is thought to be responsible for a significant proportion of toxin and siderophore production in the organism. Furthermore, it has been shown that 4'-phosphopantetheinylation is required for the activation of key enzymes involved in non-ribosomal peptide synthesis in other species. Here we report the cloning, recombinant expression and functional characterisation of a 4'-phosphopantetheinyl transferase from A. fumigatus and the identification of an atypical NRP synthetase (Afpes1), spanning 14.3 kb. Phylogenetic analysis has shown that the NRP synthetase exhibits greatest identity to NRP synthetases from Metarhizium anisolpiae (PesA) and Alternaria brassicae (AbrePsy1). Northern hybridisation and RT-PCR analysis have confirmed that both genes are expressed in A. fumigatus. A 120 kDa fragment of the A. fumigatus NRP synthetase, containing a putative thiolation domain, was cloned and expressed in the baculovirus expression system. Detection of a 4'-phosphopantetheinylated peptide (SFSAMK) from this protein, by MALDI-TOF mass spectrometric analysis after coincubation of the 4'-phosphopantetheinyl transferase with the recombinant NRP synthetase fragment and acetyl CoA, confirms that it is competent to play a role in NRP synthetase activation in A. fumigatus. The 4'-phosphopantetheinyl transferase also activates, by 4'-phosphopantetheinylation, recombinant alpha-aminoadipate reductase (Lys2p) from Candida albicans, a key enzyme involved in lysine biosynthesis.

Redshift of the BL Lacertae object PKS 2005-489

Energy Technology Data Exchange (ETDEWEB)

Falomo, R.; Maraschi, L.; Treves, A.; Tanzi, E.G.

1987-07-01

In a high-resolution spectrum of PKS 2005-489 taken on Aug. 16, 1986 two weak emission lines (EW = about 1 A) were detected at 7031 and 7051 A. Identification with H-alpha and the 6583-A forbidden line of N II is proposed at a redshift z = 0.071. The observations correspond to a relatively faint state of the source with B = about 14.7. 12 references.

Redshift of the BL Lacertae object PKS 2005-489

International Nuclear Information System (INIS)

Falomo, R.; Maraschi, L.; Treves, A.; Tanzi, E.G.; Milano Universita, Milan, Italy; CNR, Istituto di Fisica Cosmica, Milan, Italy)

1987-01-01

In a high-resolution spectrum of PKS 2005-489 taken on Aug. 16, 1986 two weak emission lines (EW = about 1 A) were detected at 7031 and 7051 A. Identification with H-alpha and the 6583-A forbidden line of N II is proposed at a redshift z = 0.071. The observations correspond to a relatively faint state of the source with B = about 14.7. 12 references

Search for a pentaquark decaying to pKS0

Science.gov (United States)

FOCUS Collaboration; Link, J. M.; Yager, P. M.; Anjos, J. C.; Bediaga, I.; Castromonte, C.; Machado, A. A.; Magnin, J.; Massafferri, A.; de Miranda, J. M.; Pepe, I. M.; Polycarpo, E.; Dos Reis, A. C.; Carrillo, S.; Casimiro, E.; Cuautle, E.; Sánchez-Hernández, A.; Uribe, C.; Vázquez, F.; Agostino, L.; Cinquini, L.; Cumalat, J. P.; Frisullo, V.; O'Reilly, B.; Segoni, I.; Stenson, K.; Butler, J. N.; Cheung, H. W. K.; Chiodini, G.; Gaines, I.; Garbincius, P. H.; Garren, L. A.; Gottschalk, E.; Kasper, P. H.; Kreymer, A. E.; Kutschke, R.; Wang, M.; Benussi, L.; Bertani, M.; Bianco, S.; Fabbri, F. L.; Pacetti, S.; Zallo, A.; Reyes, M.; Cawlfield, C.; Kim, D. Y.; Rahimi, A.; Wiss, J.; Gardner, R.; Kryemadhi, A.; Chung, Y. S.; Kang, J. S.; Ko, B. R.; Kwak, J. W.; Lee, K. B.; Cho, K.; Park, H.; Alimonti, G.; Barberis, S.; Boschini, M.; Cerutti, A.; D'Angelo, P.; Dicorato, M.; Dini, P.; Edera, L.; Erba, S.; Inzani, P.; Leveraro, F.; Malvezzi, S.; Menasce, D.; Mezzadri, M.; Moroni, L.; Pedrini, D.; Pontoglio, C.; Prelz, F.; Rovere, M.; Sala, S.; Davenport, T. F.; Arena, V.; Boca, G.; Bonomi, G.; Gianini, G.; Liguori, G.; Lopes Pegna, D.; Merlo, M. M.; Pantea, D.; Ratti, S. P.; Riccardi, C.; Vitulo, P.; Göbel, C.; Olatora, J.; Hernandez, H.; Lopez, A. M.; Mendez, H.; Paris, A.; Quinones, J.; Ramirez, J. E.; Zhang, Y.; Wilson, J. R.; Handler, T.; Mitchell, R.; Engh, D.; Givens, K. M.; Hosack, M.; Johns, W. E.; Luiggi, E.; Nehring, M.; Sheldon, P. D.; Vaandering, E. W.; Webster, M.; Sheaff, M.

2006-08-01

We present a search for a pentaquark decaying strongly to pKS0 in γN collisions at a center-of-mass energy up to 25 GeV. Finding no evidence for such a state in the mass range of 1470 MeV/c to 2200 MeV/c, we set limits on the yield and on the cross section times branching ratio relative to Σ1385 and K892.

Bioactivity Assessment of Indian Origin-Mangrove Actinobacteria against Candida albicans.

Science.gov (United States)

Pavan Kumar, J G S; Gomathi, Ajitha; Gothandam, K M; Vasconcelos, Vitor

2018-02-12

Actinobacteria is found to have a potent metabolic activity against pathogens. The present study reveals the assessment of potent antifungal secondary metabolites from actinobacteria isolated from Indian marine mangrove sediments. The samples were collected from the coastal regions of Muthupet, Andaman and the Nicobar Islands. Identification was carried out using 16S rRNA analysis and biosynthetic genes (Polyketide synthase type I/II and Non-ribosomal peptide synthase) were screened. Actinobacteria were assayed for their antifungal activity against 16 clinical Candida albicans and the compound analysis was performed using gas chromatography-mass spectrometry GC-MS. The 31 actinobacterial strains were isolated and 16S rRNA gene sequencing revealed that this ecosystem is rich on actinobacteria, with Streptomyces as the predominant genus. The PCR based screening of biosynthetic genes revealed the presence of PKS-I in six strains, PKS-II in four strains and NRPS in 11 strains. The isolated actinobacteria VITGAP240 and VITGAP241 (two isolates) were found to have a potential antifungal activity against all the tested C. albicans . GC-MS results revealed that the actinobacterial compounds were belonging to heterocyclic, polyketides and peptides. Overall, the strains possess a wide spectrum of antifungal properties which affords the production of significant bioactive metabolites as potential antibiotics.

Structural and bioinformatic characterization of an Acinetobacter baumannii type II carrier protein

International Nuclear Information System (INIS)

Allen, C. Leigh; Gulick, Andrew M.

2014-01-01

The high-resolution crystal structure of a free-standing carrier protein from Acinetobacter baumannii that belongs to a larger NRPS-containing operon, encoded by the ABBFA-003406–ABBFA-003399 genes of A. baumannii strain AB307-0294, that has been implicated in A. baumannii motility, quorum sensing and biofilm formation, is presented. Microorganisms produce a variety of natural products via secondary metabolic biosynthetic pathways. Two of these types of synthetic systems, the nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), use large modular enzymes containing multiple catalytic domains in a single protein. These multidomain enzymes use an integrated carrier protein domain to transport the growing, covalently bound natural product to the neighboring catalytic domains for each step in the synthesis. Interestingly, some PKS and NRPS clusters contain free-standing domains that interact intermolecularly with other proteins. Being expressed outside the architecture of a multi-domain protein, these so-called type II proteins present challenges to understand the precise role they play. Additional structures of individual and multi-domain components of the NRPS enzymes will therefore provide a better understanding of the features that govern the domain interactions in these interesting enzyme systems. The high-resolution crystal structure of a free-standing carrier protein from Acinetobacter baumannii that belongs to a larger NRPS-containing operon, encoded by the ABBFA-003406–ABBFA-003399 genes of A. baumannii strain AB307-0294, that has been implicated in A. baumannii motility, quorum sensing and biofilm formation, is presented here. Comparison with the closest structural homologs of other carrier proteins identifies the requirements for a conserved glycine residue and additional important sequence and structural requirements within the regions that interact with partner proteins

Structural and bioinformatic characterization of an Acinetobacter baumannii type II carrier protein

Energy Technology Data Exchange (ETDEWEB)

Allen, C. Leigh; Gulick, Andrew M., E-mail: gulick@hwi.buffalo.edu [University at Buffalo, Buffalo, NY 14203 (United States)

2014-06-01

The high-resolution crystal structure of a free-standing carrier protein from Acinetobacter baumannii that belongs to a larger NRPS-containing operon, encoded by the ABBFA-003406–ABBFA-003399 genes of A. baumannii strain AB307-0294, that has been implicated in A. baumannii motility, quorum sensing and biofilm formation, is presented. Microorganisms produce a variety of natural products via secondary metabolic biosynthetic pathways. Two of these types of synthetic systems, the nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), use large modular enzymes containing multiple catalytic domains in a single protein. These multidomain enzymes use an integrated carrier protein domain to transport the growing, covalently bound natural product to the neighboring catalytic domains for each step in the synthesis. Interestingly, some PKS and NRPS clusters contain free-standing domains that interact intermolecularly with other proteins. Being expressed outside the architecture of a multi-domain protein, these so-called type II proteins present challenges to understand the precise role they play. Additional structures of individual and multi-domain components of the NRPS enzymes will therefore provide a better understanding of the features that govern the domain interactions in these interesting enzyme systems. The high-resolution crystal structure of a free-standing carrier protein from Acinetobacter baumannii that belongs to a larger NRPS-containing operon, encoded by the ABBFA-003406–ABBFA-003399 genes of A. baumannii strain AB307-0294, that has been implicated in A. baumannii motility, quorum sensing and biofilm formation, is presented here. Comparison with the closest structural homologs of other carrier proteins identifies the requirements for a conserved glycine residue and additional important sequence and structural requirements within the regions that interact with partner proteins.

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.

Science.gov (United States)

Chevrette, Marc G; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R; Medema, Marnix H

2017-10-15

Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use. Here, we introduce prediCAT, a new phylogenetics-inspired algorithm, which quantitatively estimates the degree of predictability of each A-domain. We then systematically benchmarked all algorithms on a newly gathered, independent test set of 434 A-domain sequences, showing that active-site-motif-based algorithms outperform whole-domain-based methods. Subsequently, we developed SANDPUMA, a powerful ensemble algorithm, based on newly trained versions of all high-performing algorithms, which significantly outperforms individual methods. Finally, we deployed SANDPUMA in a systematic investigation of 7635 Actinobacteria genomes, suggesting that NRP chemical diversity is much higher than previously estimated. SANDPUMA has been integrated into the widely used antiSMASH biosynthetic gene cluster analysis pipeline and is also available as an open-source, standalone tool. SANDPUMA is freely available at https://bitbucket.org/chevrm/sandpuma and as a docker image at https://hub.docker.com/r/chevrm/sandpuma/ under the GNU Public License 3 (GPL3). chevrette@wisc.edu or marnix.medema@wur.nl. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Identification of PaPKS1, a polyketide synthase involved in melanin formation and its use as a genetic tool in Podospora anserina.

Science.gov (United States)

Coppin, Evelyne; Silar, Philippe

2007-08-01

In the filamentous fungus Podospora anserina, many pigmentation mutations map to the median region of the complex locus '14', called segment '29'. The data presented in this paper show that segment 29 corresponds to a gene encoding a polyketide synthase, designated PaPKS1, and identifies two mutations that completely or partially abolish the activity of the PaPKS1 polypeptide. We present evidence that the P. anserina green pigment is a (DHN)-melanin. Using the powerful genetic system of PaPKS1 cloning, we demonstrate that in P. anserina trans-duplicated sequences are subject to the RIP process as previously demonstrated for the cis-duplicated regions.

FERMI/LARGE AREA TELESCOPE DISCOVERY OF GAMMA-RAY EMISSION FROM THE FLAT-SPECTRUM RADIO QUASAR PKS 1454-354

International Nuclear Information System (INIS)

Abdo, A. A.; Ackermann, M.; Bechtol, K.; Berenji, B.; Blandford, R. D.; Bloom, E. D.; Borgland, A. W.; Atwood, W. B.; Axelsson, M.; Baldini, L.; Bellazzini, R.; Bregeon, J.; Brez, A.; Ballet, J.; Barbiellini, G.; Bastieri, D.; Baughman, B. M.; Bogaert, G.; Bonamente, E.; Brigida, M.

2009-01-01

We report the discovery by the Large Area Telescope (LAT) onboard the Fermi Gamma-Ray Space Telescope of high-energy γ-ray (GeV) emission from the flat-spectrum radio quasar PKS 1454-354 (z = 1.424). On 2008 September 4, the source rose to a peak flux of (3.5 ± 0.7) x 10 -6 ph cm -2 s -1 (E > 100 MeV) on a timescale of hours and then slowly dropped over the following 2 days. No significant spectral changes occurred during the flare. Fermi/LAT observations also showed that PKS 1454-354 is the most probable counterpart of the unidentified EGRET source 3EG J1500-3509. Multiwavelength measurements performed during the following days (7 September with Swift; 6-7 September with the ground-based optical telescope Automated Telescope for Optical Monitoring; 13 September with the Australia Telescope Compact Array) resulted in radio, optical, UV, and X-ray fluxes greater than archival data, confirming the activity of PKS 1454-354.

[Diversity and bioactivity analysis of actinomycetes isolated from grand Shangri-La soil].

Science.gov (United States)

Cao, Yanru; Jiang, Yi; Xu, Lihua

2009-01-01

To obtain new pharmaceuticals and enzymes with high activity,we studied the composition as well as antimicrobial and enzyme activities of actinomycetes in Grand Shangri-La. Using 4 media,we isolated mesophilic and psychrophilic actinomycetes from 220 soil samples collected from areas with different altitudes in Grand Shangri-La. Twenty-five representative isolates were phylogenetically analyzed based on their 16S rRNA gene sequences. Antimicrobial activities against four bacteria and seven fungi were tested using agar well diffusion method. Genes encoding type I and II polyketide synthases (PKS I, PKS II), nonribosomal peptide synthase (NRPS) and polyene cytochrome P450 hydroxylase (CYP) were screened by PCR. Furthermore,several enzyme activities of psychrophilic actinomycetes were examined. The 25 representative strains belonged to 6 suborders, 12 families and 15 genera of the order Actinomycetals. For NRPS and CYP genes screening, positive strains were 14 and 11, respectively. Among the 111 actinomycetes isolated under low-temperature conditions, 88% were psychrotroph strains, 12% were psychrophilic actinomycetes, and most of them utilized gelatin, cellulose and chitin. Actinomycetes diversity is rich in Grand Shangri-la, and has the potential for conservation and utilization of actinomycetes resources.

Crystallization and preliminary X-ray diffraction studies of polyketide synthase-1 (PKS-1) from Cannabis sativa

International Nuclear Information System (INIS)

Taguchi, Chiho; Taura, Futoshi; Tamada, Taro; Shoyama, Yoshinari; Shoyama, Yukihiro; Tanaka, Hiroyuki; Kuroki, Ryota; Morimoto, Satoshi

2008-01-01

Polyketide synthase-1 from C. sativa has been crystallized. The crystal diffracted to 1.55 Å resolution with sufficient quality for further structure determination. Polyketide synthase-1 (PKS-1) is a novel type III polyketide synthase that catalyzes the biosynthesis of hexanoyl triacetic acid lactone in Cannabis sativa (Mexican strain). PKS-1 was overproduced in Escherichia coli, purified and finally crystallized in two different space groups. The crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M calcium acetate and 20%(w/v) polyethylene glycol 3350 diffracted to 1.65 Å resolution and belonged to space group P1, with unit-cell parameters a = 54.3, b = 59.3, c = 62.6 Å, α = 69, β = 81, γ = 80°. Another crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M sodium chloride and 20%(w/v) polyethylene glycol 3350 diffracted to 1.55 Å resolution and belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 54.3, b = 110, c = 130 Å. These data will enable us to determine the crystal structure of PKS-1

Crystallization and preliminary X-ray diffraction studies of polyketide synthase-1 (PKS-1) from Cannabis sativa

Energy Technology Data Exchange (ETDEWEB)

Taguchi, Chiho [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Taura, Futoshi [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Tamada, Taro; Shoyama, Yoshinari [Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Shoyama, Yukihiro; Tanaka, Hiroyuki [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Kuroki, Ryota [Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Morimoto, Satoshi [Faculty of Pharmaceutical Sciences, Kyushu University (Japan)

2008-03-01

Polyketide synthase-1 from C. sativa has been crystallized. The crystal diffracted to 1.55 Å resolution with sufficient quality for further structure determination. Polyketide synthase-1 (PKS-1) is a novel type III polyketide synthase that catalyzes the biosynthesis of hexanoyl triacetic acid lactone in Cannabis sativa (Mexican strain). PKS-1 was overproduced in Escherichia coli, purified and finally crystallized in two different space groups. The crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M calcium acetate and 20%(w/v) polyethylene glycol 3350 diffracted to 1.65 Å resolution and belonged to space group P1, with unit-cell parameters a = 54.3, b = 59.3, c = 62.6 Å, α = 69, β = 81, γ = 80°. Another crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M sodium chloride and 20%(w/v) polyethylene glycol 3350 diffracted to 1.55 Å resolution and belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 54.3, b = 110, c = 130 Å. These data will enable us to determine the crystal structure of PKS-1.

Some physical and mechanical properties of palm kernel shell (PKS ...

African Journals Online (AJOL)

In this study, some of the mechanical and physical properties of palm kernel shells (PKS) were evaluated. These are moisture content, 7.8325 ± 0.6672%; true density, 1.254 ± 5.292 x 10-3 g/cm3; bulk density, 1.1248g/cm3; mean rupture force along width, and thickness were 3174.52 ± 270.70N and 2806.94 ± 498.45N for ...

Biosynthetic potential for polyketides in Talaromyces atroroseus

DEFF Research Database (Denmark)

Rasmussen, Kasper Bøwig; Mortensen, Uffe Hasbro; Thrane, Ulf

11, and deletion of PKS11 results in the loss of Monascus pigment production. T. atroroseus PKS11 is delivering a precursor for both the mitorubrins and the Monascus pigments. Based on this finding we propose hypothetical models for the evolution of azaphilone pigment PKS clusters in Talaromyces......Talaromyces atroroseus is an efficient producer of red Monascus pigments. We genome sequenced Talaromyces atroroseus IBT11181 and found it to lack the Monascus pigment PKS with the rest of the Monascus pigment cluster intact. The PKS closest related to the Monascus pigment PKS is the mitorubrin PKS...

Potency of sponge-associated bacteria producing bioactive compounds as biological control of vibriosis on shrimp

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Adityawati Fajar Rini

2017-07-01

Full Text Available ABSTRACT The aims of this study were to obtain sponge-associated bacteria as biocontrol to inhibit vibriosis in vitro and in vivo, to identify the bacterial isolates based on 16S-rRNA gene, and to detect the presence of nonribosomal peptide synthetase (NRPS, and polyketide synthase (PKS genes to prove its ability of bioactive compounds synthesis. Aaptos sp. and Hyrtios sp. sponges were collected from Pramuka Island, Jakarta. The isolation using sea water complete (SWC and  zobel marine agar (ZMA medium obtained 174 isolates. A total 69 isolates were screened successfully based on their antibacterial activity. 47 isolates showed negative haemolysis through hemolytic assays. The pathogenicity test used twelve selected isolates that have a broad spectrum of antibacterial activity and haemolysis negative. The result of pathogenicity test showed  that 12 isolates were not pathogenic to the shrimp post larvae with no significantly different (P>0.05 between treatment and negative control. Results of challenge test with Vibrio harveyi have a significant difference survival (70±5.0–90±0.0% (P<0.05 compared with positive control (38.3±2.9%. Genetic analysis based on 16S-rRNA revealed the groups of three genera belonged to Pseudomonas, Staphylococcus, and Alcaligenes. Based on amplification of NRPS and PKS genes, four bacterial isolates have been detected to have only NRPS gene, one isolate has only PKS, and one isolate has both genes. The results indicate that the potency of six sponge-associated bacteria as bioactive compounds producers. Keywords: NRPS, PKS, anti-vibriosis, Pacific white shrimp  ABSTRAK Penelitian ini bertujuan untuk memperoleh isolat bakteri asosiasi spons yang mempunyai kemampuan dalam menghambat vibriosis secara in vitro, in vivo dan mendeteksi gen 16S-rRNA, nonribosomal peptide synthase (NRPS serta polyketide synthase (PKS untuk memastikan kemampuan mensintesis senyawa bioaktif. Spons Aaptos sp. dan Hyrtios sp. berhasil

ALMA observations of AGN fuelling. The case of PKS B1718-649

Science.gov (United States)

Maccagni, F. M.; Morganti, R.; Oosterloo, T. A.; Oonk, J. B. R.; Emonts, B. H. C.

2018-06-01

We present ALMA observations of the 12CO (2-1) line of the newly born (tradio 102 years) active galactic nucleus (AGN), PKS B1718-649. These observations reveal that the carbon monoxide in the innermost 15 kpc of the galaxy is distributed in a complex warped disk. In the outer parts of this disk, the CO gas follows the rotation of the dust lane and of the stellar body of the galaxy hosting the radio source. In the innermost kiloparsec, the gas abruptly changes orientation and forms a circumnuclear disk (r ≲ 700 pc) with its major axis perpendicular to that of the outer disk. Against the compact radio emission of PKS B1718-649 (r 2 pc), we detect an absorption line at red-shifted velocities with respect to the systemic velocity (Δv = +365 ± 22 km s-1). This absorbing CO gas could trace molecular clouds falling onto the central super-massive black hole. A comparison with the near-infrared H2 1-0 S(1) observations shows that the clouds must be close to the black hole (r ≲ 75 pc). The physical conditions of these clouds are different from the gas at larger radii, and are in good agreement with the predictions for the conditions of the gas when cold chaotic accretion triggers an active galactic nucleus. These observations on the centre of PKS B1718-649 provide one of the best indications that a population of cold clouds is falling towards a radio AGN, likely fuelling its activity. The reduced datacube is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/614/A42

Comparative analysis of oligonucleotide primers for high-throughput screening of genes encoding adenylation domains of nonribosomal peptide synthetases in actinomycetes

Czech Academy of Sciences Publication Activity Database

Bakal, Tomáš; Goo, K.-S.; Najmanová, Lucie; Plháčková, Kamila; Kadlčík, Stanislav; Ulanová, Dana

2015-01-01

Roč. 108, č. 5 (2015), s. 1267-1274 ISSN 0003-6072 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : Nonribosomal peptide synthetase * Adenylation domain * Actinomycetes Subject RIV: EE - Microbiology, Virology Impact factor: 1.944, year: 2015

Diversity of Nonribosomal Peptide Synthetases Involved in the Biosynthesis of Lipopeptide Biosurfactants

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Niran Roongsawang

2010-12-01

Full Text Available Lipopeptide biosurfactants (LPBSs consist of a hydrophobic fatty acid portion linked to a hydrophilic peptide chain in the molecule. With their complex and diverse structures, LPBSs exhibit various biological activities including surface activity as well as anti-cellular and anti-enzymatic activities. LPBSs are also involved in multi-cellular behaviors such as swarming motility and biofilm formation. Among the bacterial genera, Bacillus (Gram-positive and Pseudomonas (Gram-negative have received the most attention because they produce a wide range of effective LPBSs that are potentially useful for agricultural, chemical, food, and pharmaceutical industries. The biosynthetic mechanisms and gene regulation systems of LPBSs have been extensively analyzed over the last decade. LPBSs are generally synthesized in a ribosome-independent manner with megaenzymes called nonribosomal peptide synthetases (NRPSs. Production of active‑form NRPSs requires not only transcriptional induction and translation but also post‑translational modification and assemblage. The accumulated knowledge reveals the versatility and evolutionary lineage of the NRPSs system. This review provides an overview of the structural and functional diversity of LPBSs and their different biosynthetic mechanisms in Bacillus and Pseudomonas, including both typical and unique systems. Finally, successful genetic engineering of NRPSs for creating novel lipopeptides is also discussed.

Structural pattern matching of nonribosomal peptides

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Leclère Valérie

2009-03-01

Full Text Available Abstract Background Nonribosomal peptides (NRPs, bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents. NRPs are mainly composed of amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there are several hundred different monomers that can be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently stores more than 700 NRPs annotated with their monomeric peptide structure encoded by undirected labeled graphs. This opens a way to a systematic analysis of structural patterns occurring in NRPs. Such studies can investigate the functional role of some monomeric chains, or analyse NRPs that have been computationally predicted from the synthetase protein sequence. A basic operation in such analyses is the search for a given structural pattern in the database. Results We developed an efficient method that allows for a quick search for a structural pattern in the NORINE database. The method identifies all peptides containing a pattern substructure of a given size. This amounts to solving a variant of the maximum common subgraph problem on pattern and peptide graphs, which is done by computing cliques in an appropriate compatibility graph. Conclusion The method has been incorporated into the NORINE database, available at http://bioinfo.lifl.fr/norine. Less than one second is needed to search for a pattern in the entire database.

An unusually strong Einstein ring in the radio source PKS1830-211

International Nuclear Information System (INIS)

Jauncey, D.L.

1991-01-01

RADIO observations of the strong, flat-spectrum radio source PKS1830-211 revealed a double structure, with a separation of 1 arcsec, suggesting that it might be a gravitationally lensed object. We have now obtained high-resolution radio images of PKS1830-211 from several interferometric radiotelescope networks, which show an unusual elliptical ring-like structure connecting the two brighter components. The presence of the ring, and the similarity of the two brighter spots, argue strongly that this is indeed a gravitationally lensed system, specifically an Einstein ring in which lens and lensed object are closely aligned. Although the source is close to the galactic plane, it seems that both the lens and background (lensed) object are extragalactic. This object is one hundred times brighter than either of the two previously discovered radio Einstein rings, and is among the six brightest flat-spectrum sources in the sky. Its brightness makes it a peculiar object: it must involve either a chance alignment of a lensing object with an unusually bright background source, or an alignment with a less bright object but amplified to an unusual degree. (author)

New bounds on axionlike particles from the Fermi Large Area Telescope observation of PKS 2155 -304

Science.gov (United States)

Zhang, Cun; Liang, Yun-Feng; Li, Shang; Liao, Neng-Hui; Feng, Lei; Yuan, Qiang; Fan, Yi-Zhong; Ren, Zhong-Zhou

2018-03-01

The axionlike particle (ALP)-photon mixing in the magnetic field around γ -ray sources or along the line of sight could induce oscillation between photons and ALPs, which then causes irregularities in the γ -ray spectra. In this work we search for such spectral irregularities in the spectrum of PKS 2155 -304 using 8.6 years of data from the Fermi Large Area Telescope (Fermi-LAT). No significant evidence for the presence of ALP-photon oscillation is obtained, and the parameter space of ALPs is constrained. The exclusion region sensitively depends on the poorly known magnetic field of the host galaxy cluster of PKS 2155 -304 . If the magnetic field is as high as ˜10 μ G , the "holelike" parameter region allowed in Ref. [1] can be ruled out.

Multi-Wavelength Variability in PKS 2155-304 Y. G. Zheng1,2, L ...

Indian Academy of Sciences (India)

2009), we attempt to model the multi-wavelength variability in PKS 2155-304. We assume that the acceleration process is a stochastic process and we describe it as the diffusion of the particle momentum. Throughout the paper, we assume the. Hubble constant H0 = 70 km s−1. Mpc. −1. , the matter energy density M = 0.27,.

Multifrequency observations of the Blazar PKS 0537-441 in a moderately active state

International Nuclear Information System (INIS)

Tanzi, E.G.; Chiappetti, L.; Barr, P.; Bouchet, P.; Cristiani, S.; EXOSAT Observatory, Darmstadt, West Germany; European Southern Observatory, La Silla, Chile)

1986-01-01

PKS 0537-441 was observed during an active state in February 1985 at infrared, optical, UV, and X-ray frequencies. Comparison with earlier measurements indicates that the source brightened by a factor of approximately 2 in all bands. This suggests that the same spatial region may be responsible for the emission in the whole spectral range observed. 19 references

Multifrequency observations of the Blazar PKS 0537-441 in a moderately active state

Energy Technology Data Exchange (ETDEWEB)

Tanzi, E.G.; Chiappetti, L.; Barr, P.; Bouchet, P.; Cristiani, S.

1986-12-01

PKS 0537-441 was observed during an active state in February 1985 at infrared, optical, UV, and X-ray frequencies. Comparison with earlier measurements indicates that the source brightened by a factor of approximately 2 in all bands. This suggests that the same spatial region may be responsible for the emission in the whole spectral range observed. 19 references.

First detection in gamma-rays of a young radio galaxy: Fermi -LAT observations of the compact symmetric object PKS 1718−649

Energy Technology Data Exchange (ETDEWEB)

Migliori, G.; Loh, A.; Corbel, S. [Laboratoire AIM (CEA/IRFU—CNRS/INSU—Université Paris Diderot), CEA DSM/SAp, F-91191 Gif-sur-Yvette (France); Siemiginowska, A.; Sobolewska, M. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Ostorero, L. [Dipartimento di Fisica, Università degli Studi di Torino and Istituto Nazionale di Fisica Nucleare (INFN), Via P. Giuria 1, I-10125 Torino (Italy); Stawarz, Ł., E-mail: giulia.migliori@cea.fr [Astronomical Observatory, Jagiellonian University, ul. Orla 171, 30-244 Kraków (Poland)

2016-04-20

We report the γ -ray detection of a young radio galaxy, PKS 1718−649, belonging to the class of compact symmetric objects (CSOs), with the Large Area Telescope (LAT) on board the Fermi satellite. The third Fermi Gamma-ray LAT catalog (3FGL) includes an unassociated γ -ray source, 3FGL J1728.0−6446, located close to PKS 1718−649. Using the latest Pass 8 calibration, we confirm that the best-fit 1 σ position of the γ -ray source is compatible with the radio location of PKS 1718−649. Cross-matching of the γ -ray source position with the positions of blazar sources from several catalogs yields negative results. Thus, we conclude that PKS 1718−649 is the most likely counterpart to the unassociated LAT source. We obtain a detection test statistics TS ∼ 36 (>5 σ ) with a best-fit photon spectral index Γ = 2.9 ± 0.3 and a 0.1–100 GeV photon flux density F {sub 0.1−100} {sub GeV} = (11.5 ± 0.3) × 10{sup −9} ph cm{sup −2} s{sup −1}. We argue that the linear size (∼2 pc), the kinematic age (∼100 years), and the source distance ( z = 0.014) make PKS 1718−649 an ideal candidate for γ -ray detection in the framework of the model proposing that the most compact and the youngest CSOs can efficiently produce GeV radiation via inverse-Compton scattering of the ambient photon fields by the radio lobe non-thermal electrons. Thus, our detection of the source in γ -rays establishes young radio galaxies as a distinct class of extragalactic high-energy emitters and yields a unique insight on the physical conditions in compact radio lobes interacting with the interstellar medium of the host galaxy.

In silico Design of "Un-Natural" Natural Products

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Zucko; J. ...(et al.

2008-05-01

Full Text Available Polyketides and non-ribosomal peptides represent a large class of structurally diverse natural products much studied over recent years because the enzymes that synthesise them, the modular polyketide synthases (PKSs and the non-ribosomal peptide synthetases (NRPSs, share striking architectural similarities that can be exploited to generate "un-natural" natural products. PKS and NRPS proteins are multifunctional, composed of a co-linear arrangement of discrete protein domains representing each enzymic activity needed for chain elongation using either carboxylic acid or amino acid building blocks. Each domain is housed within larger modules which form the complex. Polyketide and peptide antibiotics, antifungals, antivirals, cytostatics, immunosuppressants, antihypertensives, antidiabetics, antimalarials and anticholesterolemics are in clinical use. Of commercial importance are also polyketide and peptide antiparasitics, coccidiostatics,animal growth promoters and natural insecticides.Polyketides are assembled through serial condensations of activated coenzyme-A thioester monomers derived from simple organic acids such as acetate, propionate and butyrate. The choice of organic acid allows the introduction of different chiral centres into the polyketide backbone. The active sites required for condensation include an acyltransferase (AT, an acyl carrier protein (ACP and a ß-ketoacylsynthase (KS. Each condensation results in a ß-keto group that undergoes all, some or none of a series of processing steps. Active sites that perform these reactions are contained within the following domains; ketoreductase (KR, dehydratase (DH and an enoylreductase (ER. The absence of any ß-keto processing results in the incorporation of a ketone group into the growing polyketide chain, a KR alone gives rise to a hydroxyl moiety, a KR and DH produce an alkene, while the combination of KR, DH and ER domains lead to complete reduction to an alkane. Most often, the last

Galaxy at a redshift of 3.215 - further studies of the PKS 1614+051 system

International Nuclear Information System (INIS)

Djorgovski, S.; Strauss, M.A.; Spinrad, H.; Mccarthy, P.; Perley, R.A.; California Univ., Berkeley; National Radio Astronomy Observatory, Charlottesville, VA)

1987-01-01

A narrow-emission-line companion of the quasar PKS 1614+051 was reported earlier as a probable galaxy at a redshift of 3.218, which would have made it by far the most distant galaxy known at the time. New radio and optical imaging, and optical and near-IR spectroscopy of the PKS 1614+051 system is reported here. It is argued that the data support and reinforce the original interpretation of the companion object as a mildly active galaxy, possibly a marginal Seyfert 2. The object has a detectable and marginally resolved optical continuum, but was not detected at radio wavelengths. The ionization state is low, and the emission lines are fairly narrow. The improved redshift for the companion, based on the Ly-alpha line alone, is 3.215 + or - 0.002. New Ly-alpha images show interesting morphology of extended emission-line gas, suggestive of a possible tidal interaction with the neighboring QSO. 24 references

Long-term Study of the Light Curve of PKS 1510-089 in GeV Energies

Energy Technology Data Exchange (ETDEWEB)

Prince, Raj; Gupta, Nayantara [Raman Research Institute, Sadashivanagar, Bangalore 560080 (India); Majumdar, Pratik, E-mail: rajprince@rri.res.in [Saha Institute of Nuclear Physics, HBNI, Kolkata, West Bengal 700064 (India)

2017-07-20

We have analyzed data from the flat-spectrum radio quasar PKS 1510-089 collected over a period of eight years from 2008 August to 2016 December with the Fermi -LAT. We have identified several flares of this highly variable source, studied their temporal and spectral properties in detail, and compared with previous works on flares of PKS 1510-089. Five major flares and a few subflares or substructures have been identified in our study. The fastest variability time is found to be 1.30 ± 0.18 hr between MJD 55852.063 and 55852.188, where we estimate the minimum size of the emission region to be 4.85 × 10{sup 15} cm. In most of the flares, the spectral energy distributions are better fitted with a log-parabolic distribution compared to a simple power law or a power law with exponential cutoffs. This has strong physics implications regarding the nature of the high-energy gamma-ray emission region.

Unveiling the nature of the γ-ray emitting active galactic nucleus PKS 0521-36

International Nuclear Information System (INIS)

D'Ammando, F.; Istituto Nazionale di Astrofisica; Orienti, M.; Tavecchio, F.; Ghisellini, G.

2015-01-01

PKS 0521-36 is an active galactic nucleus (AGN) with uncertain classification. Here, we investigate the properties of this source from radio to γ-rays. The broad emission lines in the optical and ultraviolet bands and steep radio spectrum indicate a possible classification as an intermediate object between broad-line radio galaxies (BLRG) and steep spectrum radio quasars (SSRQ). On pc-scales PKS 0521-36 shows a knotty structure similar to misaligned AGN. The core dominance and the γ-ray properties are similar to those estimated for other SSRQ and BLRG detected in γ-rays, suggesting an intermediate viewing angle with respect to the observer. In this context the flaring activity detected from this source by Fermi-Large Area Telescope between 2010 June and 2012 February is very intriguing. We discuss the γ-ray emission of this source in the framework of the structured jet scenario, comparing the spectral energy distribution (SED) of the flaring state in 2010 June with that of a low state. We present three alternative models corresponding to three different choices of the viewing angles θv = 6°, 15°, and 20°. We obtain a good fit for the first two cases, but the SED obtained with θv = 15° if observed at a small angle does not resemble that of a typical blazar since the synchrotron emission should dominate by a large factor (~100) the inverse Compton component. This suggests that a viewing angle between 6° and 15° is preferred, with the rapid variability observed during γ-ray flares favouring a smaller angle. However, we cannot rule out that PKS 0521-36 is the misaligned counterpart of a synchrotron-dominated blazar.

The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variation

DEFF Research Database (Denmark)

Harris, Abigail K P; Williamson, Neil R; Slater, Holly

2004-01-01

The prodigiosin biosynthesis gene cluster (pig cluster) from two strains of Serratia (S. marcescens ATCC 274 and Serratia sp. ATCC 39006) has been cloned, sequenced and expressed in heterologous hosts. Sequence analysis of the respective pig clusters revealed 14 ORFs in S. marcescens ATCC 274...... and 15 ORFs in Serratia sp. ATCC 39006. In each Serratia species, predicted gene products showed similarity to polyketide synthases (PKSs), non-ribosomal peptide synthases (NRPSs) and the Red proteins of Streptomyces coelicolor A3(2). Comparisons between the two Serratia pig clusters and the red cluster...... from Str. coelicolor A3(2) revealed some important differences. A modified scheme for the biosynthesis of prodigiosin, based on the pathway recently suggested for the synthesis of undecylprodigiosin, is proposed. The distribution of the pig cluster within several Serratia sp. isolates is demonstrated...

Effects of disrupting the polyketide synthase gene WdPKS1 in Wangiella [Exophiala] dermatitidis on melanin production and resistance to killing by antifungal compounds, enzymatic degradation, and extremes in temperature

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Mandal Piyali

2006-06-01

Full Text Available Abstract Background Wangiella dermatitidis is a human pathogenic fungus that is an etiologic agent of phaeohyphomycosis. W. dermatitidis produces a black pigment that has been identified as a dihydroxynaphthalene melanin and the production of this pigment is associated with its virulence. Cell wall pigmentation in W. dermatitidis depends on the WdPKS1 gene, which encodes a polyketide synthase required for generating the key precursor for dihydroxynaphthalene melanin biosynthesis. Results We analyzed the effects of disrupting WdPKS1 on dihydroxynaphthalene melanin production and resistance to antifungal compounds. Transmission electron microscopy revealed that wdpks1Δ-1 yeast had thinner cell walls that lacked an electron-opaque layer compared to wild-type cells. However, digestion of the wdpks1Δ-1 yeast revealed small black particles that were consistent with a melanin-like compound, because they were acid-resistant, reacted with melanin-binding antibody, and demonstrated a free radical signature by electron spin resonance analysis. Despite lacking the WdPKS1 gene, the mutant yeast were capable of catalyzing the formation of melanin from L-3,4-dihyroxyphenylalanine. The wdpks1Δ-1 cells were significantly more susceptible to killing by voriconazole, amphotericin B, NP-1 [a microbicidal peptide], heat and cold, and lysing enzymes than the heavily melanized parental or complemented strains. Conclusion In summary, W. dermatitidis makes WdPKS-dependent and -independent melanins, and the WdPKS1-dependent deposition of melanin in the cell wall confers protection against antifungal agents and environmental stresses. The biological role of the WdPKS-independent melanin remains unclear.

Optimization of nonribosomal peptides production by a psychrotrophic fungus: Trichoderma velutinum ACR-P1.

Science.gov (United States)

Sharma, Richa; Singh, Varun P; Singh, Deepika; Yusuf, Farnaz; Kumar, Anil; Vishwakarma, Ram A; Chaubey, Asha

2016-11-01

Trichoderma is an anamorphic filamentous fungal genus with immense potential for production of small valuable secondary metabolites with indispensable biological activities. Microbial dynamics of a psychrotrophic strain Trichoderma velutinum ACR-P1, isolated from unexplored niches of the Shiwalik region, bestowed with rich biodiversity of microflora, was investigated for production of nonribosomal peptides (NRPs) by metabolite profiling by intact-cell mass spectrometry (ICMS) employing matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer. Being the first report on NRPs production by T. velutinum, studies on optimization of growth conditions by Response Surface Methodology (RSM) for production of NRPs by ACR-P1 was carried out strategically. Multifold enhancement in the yield of NRPs belonging to subfamily SF4 with medium chain of amino acid residues having m/z 1437.9, 1453.9, and 1452.0 at pH 5.9 at 20 °C and of subfamily SF1 with long-chain amino acid residues having m/z 1770.2, 1784.2, 1800.1, 1802.1, and 1815.1 was achieved at pH 7.0 at 25 °C. Complexities of natural mixtures were thus considerably reduced under respective optimized culture conditions accelerating the production of novel microbial natural products by saving time and resources.

Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae.

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Ana Patrícia Graça

Full Text Available Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA, Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus, fish pathogen (Aliivibrio fischeri and environmentally relevant bacteria (Vibrio harveyi. The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%, Vibrio (22.7% and Bacillus (7.6%. Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I and nonribosomal peptide synthetases (NRPSs genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds.

Endophytic Actinobacteria Associated with Dracaena cochinchinensis Lour.: Isolation, Diversity, and Their Cytotoxic Activities.

Science.gov (United States)

Salam, Nimaichand; Khieu, Thi-Nhan; Liu, Min-Jiao; Vu, Thu-Trang; Chu-Ky, Son; Quach, Ngoc-Tung; Phi, Quyet-Tien; Narsing Rao, Manik Prabhu; Fontana, Angélique; Sarter, Samira; Li, Wen-Jun

2017-01-01

Dracaena cochinchinensis Lour. is an ethnomedicinally important plant used in traditional Chinese medicine known as dragon's blood. Excessive utilization of the plant for extraction of dragon's blood had resulted in the destruction of the important niche. During a study to provide a sustainable way of utilizing the resources, the endophytic Actinobacteria associated with the plant were explored for potential utilization of their medicinal properties. Three hundred and four endophytic Actinobacteria belonging to the genera Streptomyces , Nocardiopsis , Brevibacterium , Microbacterium , Tsukamurella , Arthrobacter , Brachybacterium , Nocardia , Rhodococcus , Kocuria , Nocardioides , and Pseudonocardia were isolated from different tissues of D. cochinchinensis Lour. Of these, 17 strains having antimicrobial and anthracyclines-producing activities were further selected for screening of antifungal and cytotoxic activities against two human cancer cell lines, MCF-7 and Hep G2. Ten of these selected endophytic Actinobacteria showed antifungal activities against at least one of the fungal pathogens, of which three strains exhibited cytotoxic activities with IC 50 -values ranging between 3 and 33  μ g·mL -1 . Frequencies for the presence of biosynthetic genes, polyketide synthase- (PKS-) I, PKS-II, and nonribosomal peptide synthetase (NRPS) among these 17 selected bioactive Actinobacteria were 29.4%, 70.6%, and 23.5%, respectively. The results indicated that the medicinal plant D. cochinchinensis Lour. is a good niche of biologically important metabolites-producing Actinobacteria.

Results of the first simultaneous X-ray, optical, and radio campaign on the blazar PKS 1622-297

NARCIS (Netherlands)

Meyer, Angela Osterman; Miller, H. Richard; Marshall, Kevin; Ryle, Wesley T.; Aller, Hugh; Aller, Margo; McFarland, John P.; Pollock, Joseph T.; Reichart, Daniel E.; Crain, J. Adam; Ivarsen, Kevin M.; LaCluyze, Aaron P.; Nysewander, Melissa C.

Coordinated X-ray, optical, and radio observations of the blazar PKS 1622-297 were obtained during a three-week campaign in 2006 using the Rossi X-Ray Timing Explorer (RXTE), the University of Michigan Radio Astronomy Observatory, and optical telescopes at Cerro Tololo Inter-American Observatory.

Multifrequency observations of the BL Lacertae object PKS 0537 - 441

Science.gov (United States)

Maraschi, L.; Treves, A.; Schwartz, D. A.; Tanzi, E. G.

1985-01-01

PKS 0537 - 441 was repeatedly observed in the UV band with the International Ultraviolet Explorer and in the X-ray with the Einstein Observatory. On September 27, 1980, simultaneous observations in the two bands were obtained. Near-infrared photometry preceding and following the simultaneous observations by about one month is available from the literature, as is radio monitoring at 408 and 5000 MHz. Comparison of the observed X-ray flux with that predicted by the standard synchrotron self-Compton formalism, with a source dimension deduced from radio variability at 5 GHz, indicates that this component of the radio emission must be moving at relativistic speed with an effective projected Doppler beaming factor of about 10.

Multifrequency observations of the BL Lacertae object PKS 0537 - 441

Energy Technology Data Exchange (ETDEWEB)

Maraschi, L.; Treves, A.; Schwartz, D.A.; Tanzi, E.G.

1985-07-01

PKS 0537 - 441 was repeatedly observed in the UV band with the International Ultraviolet Explorer and in the X-ray with the Einstein Observatory. On September 27, 1980, simultaneous observations in the two bands were obtained. Near-infrared photometry preceding and following the simultaneous observations by about one month is available from the literature, as is radio monitoring at 408 and 5000 MHz. Comparison of the observed X-ray flux with that predicted by the standard synchrotron self-Compton formalism, with a source dimension deduced from radio variability at 5 GHz, indicates that this component of the radio emission must be moving at relativistic speed with an effective projected Doppler beaming factor of about 10. 28 references.

Multifrequency observations of the BL Lacertae object PKS 0537 - 441

International Nuclear Information System (INIS)

Maraschi, L.; Treves, A.; Schwartz, D.A.; Tanzi, E.G.; CNR, Istituto di Fisica Cosmica, Milan, Italy; Harvard-Smithsonian Center for Astrophysics, Cambridge, MA)

1985-01-01

PKS 0537 - 441 was repeatedly observed in the UV band with the International Ultraviolet Explorer and in the X-ray with the Einstein Observatory. On September 27, 1980, simultaneous observations in the two bands were obtained. Near-infrared photometry preceding and following the simultaneous observations by about one month is available from the literature, as is radio monitoring at 408 and 5000 MHz. Comparison of the observed X-ray flux with that predicted by the standard synchrotron self-Compton formalism, with a source dimension deduced from radio variability at 5 GHz, indicates that this component of the radio emission must be moving at relativistic speed with an effective projected Doppler beaming factor of about 10. 28 references

UV spectrum of the BL Lac object PKS 0521-36

Energy Technology Data Exchange (ETDEWEB)

Danziger, I.J. (European Southern Observatory, Garching (Germany, F.R.)); Bergeron, J. (Centre National de la Recherche Scientifique, 75 - Paris (France). Inst. d' Astrophysique); Fosbury, R.A.E. (Royal Greenwich Observatory, Hailsham (UK)); Maraschi, L.; Treves, A. (Consiglio Nazionale delle Ricerche, Milan (Italy). Lab. di Fisica Cosmica; Milan Univ. (Italy). Ist. di Fisica); Tanzi, E.G. (Consiglio Nazionale delle Ricerche, Milan (Italy). Lab. di Fisica Cosmica)

1983-05-01

Ultraviolet observations (1200 to 3000 A) with the IUE satellite of the BL Lac object PKS 0521-36 are presented. The only emission line which appears clearly in the spectrum is Ly..cap alpha.., which is asymmetric with a component displaced approx. 3000 km s/sup -1/ to the red. The intensity of the line and the upper limits on other lines are compared with the model calculations on QSOs and Seyfert nuclei by Kwan and Krolik. The continuous energy distribution is discussed, combining non-simultaneous observations from the ultraviolet to the infrared. The spectral range of the non-thermal source from far IR to far UV can be described by a single power law of index -1.5.

Development and Implementation of Novel Genetic Tools for Investigation of FungalSecondary Metabolism

DEFF Research Database (Denmark)

Holm, Dorte Koefoed

to produce secondary metabolites.In this study I have examined parts of the secondary metabolism in all three fungi, using dierentapproaches. For A. nidulans we have constructed an entire genome-wide polyketide synthase (PKS) deletionlibrary, which has linked the known compounds austinol and dehydroaustinol...... as a host for examination ofsecondary metabolism by heterologous expression of secondary metabolite genes from A. niger, A. aculeatus,and A. terreus.In A. niger I have investigated the products of all 37 putative PKSs by heterologous expression of the genesin A. nidulans. This approach identied the products...... to be silenced.For investigation of secondary metabolism in fungi with no available genetic tools, I have applied twodierent approaches: heterologous expression of secondary metabolite genes in A. nidulans and/or plasmidbasedgene expression in the native fungus. Heterologous expression in A. nidulans was used...

Measurement of Nonribosomal Peptide Synthetase Adenylation Domain Activity Using a Continuous Hydroxylamine Release Assay.

Science.gov (United States)

Duckworth, Benjamin P; Wilson, Daniel J; Aldrich, Courtney C

2016-01-01

Adenylation is a crucial enzymatic process in the biosynthesis of nonribosomal peptide synthetase (NRPS) derived natural products. Adenylation domains are considered the gatekeepers of NRPSs since they select, activate, and load the carboxylic acid substrate onto a downstream peptidyl carrier protein (PCP) domain of the NRPS. We describe a coupled continuous kinetic assay for NRPS adenylation domains that substitutes the PCP domain with hydroxylamine as the acceptor molecule. The pyrophosphate released from the first-half reaction is then measured using a two-enzyme coupling system, which detects conversion of the chromogenic substrate 7-methylthioguanosine (MesG) to 7-methylthioguanine. From profiling substrate specificity of unknown or engineered adenylation domains to studying chemical inhibition of adenylating enzymes, this robust assay will be of widespread utility in the broad field NRPS enzymology.

Energy distribution and variability of BL Lac objects. The cases of PKS 2155-304 and 3C 66A

International Nuclear Information System (INIS)

Maraschi, L.; Maccagni, D.; Tanzi, E.G.; Treves, A.

1983-01-01

The BL Lacertae objects, PKS 2155-304 and 3C66A have been observed in the ultraviolet and the X-ray region. The radiation flux in both regions are discussed with respect to its energy and time dependence. (Auth.)

Sponge-derived Kocuria and Micrococcus spp. as sources of the new thiazolyl peptide antibiotic kocurin.

Science.gov (United States)

Palomo, Sara; González, Ignacio; de la Cruz, Mercedes; Martín, Jesús; Tormo, José Rubén; Anderson, Matthew; Hill, Russell T; Vicente, Francisca; Reyes, Fernando; Genilloud, Olga

2013-03-28

Forty four marine actinomycetes of the family Microccocaceae isolated from sponges collected primarily in Florida Keys (USA) were selected from our strain collection to be studied as new sources for the production of bioactive natural products. A 16S rRNA gene based phylogenetic analysis showed that the strains are members of the genera Kocuria and Micrococcus. To assess their biosynthetic potential, the strains were PCR screened for the presence of secondary metabolite genes encoding nonribosomal synthetase (NRPS) and polyketide synthases (PKS). A small extract collection of 528 crude extracts generated from nutritional microfermentation arrays was tested for the production of bioactive secondary metabolites against clinically relevant strains (Bacillus subtilis, methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii and Candida albicans). Three independent isolates were shown to produce a new anti-MRSA bioactive compound that was identified as kocurin, a new member of the thiazolyl peptide family of antibiotics emphasizing the role of this family as a prolific resource for novel drugs.

PKS 2005-489 at VHE: four years of monitoring with HESS and simultaneous multi-wavelength observations

Science.gov (United States)

H.E.S.S. Collaboration; Acero, F.; Aharonian, F.; Akhperjanian, A. G.; Anton, G.; Barres de Almeida, U.; Bazer-Bachi, A. R.; Becherini, Y.; Behera, B.; Benbow, W.; Bernlöhr, K.; Bochow, A.; Boisson, C.; Bolmont, J.; Borrel, V.; Brucker, J.; Brun, F.; Brun, P.; Bühler, R.; Bulik, T.; Büsching, I.; Boutelier, T.; Chadwick, P. M.; Charbonnier, A.; Chaves, R. C. G.; Cheesebrough, A.; Chounet, L.-M.; Clapson, A. C.; Coignet, G.; Costamante, L.; Dalton, M.; Daniel, M. K.; Davids, I. D.; Degrange, B.; Deil, C.; Dickinson, H. J.; Djannati-Ataï, A.; Domainko, W.; O'C. Drury, L.; Dubois, F.; Dubus, G.; Dyks, J.; Dyrda, M.; Egberts, K.; Eger, P.; Espigat, P.; Fallon, L.; Farnier, C.; Fegan, S.; Feinstein, F.; Fiasson, A.; Förster, A.; Fontaine, G.; Füßling, M.; Gabici, S.; Gallant, Y. A.; Gérard, L.; Gerbig, D.; Giebels, B.; Glicenstein, J. F.; Glück, B.; Goret, P.; Göring, D.; Hauser, M.; Heinz, S.; Heinzelmann, G.; Henri, G.; Hermann, G.; Hinton, J. A.; Hoffmann, A.; Hofmann, W.; Hofverberg, P.; Holleran, M.; Hoppe, S.; Horns, D.; Jacholkowska, A.; de Jager, O. C.; Jahn, C.; Jung, I.; Katarzyński, K.; Katz, U.; Kaufmann, S.; Kerschhaggl, M.; Khangulyan, D.; Khélifi, B.; Keogh, D.; Klochkov, D.; Kluźniak, W.; Kneiske, T.; Komin, Nu.; Kosack, K.; Kossakowski, R.; Lamanna, G.; Lenain, J.-P.; Lohse, T.; Marandon, V.; Martineau-Huynh, O.; Marcowith, A.; Masbou, J.; Maurin, D.; McComb, T. J. L.; Medina, M. C.; Méhault, J.; Moderski, R.; Moulin, E.; Naumann-Godo, M.; de Naurois, M.; Nedbal, D.; Nekrassov, D.; Nicholas, B.; Niemiec, J.; Nolan, S. J.; Ohm, S.; Olive, J.-F.; de Oña Wilhelmi, E.; Orford, K. J.; Ostrowski, M.; Panter, M.; Paz Arribas, M.; Pedaletti, G.; Pelletier, G.; Petrucci, P.-O.; Pita, S.; Pühlhofer, G.; Punch, M.; Quirrenbach, A.; Raubenheimer, B. C.; Raue, M.; Rayner, S. M.; Renaud, M.; Rieger, F.; Ripken, J.; Rob, L.; Rosier-Lees, S.; Rowell, G.; Rudak, B.; Rulten, C. B.; Ruppel, J.; Sahakian, V.; Santangelo, A.; Schlickeiser, R.; Schöck, F. M.; Schwanke, U.; Schwarzburg, S.; Schwemmer, S.; Shalchi, A.; Sikora, M.; Skilton, J. L.; Sol, H.; Stawarz, Ł.; Steenkamp, R.; Stegmann, C.; Stinzing, F.; Superina, G.; Szostek, A.; Tam, P. H.; Tavernet, J.-P.; Terrier, R.; Tibolla, O.; Tluczykont, M.; van Eldik, C.; Vasileiadis, G.; Venter, C.; Venter, L.; Vialle, J. P.; Vincent, P.; Vivier, M.; Völk, H. J.; Volpe, F.; Wagner, S. J.; Ward, M.; Zdziarski, A. A.; Zech, A.

2010-02-01

Aims: Our aim is to study the very high energy (VHE; E>100 GeV) γ-ray emission from BL Lac objects and the evolution in time of their broad-band spectral energy distribution (SED). Methods: VHE observations of the high-frequency peaked BL Lac object PKS 2005-489 were made with the High Energy Stereoscopic System (HESS) from 2004 through 2007. Three simultaneous multi-wavelength campaigns at lower energies were performed during the HESS data taking, consisting of several individual pointings with the XMM-Newton and RXTE satellites. Results: A strong VHE signal, ~17σ total, from PKS 2005-489 was detected during the four years of HESS observations (90.3 h live time). The integral flux above the average analysis threshold of 400 GeV is ~3% of the flux observed from the Crab Nebula and varies weakly on time scales from days to years. The average VHE spectrum measured from ~300 GeV to ~5 TeV is characterized by a power law with a photon index, Γ = 3.20± 0.16_stat± 0.10_syst. At X-ray energies the flux is observed to vary by more than an order of magnitude between 2004 and 2005. Strong changes in the X-ray spectrum (ΔΓX ≈ 0.7) are also observed, which appear to be mirrored in the VHE band. Conclusions: The SED of PKS 2005-489, constructed for the first time with contemporaneous data on both humps, shows significant evolution. The large flux variations in the X-ray band, coupled with weak or no variations in the VHE band and a similar spectral behavior, suggest the emergence of a new, separate, harder emission component in September 2005. Supported by CAPES Foundation, Ministry of Education of Brazil.Now at Harvard-Smithsonian Center for Astrophysics, Cambridge, USA.Now at W.W. Hansen Experimental Physics Laboratory & Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, Stanford, USA.

The UV spectrum of the BL Lac object PKS 0521-36

International Nuclear Information System (INIS)

Danziger, I.J.; Bergeron, J.; Maraschi, L.; Treves, A.; Milan Univ.; Tanzi, E.G.

1983-01-01

Ultraviolet observations (1200 to 3000 A) with the IUE satellite of the BL Lac object PKS 0521-36 are presented. The only emission line which appears clearly in the spectrum is Lyα, which is asymmetric with a component displaced approx. 3000 km s - 1 to the red. The intensity of the line and the upper limits on other lines are compared with the model calculations on QSOs and Seyfert nuclei by Kwan and Krolik. The continuous energy distribution is discussed, combining non-simultaneous observations from the ultraviolet to the infrared. The spectral range of the non-thermal source from far IR to far UV can be described by a single power law of index -1.5. (author)

Genomics reveals traces of fungal phenylpropanoid-flavonoid metabolic pathway in the f ilamentous fungus Aspergillus oryzae.

Science.gov (United States)

Juvvadi, Praveen Rao; Seshime, Yasuyo; Kitamoto, Katsuhiko

2005-12-01

Fungal secondary metabolites constitute a wide variety of compounds which either play a vital role in agricultural, pharmaceutical and industrial contexts, or have devastating effects on agriculture, animal and human affairs by virtue of their toxigenicity. Owing to their beneficial and deleterious characteristics, these complex compounds and the genes responsible for their synthesis have been the subjects of extensive investigation by microbiologists and pharmacologists. A majority of the fungal secondary metabolic genes are classified as type I polyketide synthases (PKS) which are often clustered with other secondary metabolism related genes. In this review we discuss on the significance of our recent discovery of chalcone synthase (CHS) genes belonging to the type III PKS superfamily in an industrially important fungus, Aspergillus oryzae. CHS genes are known to play a vital role in the biosynthesis of flavonoids in plants. A comparative genome analyses revealed the unique character of A. oryzae with four CHS-like genes (csyA, csyB, csyC and csyD) amongst other Aspergilli (Aspergillus nidulans and Aspergillus fumigatus) which contained none of the CHS-like genes. Some other fungi such as Neurospora crassa, Fusarium graminearum, Magnaporthe grisea, Podospora anserina and Phanerochaete chrysosporium also contained putative type III PKSs, with a phylogenic distinction from bacteria and plants. The enzymatically active nature of these newly discovered homologues is expected owing to the conservation in the catalytic residues across the different species of plants and fungi, and also by the fact that a majority of these genes (csyA, csyB and csyD) were expressed in A. oryzae. While this finding brings filamentous fungi closer to plants and bacteria which until recently were the only ones considered to possess the type III PKSs, the presence of putative genes encoding other principal enzymes involved in the phenylpropanoid and flavonoid biosynthesis (viz

Isolation and Biosynthetic Analysis of Haliamide, a New PKS-NRPS Hybrid Metabolite from the Marine Myxobacterium Haliangium ochraceum

Directory of Open Access Journals (Sweden)

Yuwei Sun

2016-01-01

Full Text Available Myxobacteria of marine origin are rare and hard-to-culture microorganisms, but they genetically harbor high potential to produce novel antibiotics. An extensive investigation on the secondary metabolome of the unique marine myxobacterium Haliangium ochraceum SMP-2 led to the isolation of a new polyketide-nonribosomal peptide hybrid product, haliamide (1. Its structure was elucidated by spectroscopic analyses including NMR and HR-MS. Haliamide (1 showed cytotoxicity against HeLa-S3 cells with IC50 of 12 μM. Feeding experiments were performed to identify the biosynthetic building blocks of 1, revealing one benzoate, one alanine, two propionates, one acetate and one acetate-derived terminal methylene. The biosynthetic gene cluster of haliamide (hla, 21.7 kbp was characterized through the genome mining of the producer, allowing us to establish a model for the haliamide biosynthesis. The sulfotransferase (ST-thioesterase (TE domains encoded in hlaB appears to be responsible for the terminal alkene formation via decarboxylation.

OPTICAL AND INFRARED PHOTOMETRY OF THE BLAZAR PKS 0537-441: LONG AND SHORT TIMESCALE VARIABILITY

International Nuclear Information System (INIS)

Impiombato, D.; Treves, A.; Covino, S.; Foschini, L.; Fugazza, D.; Pian, E.; Tosti, G.; Ciprini, S.; Nicastro, L.

2011-01-01

We present a large collection of photometric data on the blazar PKS 0537-441 in the VRIJHK bands taken in 2004-2009. At least three flare-like episodes with months duration and >3 mag amplitude are apparent. The spectral energy distribution is consistent with a power law, and no indication of a thermal component is found. We searched for short timescale variability, and an interesting event was identified in the J band, with a duration of ∼25 minutes.

Investigating the emission mechanisms of the jet in the quasar PKS 1127-145

Science.gov (United States)

Duffy, Ryan T.; Siemiginowska, A.; Kashyap, V.; Stein, N.; Migliori, G.

2014-01-01

There is currently uncertainty surrounding the emission mechanism for X-ray photons in quasar jets, with both Inverse Compton Scattering from the Cosmic Microwave Background (IC/CMB) and synchrotron models considered possibilities. We use a 100 ks observation (Siemiginowska et al 2007) of the redshift z=1.18, radio-loud quasar PKS 1127-145 taken by the Chandra X-ray Observatory, with the hope of accurately measuring the offsets between radio and X-ray radiation peaks in order to establish the emission process for this jet. PKS 1127-145 is a bright quasar with a long jet which has several bright knots and complex morphology, making it a perfect source for this investigation. We use a Bayesian statistical method called Low-Count Image Restoration and Analysis (LIRA, Connors & van Dyk 2007, Esch et al 2004) to investigate the quasar jet. This fits the parameters of a multiscale model to the data by employing a Markov Chain Monte Carlo process. LIRA has shown the location of some jet X-ray components, although further simulations must be undertaken to determine whether these are statistically significant. We also study these jet X-ray components in both hard and soft X-ray bands in order to gain more information on the energy of the emitted photons. References: Connors, A., & van Dyk, D. A. 2007, Statistical Challenges in Modern Astronomy IV, 371, 101 Esch, D.N., Connors, A., Karovska, M., & van Dyk, D.A. 2004, ApJ, 610, 1213 Siemiginowska, A., Stawarz, L., Cheung, C.C., et al. 2007, ApJ, 657, 145

Multifrequency VLA observations of PKS 0745-191: the archetypal 'cooling flow' radio source?

International Nuclear Information System (INIS)

Baum, S.A.; O'Dea, C.P.

1991-01-01

We present 90-, 20-, 6- and 2-cm VLA observations of the high radio luminosity, cooling flow radio source PKS 0745-191. We find that the radio source has a core with a very steep spectrum and diffuse emission with an even steeper spectrum without clear indications of the jets, hotspots or double lobes found in other radio sources of comparable luminosity. The appearance of the source is highly dependent on frequency and resolution. This dependence reflects both the diffuse nature of the extended emission and the steep, but position-dependent, spectrum of the radio emission. (author)

Variability of the BL Lacertae objects PKS 2155 - 304 and OJ 287 in the far-ultraviolet

International Nuclear Information System (INIS)

Maraschi, L.; Treves, A.; Tagliaferri, G.; Tanzi, E.G.; CNR, Istituto di Fisica Cosmica, Milan, Italy)

1986-01-01

All the ultraviolet spectra of the two bright BL Lacertae objects PKS 2155 - 304 and OJ 287 taken with the International Ultraviolet Explorer in the period 1978-1984 are examined. For each spectrum the best-fitting power law is determined and a correlation between spectral slope and intensity is searched for. The correlation, if present, is weak. This is discussed in terms of models of the continuum emission of active galactic nuclei. 31 references

Variability of the BL Lacertae objects PKS 2155 - 304 and OJ 287 in the far-ultraviolet

Energy Technology Data Exchange (ETDEWEB)

Maraschi, L.; Treves, A.; Tagliaferri, G.; Tanzi, E.G.

1986-05-01

All the ultraviolet spectra of the two bright BL Lacertae objects PKS 2155 - 304 and OJ 287 taken with the International Ultraviolet Explorer in the period 1978-1984 are examined. For each spectrum the best-fitting power law is determined and a correlation between spectral slope and intensity is searched for. The correlation, if present, is weak. This is discussed in terms of models of the continuum emission of active galactic nuclei. 31 references.

H.E.S.S. discovery of very high energy γ-ray emission from PKS 0625-354

Science.gov (United States)

H.E.S.S. Collaboration; Abdalla, H.; Abramowski, A.; Aharonian, F.; Ait Benkhali, F.; Akhperjanian, A. G.; Andersson, T.; Angüner, E. O.; Arrieta, M.; Aubert, P.; Backes, M.; Balzer, A.; Barnard, M.; Becherini, Y.; Becker Tjus, J.; Berge, D.; Bernhard, S.; Bernlöhr, K.; Blackwell, R.; Böttcher, M.; Boisson, C.; Bolmont, J.; Bordas, P.; Bregeon, J.; Brun, F.; Brun, P.; Bryan, M.; Bulik, T.; Capasso, M.; Carr, J.; Casanova, S.; Cerruti, M.; Chakraborty, N.; Chalme-Calvet, R.; Chaves, R. C. G.; Chen, A.; Chevalier, J.; Chrétien, M.; Colafrancesco, S.; Cologna, G.; Condon, B.; Conrad, J.; Cui, Y.; Davids, I. D.; Decock, J.; Degrange, B.; Deil, C.; Devin, J.; deWilt, P.; Dirson, L.; Djannati-Ataï, A.; Domainko, W.; Donath, A.; Drury, L. O'C.; Dubus, G.; Dutson, K.; Dyks, J.; Dyrda, M.; Edwards, T.; Egberts, K.; Eger, P.; Ernenwein, J.-P.; Eschbach, S.; Farnier, C.; Fegan, S.; Fernandes, M. V.; Fiasson, A.; Fontaine, G.; Förster, A.; Funk, S.; Füßling, M.; Gabici, S.; Gajdus, M.; Gallant, Y. A.; Garrigoux, T.; Giavitto, G.; Giebels, B.; Glicenstein, J. F.; Gottschall, D.; Goyal, A.; Grondin, M.-H.; Hadasch, D.; Hahn, J.; Haupt, M.; Hawkes, J.; Heinzelmann, G.; Henri, G.; Hermann, G.; Hervet, O.; Hinton, J. A.; Hofmann, W.; Hoischen, C.; Holler, M.; Horns, D.; Ivascenko, A.; Jacholkowska, A.; Jamrozy, M.; Janiak, M.; Jankowsky, D.; Jankowsky, F.; Jingo, M.; Jogler, T.; Jouvin, L.; Jung-Richardt, I.; Kastendieck, M. A.; Katarzyński, K.; Katz, U.; Kerszberg, D.; Khélifi, B.; Kieffer, M.; King, J.; Klepser, S.; Klochkov, D.; Kluźniak, W.; Kolitzus, D.; Komin, Nu; Kosack, K.; Krakau, S.; Kraus, M.; Krayzel, F.; Krüger, P. P.; Laffon, H.; Lamanna, G.; Lau, J.; Lees, J.-P.; Lefaucheur, J.; Lefranc, V.; Lemière, A.; Lemoine-Goumard, M.; Lenain, J.-P.; Leser, E.; Lohse, T.; Lorentz, M.; Liu, R.; López-Coto, R.; Lypova, I.; Marandon, V.; Marcowith, A.; Mariaud, C.; Marx, R.; Maurin, G.; Maxted, N.; Mayer, M.; Meintjes, P. J.; Meyer, M.; Mitchell, A. M. W.; Moderski, R.; Mohamed, M.; Mohrmann, L.; Morâ, K.; Moulin, E.; Murach, T.; de Naurois, M.; Niederwanger, F.; Niemiec, J.; Oakes, L.; O'Brien, P.; Odaka, H.; Öttl, S.; Ohm, S.; Ostrowski, M.; Oya, I.; Padovani, M.; Panter, M.; Parsons, R. D.; Pekeur, N. W.; Pelletier, G.; Perennes, C.; Petrucci, P.-O.; Peyaud, B.; Piel, Q.; Pita, S.; Poon, H.; Prokhorov, D.; Prokoph, H.; Pühlhofer, G.; Punch, M.; Quirrenbach, A.; Raab, S.; Reimer, A.; Reimer, O.; Renaud, M.; de los Reyes, R.; Rieger, F.; Romoli, C.; Rosier-Lees, S.; Rowell, G.; Rudak, B.; Rulten, C. B.; Sahakian, V.; Salek, D.; Sanchez, D. A.; Santangelo, A.; Sasaki, M.; Schlickeiser, R.; Schüssler, F.; Schulz, A.; Schwanke, U.; Schwemmer, S.; Settimo, M.; Seyffert, A. S.; Shafi, N.; Shilon, I.; Simoni, R.; Sol, H.; Spanier, F.; Spengler, G.; Spies, F.; Stawarz, Ł.; Steenkamp, R.; Stegmann, C.; Stinzing, F.; Stycz, K.; Sushch, I.; Tavernet, J.-P.; Tavernier, T.; Taylor, A. M.; Terrier, R.; Tibaldo, L.; Tiziani, D.; Tluczykont, M.; Trichard, C.; Tuffs, R.; Uchiyama, Y.; van der Walt, D. J.; van Eldik, C.; van Rensburg, C.; van Soelen, B.; Vasileiadis, G.; Veh, J.; Venter, C.; Viana, A.; Vincent, P.; Vink, J.; Voisin, F.; Völk, H. J.; Vuillaume, T.; Wadiasingh, Z.; Wagner, S. J.; Wagner, P.; Wagner, R. M.; White, R.; Wierzcholska, A.; Willmann, P.; Wörnlein, A.; Wouters, D.; Yang, R.; Zabalza, V.; Zaborov, D.; Zacharias, M.; Zanin, R.; Zdziarski, A. A.; Zech, A.; Zefi, F.; Ziegler, A.; Żywucka, N.

2018-05-01

PKS 0625-354 (z = 0.055) was observed with the four High Energy Stereoscopic System (H.E.S.S.) telescopes in 2012 during 5.5 h. The source was detected above an energy threshold of 200 GeV at a significance level of 6.1σ. No significant variability is found in these observations. The source is well described with a power-law spectrum with photon index Γ = 2.84 ± 0.50stat ± 0.10syst and normalization (at E0 = 1.0 TeV) N0(E0) = (0.58 ± 0.22stat ± 0.12syst) × 10-12 TeV-1 cm-2 s-1. Multiwavelength data collected with Fermi-LAT, Swift-XRT, Swift-UVOT, ATOM and WISE are also analysed. Significant variability is observed only in the Fermi-LAT γ-ray and Swift-XRT X-ray energy bands. Having a good multiwavelength coverage from radio to very high energy, we performed a broad-band modelling from two types of emission scenarios. The results from a one zone lepto-hadronic and a multizone leptonic models are compared and discussed. On the grounds of energetics, our analysis favours a leptonic multizone model. Models associated to the X-ray variability constraint support previous results, suggesting a BL Lac nature of PKS 0625-354 with, however, a large-scale jet structure typical of a radio galaxy.

The Gamma-Ray Emitting Radio-Loud Narrow-Line Seyfert 1 Galaxy PKS 2004-447 II. The Radio View

Science.gov (United States)

Schulz, R.; Kreikenbohm, A.; Kadler, M.; Ojha, R.; Ros, E.; Stevens, J.; Edwards, P. G.; Carpenter, B.; Elsaesser, D.; Gehrels, N.;

DETECTION OF CA II ABSORPTION BY A HIGH-VELOCITY CLOUD IN THE DIRECTION OF THE QUASAR PKS 0837-120

NARCIS (Netherlands)

ROBERTSON, JG; SCHWARZ, UJ; VANWOERDEN, H; MURRAY, JD; MORTON, DC; HULSBOSCH, ANM

1991-01-01

We present optical absorption spectroscopy of the Ca II K and H lines along the sight line to the quasar PKS 0837-120, which lies in the direction of a high-velocity cloud (HVC) detected in H I 21-cm emission at V(LSR) = + 105 km s-1. Our data show Ca II absorption due to the HVC as well as a lower

Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes.

Science.gov (United States)

Kehr, Jan-Christoph; Gatte Picchi, Douglas; Dittmann, Elke

2011-01-01

Cyanobacteria are prolific producers of natural products. Investigations into the biochemistry responsible for the formation of these compounds have revealed fascinating mechanisms that are not, or only rarely, found in other microorganisms. In this article, we survey the biosynthetic pathways of cyanobacteria isolated from freshwater, marine and terrestrial habitats. We especially emphasize modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) pathways and highlight the unique enzyme mechanisms that were elucidated or can be anticipated for the individual products. We further include ribosomal natural products and UV-absorbing pigments from cyanobacteria. Mechanistic insights obtained from the biochemical studies of cyanobacterial pathways can inspire the development of concepts for the design of bioactive compounds by synthetic-biology approaches in the future.

Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes

Directory of Open Access Journals (Sweden)

Jan-Christoph Kehr

2011-12-01

Full Text Available Cyanobacteria are prolific producers of natural products. Investigations into the biochemistry responsible for the formation of these compounds have revealed fascinating mechanisms that are not, or only rarely, found in other microorganisms. In this article, we survey the biosynthetic pathways of cyanobacteria isolated from freshwater, marine and terrestrial habitats. We especially emphasize modular nonribosomal peptide synthetase (NRPS and polyketide synthase (PKS pathways and highlight the unique enzyme mechanisms that were elucidated or can be anticipated for the individual products. We further include ribosomal natural products and UV-absorbing pigments from cyanobacteria. Mechanistic insights obtained from the biochemical studies of cyanobacterial pathways can inspire the development of concepts for the design of bioactive compounds by synthetic-biology approaches in the future.

INTEGRAL observations of the GeV blazar PKS 1502+106 and the hard X-ray bright Seyfert galaxy Mkn 841

Czech Academy of Sciences Publication Activity Database

Pian, E.; Ubertini, P.; Bazzano, A.; Beckmann, V.; Eckert, D.; Ghisellini, G.; Pursimo, T.; Tagliaferri, G.; Tavecchio, F.; Türler, M.; Bianchi, S.; Bianchin, V.; Hudec, René; Maraschi, L.; Raiteri, C.M.; Soldi, S.; Treves, A.; Villata, M.

2011-01-01

Roč. 526, February (2011), A125/1-A125/7 ISSN 0004-6361 Grant - others:ESA(XE) ESA PECS project No.98023; GA ČR(CZ) ga102/09/0997 Institutional research plan: CEZ:AV0Z10030501 Keywords : active galaxies * blazar PKS 1502+106 Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 4.587, year: 2011

Bioprospecting Sediments from Red Sea Coastal Lagoons for Microorganisms and Their Antimicrobial Potential

KAUST Repository

Al-Amoudi, Soha

2016-12-08

Since the soils nutrient composition along with the associated biotic and abiotic factors direct the diversity of the contained microbiome and its potential to produce bioactive compounds, many studies have been focused on sediment types with unique features characteristic of extreme environments. Red Sea lagoon ecosystems are environments with such unique features as they are highly saline. However, not much is known about the potential of their microbiomes to produce bioactive compounds. Here, we explored sediment types such as mangrove mud, microbial mat, and barren soil collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL) as sources for antibiotic bioprospecting. Our antibiotic bioprospecting process started with a metagenomic study that provides a more precise view of the microbial community inhabiting these sites and serves as a preliminary screen for potential antibiotics. Taking the outcomes of the metagenomic screening into account, the next step we established a library of culturable strains from the analyzed samples. We screened each strain from that library for antibiotic activity against four target strains (Staphylococcus aureus ATCC 25923, Escherichia coli dh5 α, Pseudomonas syringae pv. tomato dc3000 and Salmonella typhimurium dt2) and for the presence of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes known to support synthesis of secondary metabolites that act like antimicrobial agents. The metagenomics study showed a shift in dominant phyla consistent with a historical exposure to hydrocarbon contamination and that AKL unexpectedly displayed more contamination than RHL. This may be due to dominant phyla in AKL being consistent with early hydrocarbon exposure (when contamination levels are still high) and the dominant phyla in RHL being consistent with late hydrocarbon exposure (when contamination levels are lower as a result of an extended period of hydrocarbon degradation). Additionally, RHL samples

Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides.

Science.gov (United States)

Gagne, Steve J; Stout, Jake M; Liu, Enwu; Boubakir, Zakia; Clark, Shawn M; Page, Jonathan E

2012-07-31

Δ(9)-Tetrahydrocannabinol (THC) and other cannabinoids are responsible for the psychoactive and medicinal properties of Cannabis sativa L. (marijuana). The first intermediate in the cannabinoid biosynthetic pathway is proposed to be olivetolic acid (OA), an alkylresorcinolic acid that forms the polyketide nucleus of the cannabinoids. OA has been postulated to be synthesized by a type III polyketide synthase (PKS) enzyme, but so far type III PKSs from cannabis have been shown to produce catalytic byproducts instead of OA. We analyzed the transcriptome of glandular trichomes from female cannabis flowers, which are the primary site of cannabinoid biosynthesis, and searched for polyketide cyclase-like enzymes that could assist in OA cyclization. Here, we show that a type III PKS (tetraketide synthase) from cannabis trichomes requires the presence of a polyketide cyclase enzyme, olivetolic acid cyclase (OAC), which catalyzes a C2-C7 intramolecular aldol condensation with carboxylate retention to form OA. OAC is a dimeric α+β barrel (DABB) protein that is structurally similar to polyketide cyclases from Streptomyces species. OAC transcript is present at high levels in glandular trichomes, an expression profile that parallels other cannabinoid pathway enzymes. Our identification of OAC both clarifies the cannabinoid pathway and demonstrates unexpected evolutionary parallels between polyketide biosynthesis in plants and bacteria. In addition, the widespread occurrence of DABB proteins in plants suggests that polyketide cyclases may play an overlooked role in generating plant chemical diversity.

A MULTIWAVELENGTH STUDY OF THE HIGH SURFACE BRIGHTNESS HOT SPOT IN PKS 1421-490

International Nuclear Information System (INIS)

Godfrey, L. E. H.; Bicknell, G. V.; Lovell, J. E. J.; Jauncey, D. L.; Gelbord, J.; Schwartz, D. A.; Birkinshaw, M.; Worrall, D. M.; Marshall, H. L.; Georganopoulos, M.; Perlman, E. S.; Murphy, D. W.

2009-01-01

Long Baseline Array imaging of the z = 0.663 broadline radio galaxy PKS 1421-490 reveals a 400 pc diameter high surface brightness hot spot at a projected distance of ∼40 kpc from the active galactic nucleus. The isotropic X-ray luminosity of the hot spot, L 2-10keV = 3 x 10 44 ergs s -1 , is comparable to the isotropic X-ray luminosity of the entire X-ray jet of PKS 0637-752, and the peak radio surface brightness is hundreds of times greater than that of the brightest hot spot in Cygnus A. We model the radio to X-ray spectral energy distribution using a one-zone synchrotron self-Compton model with a near equipartition magnetic field strength of 3 mG. There is a strong brightness asymmetry between the approaching and receding hotspots and the hot spot spectrum remains flat (α ∼ 0.5) well beyond the predicted cooling break for a 3 mG magnetic field, indicating that the hotspot emission may be Doppler beamed. A high plasma velocity beyond the terminal jet shock could be the result of a dynamically important magnetic field in the jet. There is a change in the slope of the hotspot radio spectrum at GHz frequencies, which we model by incorporating a cutoff in the electron energy distribution at γ min ∼ 650, with higher values implied if the hotspot emission is Doppler beamed. We show that a sharp decrease in the electron number density below a Lorentz factor of 650 would arise from the dissipation of bulk kinetic energy in an electron/proton jet with a Lorentz factor Γ jet ∼> 5.

Discovery of Very High Energy Gamma Rays from PKS 1424+240 and Multiwavelength Constraints on its Redshift

Energy Technology Data Exchange (ETDEWEB)

Acciari, V.A.; /Harvard-Smithsonian Ctr. Astrophys.; Aliu, E.; /Delaware U., Bartol Inst.; Arlen, T.; /UCLA; Aune, T.; /UC, Santa Cruz; Bautista, M.; /McGill U.; Beilicke, M. /Washington U., St. Louis; Benbow, W.; /Harvard-Smithsonian Ctr. Astrophys.; Bottcher, M.; /Ohio U.; Boltuch, D.; /Delaware U., Bartol Inst.; Bradbury, S.M.; /Leeds U.; Buckley, J.H.; /Washington U., St. Louis; Bugaev, V.; /Washington U., St. Louis; Byrum, K.; /Argonne; Cannon, A.; /University Coll., Dublin; Cesarini, A.; /Natl. U. of Ireland, Galway; Chow, Y.C.; /UCLA; Ciupik, L.; /Roosevelt U., Chicago; Cogan, P.; /McGill U.; Cui, W.; /Purdue U.; Duke, C.; /Grinnell Coll.; Falcone, A.; /Penn State U. /Purdue U. /Utah U. /Roosevelt U., Chicago /Harvard-Smithsonian Ctr. Astrophys. /Purdue U. /Natl. U. of Ireland, Galway /Utah U. /University Coll., Dublin /McGill U. /Roosevelt U., Chicago /McGill U. /Delaware U., Bartol Inst. /Utah U. /Chicago U., EFI /Iowa State U. /Roosevelt U., Chicago /DePauw U. /Utah U. /Pittsburg State U. /Washington U., St. Louis /Iowa State U. /Natl. U. of Ireland, Galway /Utah U. /McGill U. /Washington U., St. Louis /McGill U. /McGill U. /Purdue U. /Anderson U. /Galway-Mayo Inst. of Tech. /Iowa State U. /UCLA; /more authors..

2012-04-05

We report the first detection of very-high-energy (VHE) gamma-ray emission above 140GeV from PKS 1424+240, a BL Lac object with an unknown redshift. The photon spectrum above 140GeV measured by VERITAS is well described by a power law with a photon index of 3.8 {+-}0.5{sub stat} {+-} 0.3{sub syst} and a flux normalization at 200 GeV of (5.1 {+-} 0.9{sub stat} {+-} 0.5{sub syst}) x 10{sup -11} TeV{sup -1} cm{sup -2} s{sup -1}, where stat and syst denote the statistical and systematical uncertainty, respectively. The VHE flux is steady over the observation period between MJD 54881 and 55003 (2009 February 19 to June 21). Flux variability is also not observed in contemporaneous high energy observations with the Fermi Large Area Telescope (LAT). Contemporaneous X-ray and optical data were also obtained from the Swift XRT and MDM observatory, respectively. The broadband spectral energy distribution (SED) is well described by a one-zone synchrotron self-Compton (SSC) model favoring a redshift of less than 0.1. Using the photon index measured with Fermi in combination with recent extragalactic background light (EBL) absorption models it can be concluded from the VERITAS data that the redshift of PKS 1424+240 is less than 0.66.

DISCOVERY OF VERY HIGH ENERGY GAMMA RAYS FROM PKS 1424+240 AND MULTIWAVELENGTH CONSTRAINTS ON ITS REDSHIFT

International Nuclear Information System (INIS)

Acciari, V. A.; Benbow, W.; Aliu, E.; Boltuch, D.; Arlen, T.; Chow, Y. C.; Aune, T.; Bautista, M.; Cogan, P.; Beilicke, M.; Buckley, J. H.; Bugaev, V.; Boettcher, M.; Bradbury, S. M.; Byrum, K.; Cannon, A.; Cesarini, A.; Ciupik, L.; Cui, W.; Duke, C.

2010-01-01

We report the first detection of very high energy 83 Gamma-ray emission above 100 GeV. (VHE) gamma-ray emission above 140 GeV from PKS 1424+240, a BL Lac object with an unknown redshift. The photon spectrum above 140 GeV measured by VERITAS is well described by a power law with a photon index of 3.8 ± 0.5 stat ± 0.3 syst and a flux normalization at 200 GeV of (5.1 ± 0.9 stat ± 0.5 syst ) x 10 -11 TeV -1 cm -2 s -1 , where stat and syst denote the statistical and systematical uncertainties, respectively. The VHE flux is steady over the observation period between MJD 54881 and 55003 (from 2009 February 19 to June 21). Flux variability is also not observed in contemporaneous high-energy observations with the Fermi Large Area Telescope. Contemporaneous X-ray and optical data were also obtained from the Swift XRT and MDM observatory, respectively. The broadband spectral energy distribution is well described by a one-zone synchrotron self-Compton model favoring a redshift of less than 0.1. Using the photon index measured with Fermi in combination with recent extragalactic background light absorption models it can be concluded from the VERITAS data that the redshift of PKS 1424+240 is less than 0.66.

Quasi-simultaneous ultraviolet, optical, and infrared observations of the BL Lacertae object PKS 0048-09

International Nuclear Information System (INIS)

Falomo, R.; Bouchet, P.; Maraschi, L.; Treves, A.; Tanzi, E.G.

1988-01-01

This paper reports on quasi-simultaneous UV, optical, and IR observations of the BL Lac object PKS 0048-09, carried out on January 7-9, 1987, when the object was in a moderately high optical state. The data were used to derive a detailed energy distribution from about 10 to the 14th to about 2.5 x 10 to the 15th Hz. A comparison of observations obtained on January 7-9, 1987, with observations on September 12, 1986, pertaining to a lower state of the source, indicates spectral hardening with increasing intensity on time scales of months. 26 references

Quasi-simultaneous ultraviolet, optical, and infrared observations of the BL Lacertae object PKS 0048-09

Energy Technology Data Exchange (ETDEWEB)

Falomo, R.; Bouchet, P.; Maraschi, L.; Treves, A.; Tanzi, E.G.

1988-12-01

This paper reports on quasi-simultaneous UV, optical, and IR observations of the BL Lac object PKS 0048-09, carried out on January 7-9, 1987, when the object was in a moderately high optical state. The data were used to derive a detailed energy distribution from about 10 to the 14th to about 2.5 x 10 to the 15th Hz. A comparison of observations obtained on January 7-9, 1987, with observations on September 12, 1986, pertaining to a lower state of the source, indicates spectral hardening with increasing intensity on time scales of months. 26 references.

A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain

Directory of Open Access Journals (Sweden)

Nederbragt Alexander J

2009-08-01

Full Text Available Abstract Background Cyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS. Although some cyanobacterial NRPS gene cluster types are well described, the entire NRPS genomic content within a single cyanobacterial strain has never been investigated. Here we have combined a genome-wide analysis using massive parallel pyrosequencing ("454" and mass spectrometry screening of oligopeptides produced in the strain Planktothrix rubescens NIVA CYA 98 in order to identify all putative gene clusters for oligopeptides. Results Thirteen types of oligopeptides were uncovered by mass spectrometry (MS analyses. Microcystin, cyanopeptolin and aeruginosin synthetases, highly similar to already characterized NRPS, were present in the genome. Two novel NRPS gene clusters were associated with production of anabaenopeptins and microginins, respectively. Sequence-depth of the genome and real-time PCR data revealed three copies of the microginin gene cluster. Since NRPS gene cluster candidates for microviridin and oscillatorin synthesis could not be found, putative (gene encoded precursor peptide sequences to microviridin and oscillatorin were found in the genes mdnA and oscA, respectively. The genes flanking the microviridin and oscillatorin precursor genes encode putative modifying enzymes of the precursor oligopeptides. We therefore propose ribosomal pathways involving modifications and cyclisation for microviridin and oscillatorin. The microviridin, anabaenopeptin and cyanopeptolin gene clusters are situated in close proximity to each other, constituting an oligopeptide island. Conclusion Altogether seven nonribosomal peptide synthetase (NRPS gene clusters and two gene clusters putatively encoding ribosomal oligopeptide biosynthetic pathways were revealed. Our results demonstrate that whole genome shotgun sequencing combined with MS-directed determination of oligopeptides successfully

Structure Elucidation and Activity of Kolossin A, the D-/L-Pentadecapeptide Product of a Giant Nonribosomal Peptide Synthetase.

Science.gov (United States)

Bode, Helge B; Brachmann, Alexander O; Jadhav, Kirtikumar B; Seyfarth, Lydia; Dauth, Christina; Fuchs, Sebastian W; Kaiser, Marcel; Waterfield, Nick R; Sack, Holger; Heinemann, Stefan H; Arndt, Hans-Dieter

2015-08-24

The largest continuous bacterial nonribosomal peptide synthetase discovered so far is described. It consists of 15 consecutive modules arising from an uninterrupted, fully functional gene in the entomopathogenic bacterium Photorhabdus luminescens. The identification of its cryptic biosynthesis product was achieved by using a combination of genome analysis, promoter exchange, isotopic labeling experiments, and total synthesis of a focused collection of peptide candidates. Although it belongs to the growing class of D-/ L-peptide natural products, the encoded metabolite kolossin A was found to be largely devoid of antibiotic activity and is likely involved in interspecies communication. A stereoisomer of this peculiar natural product displayed high activity against Trypanosoma brucei rhodesiense, a recalcitrant parasite that causes the deadly disease African sleeping sickness. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The expression of selected non-ribosomal peptide synthetases in Aspergillus fumigatus is controlled by the availability of free iron.

Science.gov (United States)

Reiber, Kathrin; Reeves, Emer P; Neville, Claire M; Winkler, Robert; Gebhardt, Peter; Kavanagh, Kevin; Doyle, Sean

2005-07-01

Three non-ribosomal peptide synthetase genes, termed sidD, sidC and sidE, have been identified in Aspergillus fumigatus. Gene expression analysis by RT-PCR confirms that expression of both sidD and C was reduced by up to 90% under iron-replete conditions indicative of a likely role in siderophore biosynthesis. SidE expression was less sensitive to iron levels. In addition, two proteins purified from mycelia grown under iron-limiting conditions corresponded to SidD ( approximately 200 kDa) and SidC (496 kDa) as determined by MALDI ToF peptide mass fingerprinting and MALDI LIFT-ToF/ToF. Siderophore synthetases are unique in bacteria and fungi and represent an attractive target for antimicrobial chemotherapy.

Suzaku View of the Swift/BAT Active Galactic Nuclei. V. Torus Structure of Two Luminous Radio-Loud Active Galactic Nuclei (3C 206 and PKS 0707-35)

Science.gov (United States)

Tazaki, Fumie; Ueda, Yoshihiro; Terashima, Yuichi; Mushotzky, Richard F.; Tombesi, Francesco

2013-01-01

We present the results from broadband X-ray spectral analysis of 3C 206 and PKS 0707-35 with Suzaku and Swift/BAT, two of the most luminous unobscured and obscured radio-loud active galactic nuclei (AGNs) with hard X-ray luminosities of 10(sup 45.5) erg per second and 10(sup 44.9) erg per second (14-195 keV), respectively. Based on the radio core luminosity, we estimate that the X-ray spectrum of 3C 206 contains a significant (60% in the 14-195 keV band) contribution from the jet, while it is negligible in PKS 0707-35.We can successfully model the spectra with the jet component (for 3C 206), the transmitted emission, and two reflection components from the torus and the accretion disk. The reflection strengths from the torus are found to be R(sub torus)(=Omega/2pi) = 0.29 +/- 0.18 and 0.41 +/- 0.18 for 3C 206 and PKS 0707-35, respectively, which are smaller than those in typical Seyfert galaxies. Utilizing the torus model by Ikeda et al., we quantify the relation between the half-opening angle of a torus (theta(sub oa)) and the equivalent width of an iron-K line. The observed equivalent width of 3C 206, less than 71 eV, constrains the column density in the equatorial plane to N(sup eq)(sub H) lesst han 10(sup 23) per square centimeter, or the half-opening angle to theta(sub oa) greater than 80 deg. if N(sup eq)(sub H) = 10(sup 24) per square centimeter is assumed. That of PKS 0707-35, 72 +/- 36 eV, is consistent with N(sup eq)(sub H) 10(sup 23) per square centimeter. Our results suggest that the tori in luminous radio-loud AGNs are only poorly developed. The trend is similar to that seen in radio-quiet AGNs, implying that the torus structure is not different between AGNs with jets and without jets.

Engineered fungal polyketide biosynthesis in Pichia pastoris: a potential excellent host for polyketide production.

Science.gov (United States)

Gao, Limei; Cai, Menghao; Shen, Wei; Xiao, Siwei; Zhou, Xiangshan; Zhang, Yuanxing

2013-09-08

Polyketides are one of the most important classes of secondary metabolites and usually make good drugs. Currently, heterologous production of fungal polyketides for developing a high potential industrial application system with high production capacity and pharmaceutical feasibility was still at its infancy. Pichia pastoris is a highly successful system for the high production of a variety of heterologous proteins. In this work, we aim to develop a P. pastoris based in vivo fungal polyketide production system for first time and evaluate its feasibility for future industrial application. A recombinant P. pastoris GS115-NpgA-ATX with Aspergillus nidulans phosphopantetheinyl transferase (PPtase) gene npgA and Aspergillus terrus 6-methylsalicylic acid (6-MSA) synthase (6-MSAS) gene atX was constructed. A specific compound was isolated and identified as 6-MSA by HPLC, LC-MS and NMR. Transcription of both genes were detected. In 5-L bioreactor, the GS115-NpgA-ATX grew well and produced 6-MSA quickly until reached a high value of 2.2 g/L by methanol induction for 20 hours. Thereafter, the cells turned to death ascribing to high concentration of antimicrobial 6-MSA. The distribution of 6-MSA changed that during early and late induction phase it existed more in supernatant while during intermediate stage it mainly located intracellular. Different from 6-MSA production strain, recombinant M. purpureus pksCT expression strains for citrinin intermediate production, no matter PksCT located in cytoplasm or in peroxisomes, did not produce any specific compound. However, both npgA and pksCT transcripted effectively in cells and western blot analysis proved the expression of PPtase. Then the PPTase was expressed and purified, marked by fluorescent probes, and reacted with purified ACP domain and its mutant ACPm of PksCT. Fluoresence was only observed in ACP but not ACPm, indicating that the PPTase worked well with ACP to make it bioactive holo-ACP. Thus, some other factors may

Penentuan Kadar Air Dan Kadar Kotoran Minyak Inti Sawit Di PTPN III PKS Kebun Rambutan – Tebing Tinggi

OpenAIRE

Nadapdap, Nova Dana Isabela

2010-01-01

PTPN III PKS Kebun Rambutan – tebing tinggi is factory which manufactures CPO starting from fresh fruit bunch to be crude oil.And the second product produced by PTPN III is Palm kernel.The proses of palm kernel oil within several steps are separation,solution,drying and storage.In other to be distributed,palm kernel must the following the quality specification free fatty acid 0,5 %,water content 7,0 %,pollutant content 6,0 %,ang these are the standart for obtaining high quality palm kernel.An...

First Nustar Observations of the Bl Lac-Type Blazar Pks 2155-304: Constraints on the Jet Content and Distribution of Radiating Particles

DEFF Research Database (Denmark)

Madejski, G. M.; Nalewajko, K.; Madsen, K. K.

2016-01-01

We report the first hard X-ray observations with NuSTAR of the BL Lac-type blazar PKS 2155-304, augmented with soft X-ray data from XMM-Newton and γ-ray data from the Fermi Large Area Telescope, obtained in 2013 April when the source was in a very low flux state. A joint NuSTAR and XMM spectrum, ...

Swift detections of the flaring blazar GAIA 18ayp (PKS 2333-415) in X-rays and the UV

Science.gov (United States)

Grupe, Dirk; Komossa, S.; Angioni, R.; Schartel, N.

2018-04-01

We report Swift observations of the z=1.41 QSO GAIA 18ayp (PKS 2333-415) which was detected by GAIA in an optically flaring state on 2018-April-14. Swift observed GAIA 18ayp on 2018 April 23 for a total of 1.4 ks. The QSO is clearly detected in X-rays and the UV. The X-ray position found using the enhanced XRT position (Goad et al. 2007, Evans et al. 2009) is RA-2000 = 23 36 34.1, Dec-2000 = -41 15 21.4 with an uncertainty of 3.0".

Genome-scale Evaluation of the Biotechnological Potential of Red Sea Bacilli Strains

KAUST Repository

Othoum, Ghofran K.

2018-02-01

The increasing spectrum of multidrug-resistant bacteria has caused a major global public health concern, necessitating the discovery of novel antimicrobial agents. Additionally, recent advancements in the use of microbial cells for the scalable production of industrial enzymes has encouraged the screening of new environments for efficient microbial cell factories. The unique ecological niche of the Red Sea points to the promising metabolic and biosynthetic potential of its microbial system. Here, ten sequenced Bacilli strains, that are isolated from microbial mat and mangrove mud samples from the Red Sea, were evaluated for their use as platforms for protein production and biosynthesis of bioactive compounds. Two of the species (B.paralicheniformis Bac48 and B. litoralis Bac94) were found to secrete twice as much protein as Bacillus subtilis 168, and B. litoralis Bac94 had complete Tat and Sec protein secretion systems. Additionally, four Red Sea Species (B. paralicheniformis Bac48, Virgibacillus sp. Bac330, B. vallismortis Bac111, B. amyloliquefaciens Bac57) showed capabilities for genetic transformation and possessed competence genes. More specifically, the distinctive biosynthetic potential evident in the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 was assessed and compared to nine available complete genomes of B. licheniformis and three genomes of B. paralicheniformis. A uniquely-structured trans-acyltransferase (trans-AT) polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) cluster in strains of this species was identified in the genome of B. paralicheniformis 48. In total, the two B. paralicheniformis Red Sea strains were found to be more enriched in modular clusters compared to B. licheniformis strains and B. paralicheniformis strains from other environments. These findings provided more insights into the potential of B. paralicheniformis 48 as a microbial cell factory and encouraged further focus on the strain�

Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase

DEFF Research Database (Denmark)

Yuzawa, Satoshi; Bailey, Constance B.; Fujii, Tatsu A.

2017-01-01

Streptomyces-derived, Well-characterized modular, polyketide synthase (PKS). Using this enzyme as a model, we experimentally investigated the effects of alternative TSSs using a heterologous host, Streptomyces venezuelae. One of the TSSs employed boosted the protein level by 59-fold and the product yield by 23...

Aromatic Polyketide GTRI-02 is a Previously Unidentified Product of the act Gene Cluster in Streptomyces coelicolor A3(2).

Science.gov (United States)

Wu, Changsheng; Ichinose, Koji; Choi, Young Hae; van Wezel, Gilles P

2017-07-18

The biosynthesis of aromatic polyketides derived from type II polyketide synthases (PKSs) is complex, and it is not uncommon that highly similar gene clusters give rise to diverse structural architectures. The act biosynthetic gene cluster (BGC) of the model actinomycete Streptomyces coelicolor A3(2) is an archetypal type II PKS. Here we show that the act BGC also specifies the aromatic polyketide GTRI-02 (1) and propose a mechanism for the biogenesis of its 3,4-dihydronaphthalen-1(2H)-one backbone. Polyketide 1 was also produced by Streptomyces sp. MBT76 after activation of the act-like qin gene cluster by overexpression of the pathway-specific activator. Mining of this strain also identified dehydroxy-GTRI-02 (2), which most likely originated from dehydration of 1 during the isolation process. This work shows that even extensively studied model gene clusters such as act of S. coelicolor can still produce new chemistry, offering new perspectives for drug discovery. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biocombinatorial Engineering of Fungal PKS-NRPS Hybrids for Production of Novel Synthetic Natural Products

DEFF Research Database (Denmark)

Nielsen, Maria Lund

encoding a PKS-NRPS hybrid responsible for the production of a medically relevant compound in Talaromyces atroroseus. To the best of my knowledge, this study represents the first example of reverse engineering of a Talaromyces species. In the fourth study (chapter 5), I used the CRISPR-Cas9 system...... structure optimization. Within the last decade, an alternative approach for expanding natural product chemodiversity has been applied. This strategy, known as combinatorial biosynthesis, involves the re-engineering of biosynthetic pathways and ultimately the rational engineering of new natural product...... analogs. This field, however, has proved very challenging and many engineering efforts have resulted in enzymatic loss-of-function or reduced yields. Thus, the future success in combinatorial biosynthetic studies requires a thorough understanding of the structure and function of biosynthetic enzymes...

Examining the nature of very-high-energy gamma-ray emission from the AGN PKS 1222+216 and 3C 279

Science.gov (United States)

Price, Sharleen; Brill, Ari; Mukherjee, Reshmi; VERITAS

2018-01-01

Blazars are a type of active galactic nuclei (AGN) that emit jets of ionized matter which move towards the Earth at relativistic speeds. In this research we carried out a study of two objects, 3C 279 and PKS 1222+216, which belong to the subset of blazars known as FSRQs (flat spectrum radio quasars), the most powerful TeV-detected sources at gamma-ray energies with bolometric luminosities exceeding 1048 erg/s. The high-energy emission of quasars peaks in the MeV-GeV band, making these sources very rarely detectable in the TeV energy range. In fact, only six FSRQs have ever been detected in this range by very-high-energy gamma-ray telescopes. We will present results from observing campaigns on 3C 279 in 2014 and 2016, when the object was detected in high flux states by Fermi-LAT. Observations include simultaneous coverage with the Fermi-LAT satellite and the VERITAS ground-based array spanning four decades in energy from 100 MeV to 1 TeV. We will also report VERITAS observations of PKS 1222+216 between 2008 and 2017. The detection/non-detection of TeV emission during flaring episodes at MeV energies will further contribute to our understanding of particle acceleration and gamma-ray emission mechanisms in blazar jets.

Polyketide family of novel antibacterial 7-O-methyl-5'-hydroxy-3'-heptenoate-macrolactin from seaweed-associated Bacillus subtilis MTCC 10403.

Science.gov (United States)

Chakraborty, Kajal; Thilakan, Bini; Raola, Vamshi Krishna

2014-12-17

Seaweed-associated heterotrophic bacterial communities were screened to isolate potentially useful antimicrobial strains, which were characterized by phylogenetic analysis. The bacteria were screened for the presence of metabolite genes involved in natural product biosynthetic pathway, and the structural properties of secondary metabolites were correlated with the genes. Bioactivity-guided isolation of polyene antibiotic 7-O-methyl-5'-hydroxy-3'-heptenoate-macrolactin from Bacillus subtilis MTCC10403 associated with seaweed Anthophycus longifolius using mass spectrometry and extensive 2D-NMR studies was carried out. The newly isolated macrolactin compound is a bactericidal antibiotic with broad spectrum activity against human opportunistic clinical pathogens. The biosynthetic pathway of 7-O-methyl-5'-hydroxy-3'-heptenoate-macrolactin by means of a stepwise, decarboxylative condensation pathway established the PKS-assisted biosynthesis of the parent macrolactin and the side-chain 5-hydroxyhept-3-enoate moiety attached to the macrolactin ring system at C-7. Antimicrobial activity analysis combined with the results of amplifying genes encoding for polyketide synthetase and nonribosomal peptide synthetase showed that seaweed-associated bacteria had broad-spectrum antimicrobial activity. The present work may have an impact on the exploitation of macrolactins for pharmaceutical and biotechnological applications.

Molecular hydrogen in the z = 2.811 absorbing material toward the quasar PKS 0528-250

International Nuclear Information System (INIS)

Levshakov, S.A.; Varshalovich, D.A.

1985-01-01

Among the previously unidentified absorbtion features in the spectrum of the quasar PKS 0528-250 obtained by previous authors tentative evidence has been found for H 2 lines at the same redshift (z = 2.811) as that of the well-known absorption-line system. The column density of molecules has been estimated from the curve of growth; the fraction of H 2 appears to be about 2 x 10 -5 . The ortho- to para-H 2 ratio corresponds to the excitation temperature of Tsub(ex)(H 2 ) = 300 +- 150 K, though the upper rotational levels J >= 3 turn out be overpopulated. The results obtained seem to provide substantial evidence for the existence of molecular hydrogen at the early cosmological epoch with z approx. 3. (author)

On the intrinsic spectrum of PKS 2155-304 from H.E.S.S. 2003 data

International Nuclear Information System (INIS)

Costamante, L.; Benbow, W.; Horns, D.; Reimer, A.; Reimer, O.

2005-01-01

In 2003, PKS 2155-304 has been significantly detected by H.E.S.S. at Very High Energies (VHE), with an average spectrum of Γ = 3.3. Due to absorption by the Extragalactic Background Light (EBL), the intrinsic spectrum is heavily modified both in shape and intensity. To correct for this effect, and locate the Inverse Compton (IC) peak of the Spectral Energy Distribution (SED), we used three EBL models (representatives of three different flux levels for the stellar peak component). The resulting TeV spectrum has a peak around 1 TeV for stellar peak fluxes above the Primack (2001) calculation, while the spectrum is steeper than Γ = 2 (thus locating the IC peak 19 (for historical SED fluxes and 2 hours variability timescale)

Multi-Frequency Monitoring of the Flat Spectrum Radio Quasar PKS 1222+216 in 2008–2015

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Ivan Troitskiy

2016-11-01

Full Text Available We analyze the broadband activity of the flat spectrum radio quasar PKS 1222+216 from 2008 to 2015 using multi-frequency monitoring which involves γ-ray data from the Fermi Large Area Telescope, total intensity and linear polarization observations from different optical telescopes in R band, and imaging of the inner jet structure with the Very Long Baseline Array (VLBA at 43 GHz. During the observations, the source showed several dramatic flares at γ rays and optical bands, with the rising branch of a γ-ray flare accompanied by a rapid rotation of the polarization position angle (EVPA, a fast increase of the degree of polarization in the optical band, brightening of the VLBI core, and appearance of a new superluminal component in the parsec-scale jet. The rapid variability of the optical linear polarization may be explained by a strong turbulence in the jet plasma. We find a correlation between the γ rays, optical R band, and 43 GHz variability on a long-term scale (months and years, and a good general alignment between EVPAs in R band and at 43 GHz, while the correlation between short-term variations (days and weeks is weaker. Synchronous activity across the bands supports the idea that the emission regions responsible for the γ-ray and optical flares are co-spatial and located in the vicinity of the mm-wave core of the parsec-scale jet. However, these connections do not completely explain the challenging behaviour of PKS 1222+216, since there are some γ-ray flares which are not accompanied by jet events, and vice versa. We need a continuation of multi-frequency monitoring along with high resolution imaging of the parsec-scale jet to understand in detail the origin of high energy emission in blazars.

Gamma-Ray Flaring Activity from the Gravitationally Lensed Blazar PKS 1830-211 Observed by Fermi LAT

Energy Technology Data Exchange (ETDEWEB)

Abdo, A. A.; et al.

2015-01-23

The Large Area Telescope (LAT) on board the Fermi Gamma-ray Space Telescope routinely detects the MeV-peaked flat-spectrum radio quasar PKS 1830–211 (z = 2.507). Its apparent isotropic γ-ray luminosity (E > 100 MeV), averaged over ~3 years of observations and peaking on 2010 October 14/15 at 2.9 × 10(50) erg s(–)(1), makes it among the brightest high-redshift Fermi blazars. No published model with a single lens can account for all of the observed characteristics of this complex system. Based on radio observations, one expects time-delayed variability to follow about 25 days after a primary flare, with flux about a factor of 1.5 less. Two large γ-ray flares of PKS 1830–211 have been detected by the LAT in the considered period, and no substantial evidence for such a delayed activity was found. This allows us to place a lower limit of about 6 on the γ-ray flux ratio between the two lensed images. Swift XRT observations from a dedicated Target of Opportunity program indicate a hard spectrum with no significant correlation of X-ray flux with the γ-ray variability. The spectral energy distribution can be modeled with inverse Compton scattering of thermal photons from the dusty torus. The implications of the LAT data in terms of variability, the lack of evident delayed flare events, and different radio and γ-ray flux ratios are discussed. Microlensing effects, absorption, size and location of the emitting regions, the complex mass distribution of the system, an energy-dependent inner structure of the source, and flux suppression by the lens galaxy for one image path may be considered as hypotheses for understanding our results.

The ultraviolet to infrared energy distribution of the BL Lacertae object PKS 0422+00 at two different brightness levels

Energy Technology Data Exchange (ETDEWEB)

Falomo, R.; Bouchet, P.; Maraschi, L.; Treves, A.; Tanzi, E.G. (Padova, Osservatorio Astronomico, Padua (Italy) European Southern Observatory, La Silla (Chile) Milano Universita, Milan (Italy) CNR, Istituto di Fisica Cosmica, Milan (Italy))

1989-10-01

The BL Lacertae object PKS 0422+00 was observed with IUE (International Ultraviolet Explorer) on August 31-September 1, 1987, when the visual magnitude of the object was V = 16.2, and again about 4 months later (January 10, 1988) during an active state (V = 15.6). Quasi-simultaneous optical to infrared observations allow deriving a detailed spectral flux distribution from 8 x 10 to the 13th to 2.5 x 10 the 15th Hz, for each epoch. Fits in terms of broken power laws and logarithmic parabolas are discussed. 32 refs.

The ultraviolet to infrared energy distribution of the BL Lacertae object PKS 0422+00 at two different brightness levels

International Nuclear Information System (INIS)

Falomo, R.; Bouchet, P.; Maraschi, L.; Treves, A.; Tanzi, E.G.

1989-01-01

The BL Lacertae object PKS 0422+00 was observed with IUE (International Ultraviolet Explorer) on August 31-September 1, 1987, when the visual magnitude of the object was V = 16.2, and again about 4 months later (January 10, 1988) during an active state (V = 15.6). Quasi-simultaneous optical to infrared observations allow deriving a detailed spectral flux distribution from 8 x 10 to the 13th to 2.5 x 10 the 15th Hz, for each epoch. Fits in terms of broken power laws and logarithmic parabolas are discussed. 32 refs

Combined genetic and bioactivity-based prioritization leads to the isolation of an endophyte-derived antimycobacterial compound.

Science.gov (United States)

Alvin, A; Kalaitzis, J A; Sasia, B; Neilan, B A

2016-05-01

To initiate a genetic and bioactivity-based screening programme of culturable endophytes to identify micro-organisms capable of producing bioactive polyketides and peptides. Fungal endophytes were isolated from flowers, leaves and roots of Rhoeo spathacea, revealing a community consisting of Colletotrichum sp., Fusarium sp., Guignardia sp., Phomopsis sp., Phoma sp. and Microdochium sp. Genetic screening showed that all isolates had polyketide synthase (PKS) genes and most had nonribosomal peptide synthetase (NRPS) genes. Ethyl acetate extracts of the fungal isolates exhibited antiproliferative activity against at least one of the seven bacterial and mycobacterial test strains. Nuclear Magnetic Resonance -guided fractionation of the crude extract from a Fusarium sp. strain which exhibited strong antiproliferative activity against Mycobacterium tuberculosis resulted in the isolation of the polyketide javanicin. This compound was active against Myco. tuberculosis (MIC = 25 μg ml(-1)) and Mycobacterium phlei (MIC = 50 μg ml(-1)). The medicinal plant R. spathacea hosts a variety of fungal endophytes capable of producing antibacterial and antimycobacterial compounds. There is a positive correlation between the presence of PKS and/or NRPS encoding genes in endophytes and the bioactivity of their respective organic extracts. This is the first report on the fungal endophytic diversity of R. spathacea, and the isolation of an antimycobacterial compound from the plant which has been traditionally used for the treatment of tuberculosis symptoms. © 2016 The Society for Applied Microbiology.

Analysis of the Sequences, Structures, and Functions of Product-Releasing Enzyme Domains in Fungal Polyketide Synthases

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Lu Liu

2017-09-01

Full Text Available Product-releasing enzyme (PRE domains in fungal non-reducing polyketide synthases (NR-PKSs play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I–VIII. It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE, reductase (R, and metallo-β-lactamase-type TE (MβL-TE. The widely distributed TE or TE-like domains were involved in NR-PKSs of groups I–IV, VI, and VIII. The R domains appeared in NR-PKSs of groups IV and VII, while the physically discrete MβL-TE domains were employed by most NR-PKSs of group V. The changes of catalytic sites and structural characteristics resulted in PRE functional differentiations. The phylogeny revealed that the evolution of TE domains was accompanied by complex functional divergence. The diverse sequence lengths of TE lid-loops affected substrate specificity with different chain lengths. The volume diversification of TE catalytic pockets contributed to catalytic mechanisms with functional differentiations. The above findings may help to understand the crucial catalysis of fungal aromatic polyketide biosyntheses and govern recombination of NR-PKSs to obtain unnatural target products.

Genetic determinants of reutericyclin biosynthesis in Lactobacillus reuteri.

Science.gov (United States)

Lin, Xiaoxi B; Lohans, Christopher T; Duar, Rebbeca; Zheng, Jinshui; Vederas, John C; Walter, Jens; Gänzle, Michael

2015-03-01

Reutericyclin is a unique antimicrobial tetramic acid produced by some strains of Lactobacillus reuteri. This study aimed to identify the genetic determinants of reutericyclin biosynthesis. Comparisons of the genomes of reutericyclin-producing L. reuteri strains with those of non-reutericyclin-producing strains identified a genomic island of 14 open reading frames (ORFs) including genes coding for a nonribosomal peptide synthetase (NRPS), a polyketide synthase (PKS), homologues of PhlA, PhlB, and PhlC, and putative transport and regulatory proteins. The protein encoded by rtcN is composed of a condensation domain, an adenylation domain likely specific for d-leucine, and a thiolation domain. rtcK codes for a PKS that is composed of a ketosynthase domain, an acyl-carrier protein domain, and a thioesterase domain. The products of rtcA, rtcB, and rtcC are homologous to the diacetylphloroglucinol-biosynthetic proteins PhlABC and may acetylate the tetramic acid moiety produced by RtcN and RtcK, forming reutericyclin. Deletion of rtcN or rtcABC in L. reuteri TMW1.656 abrogated reutericyclin production but did not affect resistance to reutericyclin. Genes coding for transport and regulatory proteins could be deleted only in the reutericyclin-negative L. reuteri strain TMW1.656ΔrtcN, and these deletions eliminated reutericyclin resistance. The genomic analyses suggest that the reutericyclin genomic island was horizontally acquired from an unknown source during a unique event. The combination of PhlABC homologues with both an NRPS and a PKS has also been identified in the lactic acid bacteria Streptococcus mutans and Lactobacillus plantarum, suggesting that the genes in these organisms and those in L. reuteri share an evolutionary origin. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Biosynthesis of antimycins with a reconstituted 3-formamidosalicylate pharmacophore in Escherichia coli.

Science.gov (United States)

Liu, Joyce; Zhu, Xuejun; Seipke, Ryan F; Zhang, Wenjun

2015-05-15

Antimycins are a family of natural products generated from a hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line. Although they possess an array of useful biological activities, their structural complexity makes chemical synthesis challenging, and their biosynthesis has thus far been dependent on slow-growing source organisms. Here, we reconstituted the biosynthesis of antimycins in Escherichia coli, a versatile host that is robust and easy to manipulate genetically. Along with Streptomyces genetic studies, the heterologous expression of different combinations of ant genes enabled us to systematically confirm the functions of the modification enzymes, AntHIJKL and AntO, in the biosynthesis of the 3-formamidosalicylate pharmacophore of antimycins. Our E. coli-based antimycin production system can not only be used to engineer the increased production of these bioactive compounds, but it also paves the way for the facile generation of novel and diverse antimycin analogues through combinatorial biosynthesis.

Multiwavelength Observations of the Powerful Gamma-ray Quasar PKS 1510-089: Clues on the Jet Composition

Energy Technology Data Exchange (ETDEWEB)

Kataoka, J.; Madejski, G.; Sikora, M.; Roming, P.; Chester, M.M.; Grupe, D.; Tsubuku, Y.; Sato, R.; Kawai, N.; Tosti, G.; Impiombato, D.; Kovalev, Y.Y.; Kovalev, Y.A.; Edwards, Philip G.; Wagner, S.J.; Moderski, R.; Stawarz, L.; Takahashi, T.; Watanabe, S.

2007-09-28

We present the results from a multiwavelength campaign conducted in August 2006 of the powerful {gamma}-ray quasar PKS 1510--089 (z = 0.361). This campaign commenced with a deep Suzaku observation lasting three days for a total exposure time of 120 ks, and continued with Swift monitoring over 18 days. Besides Swift observations, which sampled the optical/UV flux in all 6 UVOT filters as well as the X-ray spectrum in the 0.3--10 keV energy range, the campaign included ground-based optical and radio data, and yielded a quasi-simultaneous broad-band spectral energy distribution from 109 Hz to 1019 Hz. Thanks to its low instrumental background, the Suzaku observation provided a high S/N X-ray spectrum, which is well represented by an extremely hard power-law with photon index {Gamma}{approx_equal}1.2, augmented by a soft component apparent below 1 keV, which is well described by a black-body model with temperature kT {approx_equal}0.2 keV. Monitoring by Suzaku revealed temporal variability which is different between the low and high energy bands, again suggesting the presence of a second, variable component in addition to the primary power-law emission. We model the broadband spectrum of PKS 1510--089 assuming that the high energy spectral component results from Comptonization of infrared radiation produced by hot dust located in the surrounding molecular torus. In the adopted internal shock scenario, the derived model parameters imply that the power of the jet is dominated by protons but with a number of electrons/positrons exceeding a number of protons by a factor {approx} 10. We also find that inhomogeneities responsible for the shock formation, prior to the collision may produce bulk-Compton radiation which can explain the observed soft X-ray excess and possible excess at {approx} 18 keV. We note, however, that the bulk-Compton interpretation is not unique, and the observed soft excess could arise as well via some other processes discussed briefly in the text.

Analisa Kadar Silika Pada Air Umpan Ketel Dan Air Boiler Dengan Alat Lovibond Di Pks PT. Perkebunan Nusantara IV Dolok Ilir

OpenAIRE

Simamora, Evi Novita F.

2016-01-01

Analysis was performed on a silica content of boiler feed water and boiler water at the PKS PT. PTPN IV Dolok Ilir. Samples taken from the boiler feed water tank heated while the boiler water sample taken from the heating pipes in the boiler drum. Silica content in the sample is determined by comparison with a reagent Ammonium molybdat, HCL 1: 1, and oxalic acid. The determinations were performed over a period of 18 to 27 February 2015. The results showed that the silica content of boiler fee...

X-ray monitoring of the radio and γ-ray loud Narrow-Line Seyfert 1 Galaxy PKS2004–447

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Kreikenbohm A.

2013-12-01

Full Text Available We present preliminary results of the X-ray analysis of XMM-Newton and Swift observations as part of a multi-wavelength monitoring campaign in 2012 of the radio-loud narrow line Seyfert 1 galaxy PKS 2004–447. The source was recently detected in γ-rays by Fermi/LAT among only four other galaxies of that type. The 0:5 – 10 keV X-ray spectrum is well-described by a simple absorbed powerlaw (Γ ∼ 1.6. The source brightness exhibits variability on timescales of months to years with indications for spectral variability, which follows a “bluer-when-brighter” behaviour, similar to blazars.

Optical Polarimetry and Radio Observations of PKS1510-089 between 2009 and 2013

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Pedro P. B. Beaklini

2018-02-01

Full Text Available The blazar PKS 1510-089 has shown intense activity at γ -rays in the recent years. In this work, we discussed the results of our 7 mm radio continuum and optical polarimetric monitoring between 2009 and 2013. In 2009, we detected a large rotation of the optical polarization angle that we attributed to the ejection of new polarized components. In 2011, after the occurrence of several γ -rays flares, the radio emission started to increase, reaching values never observed before. We interpreted this increase as the consequence of the superposition of several new components ejected during the γ -rays flares. A delay was measured between the maximum in the radio emission and the γ -ray flares, which favors models involving expanding components like the shock-in-jet models. Finally, we tried to understand the polarization angle variability behavior filling the gaps in our observations with published results of other polarimetric campaigns, and using the criterion of minimum variation in the polarization angle between successive observations to solve the 180° multiplicity.

The Colibactin Genotoxin Generates DNA Interstrand Cross-Links in Infected Cells

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Nadège Bossuet-Greif

2018-03-01

Full Text Available Colibactins are hybrid polyketide-nonribosomal peptides produced by Escherichia coli, Klebsiella pneumoniae, and other Enterobacteriaceae harboring the pks genomic island. These genotoxic metabolites are produced by pks-encoded peptide-polyketide synthases as inactive prodrugs called precolibactins, which are then converted to colibactins by deacylation for DNA-damaging effects. Colibactins are bona fide virulence factors and are suspected of promoting colorectal carcinogenesis when produced by intestinal E. coli. Natural active colibactins have not been isolated, and how they induce DNA damage in the eukaryotic host cell is poorly characterized. Here, we show that DNA strands are cross-linked covalently when exposed to enterobacteria producing colibactins. DNA cross-linking is abrogated in a clbP mutant unable to deacetylate precolibactins or by adding the colibactin self-resistance protein ClbS, confirming the involvement of the mature forms of colibactins. A similar DNA-damaging mechanism is observed in cellulo, where interstrand cross-links are detected in the genomic DNA of cultured human cells exposed to colibactin-producing bacteria. The intoxicated cells exhibit replication stress, activation of ataxia-telangiectasia and Rad3-related kinase (ATR, and recruitment of the DNA cross-link repair Fanconi anemia protein D2 (FANCD2 protein. In contrast, inhibition of ATR or knockdown of FANCD2 reduces the survival of cells exposed to colibactin-producing bacteria. These findings demonstrate that DNA interstrand cross-linking is the critical mechanism of colibactin-induced DNA damage in infected cells.

Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata.

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Yujie Hou

Full Text Available The genus Alternaria is a group of infectious/contagious pathogenic fungi that not only invade a wide range of crops but also induce severe allergic reactions in a part of the human population. In this study, two strains Alternaria longipes cx1 and Alternaria alternata cx2 were isolated from different brown spot lesions on infected tobacco leaves. Their complete genomes were sequenced, de novo assembled, and comparatively analyzed. Phylogenetic analysis revealed that A. longipes cx1 and A. alternata cx2 diverged 3.3 million years ago, indicating a recent event of speciation. Seventeen non-ribosomal peptide synthetase (NRPS genes and 13 polyketide synthase (PKS genes in A. longipes cx1 and 13 NRPS genes and 12 PKS genes in A. alternata cx2 were identified in these two strains. Some of these genes were predicted to participate in the synthesis of non-host specific toxins (non-HSTs, such as tenuazonic acid (TeA, alternariol (AOH and alternariol monomethyl ether (AME. By comparative genome analysis, we uncovered that A. longipes cx1 had more genes putatively involved in pathogen-plant interaction, more carbohydrate-degrading enzymes and more secreted proteins than A. alternata cx2. In summary, our results demonstrate the genomic distinction between A. longipes cx1 and A. altenata cx2. They will not only improve the understanding of the phylogenetic relationship among genus Alternaria, but more importantly provide valuable genomic resources for the investigation of plant-pathogen interaction.

HUBUNGAN ANTARA PARTISIPASI BIDAN PRAKTIK MANDIRI (BPM, PERJANJIAN KERJASAMA (PKS DAN SOSIALISASI DENGAN PELAKSANAAN PROGRAM JAMPERSAL DI KOTA BOGOR

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Nawati Nawati

2016-04-01

Full Text Available Hubungan antara Partisipasi BPM, Perjanjian Kerjasama dan Sosialiasi dengan Pelaksanaan Program Jampersal di kota Bogor. Kesehatan merupakan bagian integal yang penting dalam pembangunan dan peningkatan kesejahteraan bangsa serta human capital investment baik jangka pendek maupun jangka panjang oleh karena itu pemerintah dalam suatu negara bertanggung jawab pada masalah kesehatan rakyatnya. Pemerintah sendiri adalah regulator dari penyelenggaraan pelayanan kesehatan untuk seluruh masyarakat, agar masyarakat mampu membayar kesehatan yang dibebankan kepadanya atau institusi tempat kerjanya. Tujuan penelitian ini adalah untuk diketahuinya hubungan antara Partisipasi BPM, Perjanjian Kerjasama dan Sosialiasi dengan Pelaksanaan Program Jampersal. Metode yang digunakan dalam penelitian ini adalah metode penelitian  analitik dengan pendekatan Cross sectional. Data dikumpulkan melalui wawancara dengan kuesioner pada bidan. Analisis data menggunakan uji Chi Square dan Regresi Logistik. Hasil analisis data didapatkan responden dengan OR:9,74 (95% CI:5,33-17,81 dan p-value= 0,000. Pada pendidikan responden mendapatkan nilai OR:4,56 (95% CI:3,22-16,24 dengan p-value= 0,000. Pada masa kerja responden dengan nilai OR:9,46 (95% CI:4,88-19,98 dengan p-value= 0,000. Pada karakteristik lama responden dengan OR: 66,93 (95% CI:5,89-173,07 dengan p-value= 0,000. Nilai sikap responden dengan OR:10,98 (95% CI:5,14-23,43 dengan p-value= 0,006. PKS dengan pelaksanakan Program Jampersal di Kota Bogor mempunyai nilai OR:9,46 (95% CI:4,48-19,98 dengan p-value= 0,000. Analisis multivariat ternyata variabel yang berhubungan bermakna dengan pelaksanaan program Jampersal adalah variabel PKS dengan nilai expB 3.833 p-value 0,036 dan sikap responden dengan nilai expB 3.032 dengan p-value 0,006. Dapat disimpulkan bahwa sikap responden memiliki perilaku positif dalam pelaksanaan Program Jampersal, variabel yang berhubungan bermakna dengan pelaksanaan Program Jampersal adalah

Engineering modular polyketide synthases for production of biofuels and industrial chemicals.

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Cai, Wenlong; Zhang, Wenjun

2018-04-01

Polyketide synthases (PKSs) are one of the most profound biosynthetic factories for producing polyketides with diverse structures and biological activities. These enzymes have been historically studied and engineered to make un-natural polyketides for drug discovery, and have also recently been explored for synthesizing biofuels and industrial chemicals due to their versatility and customizability. Here, we review recent advances in the mechanistic understanding and engineering of modular PKSs for producing polyketide-derived chemicals, and provide perspectives on this relatively new application of PKSs. Copyright © 2017 Elsevier Ltd. All rights reserved.

De Novo Assembly and Genome Analyses of the Marine-Derived Scopulariopsis brevicaulis Strain LF580 Unravels Life-Style Traits and Anticancerous Scopularide Biosynthetic Gene Cluster.

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Kumar, Abhishek; Henrissat, Bernard; Arvas, Mikko; Syed, Muhammad Fahad; Thieme, Nils; Benz, J Philipp; Sørensen, Jens Laurids; Record, Eric; Pöggeler, Stefanie; Kempken, Frank

2015-01-01

The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis.

Simultaneous X-ray, ultraviolet, and optical observations of the BL Lacertae object PKS 2155-304

International Nuclear Information System (INIS)

Treves, A.; Morini, M.; Chiappetti, L.; Fabian, A.; Falomo, R.

1989-01-01

A series of observations at optical, UV, and X-ray frequencies of PKS 2155-304, one of the brightest BL Lac objects is reported. Spectral fits given for various epochs show that the medium energy data are well fitted by single power laws plus absorption, with energy index between 1.5 and 2. Marginal evidence for an absorption edge at about 7 keV is found, as is evidence for some spectral depression at about 1 keV. This may be modeled with an edge at 660 + or - 26 eV with optical depth tau = 1.8 + or - 0.2. Energy distributions on several occasions are reconstructed, and the optical, UV, and X-ray intensities are found to be correlated in all cases but one. The variability amplitudes decrease and the time scales increase with decreasing frequency. These results indicate a synchrotron origin for the X-rays and distinct but connected emission regions for the X-ray, UV, and optical bands. 46 refs

The z = 1.6748 C I Absorber Toward the QSO PKS 1756+237

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Roth, Katherine C.; Bauer, James M.; Jim, Kevin T. C.

We have detected C I ground-state absorption at zabs = 1.6748 toward the QSO PKS 1756+237 (zem = 1.725), making this only the fourth known C I QSO absorber. The absence of excited-state fine-structure C I lines is compatible with the redshifted Cosmic Microwave Background Radiation at an expected temperature of TCMBR (1+z) = 7.291 K (Mather et al. 1994, ApJ, 354, L37). We find a 2 σ upper-limit on the C I excitation temperature of Tex <= 7.73(+0.53, -0.46) K (Roth & Bauer 1999, ApJ, submitted). Our Keck HIRES spectra (8.3 km s-1 FWHM) obtained in May 1997 also reveal the existence of Ni II and Fe II lines with a sub-solar Ni/Fe abundance ratio, presumably indicative of dust. We have obtained deep, high resolution (0.3'' FWHM) images in H+K' with the UH 2.2m Tip-Tilt system of the QSO field in order to identify the system responsible for the zabs = 1.6748 absorption. We detect two faint candidate systems within 1.5'' and 3'' (≅ 15 and 30 kpc, Hcirc = 65) of the QSO.

Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture

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Miller, Bradley R.; Drake, Eric J.; Shi, Ce; Aldrich, Courtney C.; Gulick, Andrew M. (UMM); (HWMRI)

2016-09-05

Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa. These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain.

Genome Assembly of the Fungus Cochliobolus miyabeanus, and Transcriptome Analysis during Early Stages of Infection on American Wildrice (Zizania palustris L..

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Claudia V Castell-Miller

Full Text Available The fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice (Oryza sativa and two North American specialty crops, American wildrice (Zizania palustris and switchgrass (Panicum virgatum. Despite the importance of C. miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C. miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C. miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta. A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses including hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. This work will facilitate future research on C. miyabeanus pathogen-associated molecular patterns and effectors, and in the identification of their corresponding wildrice defense mechanisms.

EVIDENCE FOR TWO LOGNORMAL STATES IN MULTI-WAVELENGTH FLUX VARIATION OF FSRQ PKS 1510-089

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Kushwaha, Pankaj; Misra, Ranjeev [Inter University Center for Astronomy and Astrophysics, Pune 411007 (India); Chandra, Sunil; Singh, K. P. [Department of Astronomy and Astrophysics, Tata Institute of Fundamental Research, Mumbai 400005 (India); Sahayanathan, S. [Astrophysical Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Baliyan, K. S., E-mail: pankajk@iucaa.in [Physical Research Laboratory, Ahmedabad 380009 (India)

2016-05-01

We present a systematic characterization of multi-wavelength emission from blazar PKS 1510-089 using well-sampled data at near-infrared (NIR), optical, X-ray, and γ -ray energies. The resulting flux distributions, except at X-rays, show two distinct lognormal profiles corresponding to a high and a low flux level. The dispersions exhibit energy-dependent behavior except in the LAT γ -ray and optical B-band. During the low level flux states, it is higher toward the peak of the spectral energy distribution, with γ -ray being intrinsically more variable followed by IR and then optical, consistent with mainly being a result of varying bulk Lorentz factor. On the other hand, the dispersions during the high state are similar in all bands except the optical B-band, where thermal emission still dominates. The centers of distributions are a factor of ∼4 apart, consistent with anticipation from studies of extragalactic γ -ray background with the high state showing a relatively harder mean spectral index compared to the low state.

Ancient horizontal gene transfer from bacteria enhances biosynthetic capabilities of fungi.

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Imke Schmitt

Full Text Available Polyketides are natural products with a wide range of biological functions and pharmaceutical applications. Discovery and utilization of polyketides can be facilitated by understanding the evolutionary processes that gave rise to the biosynthetic machinery and the natural product potential of extant organisms. Gene duplication and subfunctionalization, as well as horizontal gene transfer are proposed mechanisms in the evolution of biosynthetic gene clusters. To explain the amount of homology in some polyketide synthases in unrelated organisms such as bacteria and fungi, interkingdom horizontal gene transfer has been evoked as the most likely evolutionary scenario. However, the origin of the genes and the direction of the transfer remained elusive.We used comparative phylogenetics to infer the ancestor of a group of polyketide synthase genes involved in antibiotic and mycotoxin production. We aligned keto synthase domain sequences of all available fungal 6-methylsalicylic acid (6-MSA-type PKSs and their closest bacterial relatives. To assess the role of symbiotic fungi in the evolution of this gene we generated 24 6-MSA synthase sequence tags from lichen-forming fungi. Our results support an ancient horizontal gene transfer event from an actinobacterial source into ascomycete fungi, followed by gene duplication.Given that actinobacteria are unrivaled producers of biologically active compounds, such as antibiotics, it appears particularly promising to study biosynthetic genes of actinobacterial origin in fungi. The large number of 6-MSA-type PKS sequences found in lichen-forming fungi leads us hypothesize that the evolution of typical lichen compounds, such as orsellinic acid derivatives, was facilitated by the gain of this bacterial polyketide synthase.

The Kinome of Edible and Medicinal Fungus Wolfiporia cocos

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Wei Wei

2016-09-01

Full Text Available Wolfiporia cocos is an edible and medicinal fungus that grows in association with pine trees, and its dried sclerotium, known as Fuling in China, has been used as a traditional medicine in East Asian countries for centuries. Nearly 10% of the traditional Chinese medicinal preparations contain W. cocos. Currently, the commercial production of Fuling is limited because of the lack of pine-based substrate and paucity of knowledge about the sclerotial development of the fungus. Since protein kinase (PKs play significant roles in the regulation of growth, development, reproduction and environmental responses in filamentous fungi, the kinome of W. cocos was analyzed by identifying the PKs genes, studying transcript profiles and assigning PKs to orthologous groups. Of the 10 putative PKs, 11 encode atypical PKs, and 13, 10, 2, 22, and 11 could encoded PKs from the AGC, CAMK, CK, CMGC, STE and TLK Groups, respectively. The level of transcripts from PK genes associated with sclerotia formation in the mycelium and sclerotium stages were analyzed by qRT-PCR. Based on the functions of the orthologues in Sclerotinia sclerotiorum (a sclerotia-formation fungus and Saccharomyces cerevisiae, the potential roles of these W. cocos PKs were assigned. To the best of our knowledge, our study is the first identification and functional discussion of the kinome in the edible and medicinal fungus W. cocos. Our study systematically suggests potential roles of W. cocos PKs and provide comprehensive and novel insights into W. cocos sclerotial development and other economically important traits. Additionally, based on our result, genetic engineering can be employed for over expression or interference of some significant PKs genes to promote sclerotial growth and the accumulation of active compounds.

Characterization of the product of a nonribosomal peptide synthetase-like (NRPS-like) gene using the doxycycline dependent Tet-on system in Aspergillus terreus.

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Sun, Wei-Wen; Guo, Chun-Jun; Wang, Clay C C

2016-04-01

Genome sequencing of the fungus Aspergillus terreus uncovered a number of silent core structural biosynthetic genes encoding enzymes presumed to be involved in the production of cryptic secondary metabolites. There are five nonribosomal peptide synthetase (NRPS)-like genes with the predicted A-T-TE domain architecture within the A. terreus genome. Among the five genes, only the product of pgnA remains unknown. The Tet-on system is an inducible, tunable and metabolism-independent expression system originally developed for Aspergillus niger. Here we report the adoption of the Tet-on system as an effective gene activation tool in A. terreus. Application of this system in A. terreus allowed us to uncover the product of the cryptic NRPS-like gene, pgnA. Furthermore expression of pgnA in the heterologous Aspergillus nidulans host suggested that the pgnA gene alone is necessary for phenguignardic acid (1) biosynthesis. Copyright © 2016 Elsevier Inc. All rights reserved.

Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

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Studt, Lena; Niehaus, Eva-Maria; Espino, Jose J.; Huß, Kathleen; Michielse, Caroline B.; Albermann, Sabine; Wagner, Dominik; Bergner, Sonja V.; Connolly, Lanelle R.; Fischer, Andreas; Reuter, Gunter; Kleigrewe, Karin; Bald, Till; Wingfield, Brenda D.; Ophir, Ron; Freeman, Stanley; Hippler, Michael; Smith, Kristina M.; Brown, Daren W.; Proctor, Robert H.; Münsterkötter, Martin; Freitag, Michael; Humpf, Hans-Ulrich; Güldener, Ulrich; Tudzynski, Bettina

2013-01-01

The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F

Very Rapid High-amplitude Gamma-Ray Variability in Luminous Blazar PKS 1510-089 Studied with Fermi-LAT

Energy Technology Data Exchange (ETDEWEB)

Saito, S.; Stawarz, L.; Tanaka, Y.T.; Takahashi, T.; Madejski, G.; D' Ammando, F.

2013-03-20

Here we report on the detailed analysis of the γ-ray light curve of a luminous blazar PKS 1510-089 observed in the GeV range with the Large Area Telescope (LAT) onboard the Fermi satellite during the period 2011 September - December. By investigating the properties of the detected three major flares with the shortest possible time binning allowed by the photon statistics, we find a variety of temporal characteristics and variability patterns. This includes a clearly asymmetric profile (with a faster flux rise and a slower decay) of the flare resolved on sub-daily timescales, a superposition of many short uncorrelated flaring events forming the apparently coherent longer-duration outburst, and a huge single isolated outburst unresolved down to the timescale of three-hours. In the latter case we estimate the corresponding γ-ray flux doubling timescale to be below one hour, which is extreme and never previously reported for any active galaxy

Biosynthesis of t-Butyl in Apratoxin A: Functional Analysis and Architecture of a PKS Loading Module.

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Skiba, Meredith A; Sikkema, Andrew P; Moss, Nathan A; Lowell, Andrew N; Su, Min; Sturgis, Rebecca M; Gerwick, Lena; Gerwick, William H; Sherman, David H; Smith, Janet L

2018-04-27

The unusual feature of a t-butyl group is found in several marine-derived natural products including apratoxin A, a Sec61 inhibitor produced by the cyanobacterium Moorea bouillonii PNG 5-198. Here we determine that the apratoxin A t-butyl group is formed as pivaloyl acyl carrier protein (ACP) by AprA, the polyketide synthase (PKS) loading module of the apratoxin A biosynthetic pathway. AprA contains an inactive "pseudo" GCN5-related N-acetyltransferase domain (ΨGNAT) flanked by two methyltransferase domains (MT1 and MT2) that differ distinctly in sequence. Structural, biochemical, and precursor incorporation studies reveal that MT2 catalyzes unusually coupled decarboxylation and methylation reactions to transform dimethylmalonyl-ACP, the product of MT1, to pivaloyl-ACP. Further, pivaloyl-ACP synthesis is primed by the fatty acid synthase malonyl acyltransferase (FabD), which compensates for the ΨGNAT and provides the initial acyl-transfer step to form AprA malonyl-ACP. Additionally, images of AprA from negative stain electron microscopy reveal multiple conformations that may facilitate the individual catalytic steps of the multienzyme module.

Upper mantle dynamics of Bangladesh by splitting analysis of core-mantle refracted SKS, PKS, and SKKS phases

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Tiwari, Ashwani Kant; Bhushan, Kirti; Eken, Tuna; Singh, Arun

2018-06-01

New shear wave splitting measurements are obtained from the Bengal Basin using core-mantle refracted SKS, PKS, and SKKS phases. The splitting parameters, namely time delays (δ t) and fast polarization directions (ϕ), were estimated through analysis of 54 high-quality waveforms (⩾ 2.5 signal to noise ratio) from 30 earthquakes with magnitude ⩾ 5.5 recorded at ten seismic stations deployed over Bangladesh. No evidence of splitting was found, which indicates azimuthal isotropy beneath the region. These null measurements can be explained by either vertically dipping anisotropic fast axes or by the presence of multiple horizontal anisotropic layers with different fast polarization directions, where the combined effect results in a null characterization. The anisotropic fabric preserved from rifting episodes of Antarctica and India, subduction-related dynamics of the Indo-Burmese convergence zone, and northward movement of the Indian plate creating shear at the base of the lithosphere can explain the observed null measurements. The combined effect of all these most likely results in a strong vertical anisotropic heterogeneity, creating the observed null results.

Tentative detection of warm intervening gas towards PKS 0548-322 with XMM-Newton

Energy Technology Data Exchange (ETDEWEB)

Barcons, X.

2005-03-17

We present the results of a long ({approx} 93 ksec) XMM-Newton observation of the bright BL-Lac object PKS 0548-322 (z = 0.069). Our Reflection Grating Spectrometer (RGS) spectrum shows a single absorption feature at an observed wavelength {lambda} = 23.33 {+-} 0.01 {angstrom} which we interpret as OVI K{alpha} absorption at z = 0.058, i.e., {approx} 3000 km s{sup -1} from the background object. The observed equivalent width of the absorption line {approx} 30m {angstrom}, coupled with the lack of the corresponding absorption edge in the EPIC pn data, implies a column density N{sub OVI} {approx} 2 x 10{sup 16} cm{sup -2} and turbulence with a Doppler velocity parameter b > 100 km s{sup -1}. Within the limitations of our RGS spectrum, no OVII or OV K{alpha} absorption are detected. Under the assumption of ionization equilibrium by both collisions and the extragalactic background, this is only marginally consistent if the gas temperature is {approx} 2.5 x 10{sup 5} K, with significantly lower or higher values being excluded by our limits on OV or OVII. If confirmed, this would be the first X-ray detection of a large amount of intervening warm absorbing gas through OVI absorption. The existence of such a high column density absorber, much stronger than any previously detected one in OVI, would place stringent constraints on the large-scale distribution of baryonic gas in the Universe.

The z = 0.8596 damped Ly-alpha absorbing galaxy toward PKS 0454+039

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Steidel, Charles C.; Bowen, David V.; Blades, J. Chris; Dickenson, Mark

1995-01-01

We present Hubble Space Telescope (HST) and ground-based data on the Z(sub abs) = 0.8596 metal-line absorption system along the line of sight to PKS 0454+0356. The system is a moderate-redshift damped Ly-alpha system, with N(H I) = (5.7 +/- 0.3) x 10(exp 20)/sq cm as measured from the Faint Object Spectrograph (FOS) spectrum. We also present ground-based images which we use to identify the galaxy which most probably gives rise to the damped system; the most likely candidate is relatively underluminous by QSO absorber standards M(sub B) approximately -19.0 for A(sub 0) = 0.5 and H(sub 0) = 50 km/s/Mpc) and lies approximately 8.5/h kpc in projection from the QSO sight line. Ground-based measurements of Zn II, Cr II, and Fe II absorption lines from this system allow us to infer abundances of (Zn/H) = -1.1, (Cr/H) = -1.2, and (Fe/H) = -1.2 indicating overall metallicity similar to damped systems at z is greater than 2, and that the depletion of Cr and Fe onto dust grains may be even less important than in many of the high-redshift systems of comparable metallicity. Limits previously placed on the 21 cm optical depth in the z = 0.8596 system, together with our new N(H I) measurement, suggest a very high spin temperature for the H I, T(sub s) is greater than 580 K.

X-ray variability of the BL Lacertae object PKS 2155 - 304 in the 0.1-6 keV range

International Nuclear Information System (INIS)

Morini, M.; Chiappetti, L.; Maccagni, D.; Maraschi, L.; Molteni, D.; CNR, Istituto di Fisica Cosmica, Milan, Italy; CNR, Istituto di Fisica Cosmica; Milano Universita, Italy; Palermo Universita, Italy)

1986-01-01

Observations of the bright BL Lac object PKS 2155 - 304 obtained at 1-6 keV using the ME argon counters and channel-multiplier array at the focus of the Exosat LE telescope, in conjunction with the 0.05-2-keV-bandpass 3000-A Lexan filter, during a total of 30 h in October-November 1983 and November 1984 are reported. The data are presented in tables and graphs and characterized. Findings discussed include an overall variation of a factor of 10, one factor-of-four increase over 4 h, and maximum luminosity variation dL/dt = 2 x 10 to the 42nd erg/s sq for H = 100 km/s Mpc (corresponding to a lower limit of mass of 10 to the 8th solar mass and a gravitational radius of 3 x 10 to the 13th cm). The implications of these results for theoretical models of the X-ray emission source are considered. 17 references

The potential roles of bacterial communities in coral defence: A case study at Talang-talang reef

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Kuek, Felicity W. I.; Lim, Li-Fang; Ngu, Lin-Hui; Mujahid, Aazani; Lim, Po-Teen; Leaw, Chui-Pin; Müller, Moritz

2015-06-01

Complex microbial communities are known to exert significant influence over coral reef ecosystems. The Talang- Satang National Park is situated off the coast of Sematan and is one of the most diverse ecosystems found off-Sarawak. Interestingly, the Talang-talang reef thrives at above-average temperatures of 28- 30°C throughout the year. Through isolation and identification (16S rRNA) of native microbes from the coral, the surface mucus layer (SML), as well as the surrounding sediment and waters, we were able to determine the species composition and abundance of the culturable bacteria in the coral reef ecosystem. Isolates found attached to the coral are related mostly to Vibrio spp., presumably attached to the mucus from the water column and surrounding sediment. Pathogenic Vibrio spp. and Bacillus spp. were dominant amongst the isolates from the water column and sediment, while known coral pathogens responsible for coral bleaching, Vibrio coralliilyticus and Vibrio shiloi, were isolated from the coral SML and sediment samples respectively. Coral SML isolates were found to be closely related to known nitrogen fixers and antibiotic producers with tolerance towards elevated temperatures and heavy metal contamination, offering a possible explanation why the local corals are able to thrive in higher than usual temperatures. This specialized microbiota may be important for protecting the corals from pathogens by occupying entry niches and/or through the production of secondary metabolites such as antibiotics. The communities from the coral SML were tested against each other at 28, 30 and 32°C, and were also assessed for the presence of type I modular polyketides synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes which are both involved in the production of antibiotic compounds. The bacterial community from the SML exhibited antimicrobial properties under normal temperatures while pathogenic strains appeared toxic at elevated temperatures and our results

Search for a narrow baryonic state decaying to pKS0 and p‾KS0 in deep inelastic scattering at HERA

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H. Abramowicz

2016-08-01

Full Text Available A search for a narrow baryonic state in the pKS0 and p‾KS0 system has been performed in ep collisions at HERA with the ZEUS detector using an integrated luminosity of 358pb−1 taken in 2003–2007. The search was performed with deep inelastic scattering events at an ep centre-of-mass energy of 318GeV for exchanged photon virtuality, Q2, between 20 and 100GeV2. Contrary to evidence presented for such a state around 1.52 GeV in a previous ZEUS analysis using a sample of 121 pb−1 taken in 1996–2000, no resonance peak was found in the p(p‾KS0 invariant-mass distribution in the range 1.45–1.7 GeV. Upper limits on the production cross section are set.

Comparative Transcriptomics to Identify Novel Genes and Pathways in Dinoflagellates

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Ryan, D.

2016-02-01

The unarmored dinoflagellate Karenia brevis is among the most prominent harmful, bloom-forming phytoplankton species in the Gulf of Mexico. During blooms, the polyketides PbTx-1 and PbTx-2 (brevetoxins) are produced by K. brevis. Brevetoxins negatively impact human health and the Gulf shellfish harvest. However, the genes underlying brevetoxin synthesis are currently unknown. Because the K. brevis genome is extremely large ( 1 × 1011 base pairs long), and with a high proportion of repetitive, non-coding DNA, it has not been sequenced. In fact, large, repetitive genomes are common among the dinoflagellate group. High-throughput RNA sequencing technology enabled us to assemble Karenia transcriptomes de novo and investigate potential genes in the brevetoxin pathway through comparative transcriptomics. The brevetoxin profile varies among K. brevis clonal cultures. For example, well-documented Wilson-CCFWC268 typically produces 8-10 pg PbTx per cell, whereas SP1 produces differences in gene expression. Of the 85,000 transcripts in the K. brevis transcriptome, 4,600 transcripts, including novel unannotated orthologs and putative polyketide synthases (PKSs), were only expressed by brevetoxin-producing K. brevis and K. papilionacea, not K. mikimotoi. Examination of gene expression between the typical- and low-toxin Wilson clones identified about 3,500 genes with significantly different expression levels, including 2 putative PKSs. One of the 2 PKSs was only found in the brevetoxin-producing Karenia species. These transcriptomes could not have been characterized without high-throughput RNA sequencing.

Probing the Selectivity and Protein•Protein Interactions of a Non-Reducing Fungal Polyketide Synthase Using Mechanism-Based Crosslinkers

Science.gov (United States)

Bruegger, Joel; Haushalter, Bob; Vagstad, Anna; Shakya, Gaurav; Mih, Nathan; Townsend, Craig A.; Burkart, Michael D.; Tsai, Shiou-Chuan

2013-01-01

SUMMARY Protein•protein interactions, which often involve interactions between an acyl carrier protein (ACP) and its partner enzymes, are important for coordinating polyketide biosynthesis. However, the nature of such interactions is not well understood, especially in the fungal non-reducing polyketide synthases (NR-PKSs) that biosynthesize toxic and pharmaceutically important polyketides. Here, we employ a mechanism-based crosslinker to successfully probe ACP and ketosynthase (KS) domain interactions in NR-PKSs. We found that crosslinking efficiency is closely correlated with the strength of ACP•KS interactions, and that KS demonstrates strong starter unit selectivity. We further identified positively charged surface residues by KS mutagenesis, which mediate key interactions with the negatively-charged ACP surface. Such complementary/matching contact pairs can serve as “adapter surfaces” for future efforts to generate new polyketides using NR-PKSs. PMID:23993461

A hybrid non-ribosomal peptide/polyketide synthetase containing fatty-acyl ligase (FAAL synthesizes the β-amino fatty acid lipopeptides puwainaphycins in the Cyanobacterium Cylindrospermum alatosporum.

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Jan Mareš

Full Text Available A putative operon encoding the biosynthetic pathway for the cytotoxic cyanobacterial lipopeptides puwainphycins was identified in Cylindrospermum alatosporum. Bioinformatics analysis enabled sequential prediction of puwainaphycin biosynthesis; this process is initiated by the activation of a fatty acid residue via fatty acyl-AMP ligase and continued by a multidomain non-ribosomal peptide synthetase/polyketide synthetase. High-resolution mass spectrometry and nuclear magnetic resonance spectroscopy measurements proved the production of puwainaphycin F/G congeners differing in FA chain length formed by either 3-amino-2-hydroxy-4-methyl dodecanoic acid (4-methyl-Ahdoa or 3-amino-2-hydroxy-4-methyl tetradecanoic acid (4-methyl-Ahtea. Because only one puwainaphycin operon was recovered in the genome, we suggest that the fatty acyl-AMP ligase and one of the amino acid adenylation domains (Asn/Gln show extended substrate specificity. Our results provide the first insight into the biosynthesis of frequently occurring β-amino fatty acid lipopeptides in cyanobacteria, which may facilitate analytical assessment and development of monitoring tools for cytotoxic cyanobacterial lipopeptides.

Synthetic biology of polyketide synthases

DEFF Research Database (Denmark)

Yuzawa, Satoshi; Backman, Tyler W.H.; Keasling, Jay D.

2018-01-01

). The modules are composed of enzymatic domains that share sequence and functional similarity across all known PKSs. We have used the nomenclature of synthetic biology to classify the enzymatic domains and modules as parts and devices, respectively, and have generated detailed lists of both. In addition, we...... realize the potential that synthetic biology approaches bring to this class of molecules....

Exploring the diversity and antimicrobial potential of marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile

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Agustina Undabarrena

2016-07-01

Full Text Available Bioprospecting natural products in marine bacteria from fjord environments are attractive due to their unique geographical features. Although Actinobacteria are well known for producing a myriad of bioactive compounds, investigations regarding fjord-derived marine Actinobacteria are scarce. In this study, the diversity and biotechnological potential of Actinobacteria isolated from marine sediments within the Comau fjord, in Northern Chilean Patagonia, were assessed by culture-based approaches. The 16S rRNA gene sequences revealed that members phylogenetically related to the Micrococcaceae, Dermabacteraceae, Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, Dietziaceae, Nocardiaceae and Streptomycetaceae families were present at the Comau fjord. A high diversity of cultivable Actinobacteria (10 genera was retrieved by using only five different isolation media. Four isolates belonging to Arthrobacter, Brevibacterium, Corynebacterium and Kocuria genera showed 16S rRNA gene identity <98.7% suggesting that they are novel species. Physiological features such as salt tolerance, artificial sea water requirement, growth temperature, pigmentation and antimicrobial activity were evaluated. Arthrobacter, Brachybacterium, Curtobacterium, Rhodococcus and Streptomyces isolates showed strong inhibition against both Gram-negative Pseudomonas aeruginosa, Escherichia coli and Salmonella enterica and Gram-positive Staphylococcus aureus, Listeria monocytogenes. Antimicrobial activities in Brachybacterium, Curtobacterium and Rhodococcus have been scarcely reported, suggesting that non-mycelial strains are a suitable source of bioactive compounds. In addition, all strains bear at least one of the biosynthetic genes coding for NRPS (91%, PKS I (18% and PKS II (73%.Our results indicate that the Comau fjord is a promising source of novel Actinobacteria with biotechnological potential for producing biologically active compounds.

The Land-Potential Knowledge System (LandPKS): mobile apps and collaboration for optimizing climate change investments

Science.gov (United States)

Massive investments in climate change mitigation and adaptation are projected during coming decades. Many of these investments will seek to modify how land is managed. The return on both types of investments can be increased through an understanding of land potential: the potential of the land to s...

Inhibition of Grape Crown Gall by Agrobacterium vitis F2/5 Requires Two Nonribosomal Peptide Synthetases and One Polyketide Synthase.

Science.gov (United States)

Zheng, Desen; Burr, Thomas J

2016-02-01

Agrobacterium vitis nontumorigenic strain F2/5 is able to inhibit crown gall disease on grapevines. The mechanism of grape tumor inhibition (GTI) by F2/5 has not been fully determined. In this study, we demonstrate that two nonribosomal peptide synthetase (NRPS) genes (F-avi3342 and F-avi5730) and one polyketide synthase gene (F-avi4330) are required for GTI. Knockout of any one of them resulted in F/25 losing GTI capacity. We previously reported that F-avi3342 and F-avi4330 but not F-avi5730 are required for induction of grape tissue necrosis and tobacco hypersensitive response. F-avi5730 is predicted to encode a single modular NRPS. It is located in a cluster that is homologous to the siderophore vicibactin biosynthesis locus in Rhizobium species. Individual disruption of F-avi5730 and two immediate downstream genes, F-avi5731 and F-avi5732, all resulted in reduced siderophore production; however, only F-avi5730 was found to be required for GTI. Complemented F-avi5730 mutant (ΔF-avi5730(+)) restored a wild-type level of GTI activity. It was determined that, over time, populations of ΔF-avi4330, ΔF-avi3342, and ΔF-avi5730 at inoculated wound sites on grapevine did not differ from those of ΔF-avi5730(+) indicating that loss of GTI was not due to reduced colonization of wound sites by mutants.

Structural basis of the interaction of MbtH-like proteins, putative regulators of nonribosomal peptide biosynthesis, with adenylating enzymes.

Science.gov (United States)

Herbst, Dominik A; Boll, Björn; Zocher, Georg; Stehle, Thilo; Heide, Lutz

2013-01-18

The biosynthesis of nonribosomally formed peptides (NRPs), which include important antibiotics such as vancomycin, requires the activation of amino acids through adenylate formation. The biosynthetic gene clusters of NRPs frequently contain genes for small, so-called MbtH-like proteins. Recently, it was discovered that these MbtH-like proteins are required for some of the adenylation reactions in NRP biosynthesis, but the mechanism of their interaction with the adenylating enzymes has remained unknown. In this study, we determined the structure of SlgN1, a 3-methylaspartate-adenylating enzyme involved in the biosynthesis of the hybrid polyketide/NRP antibiotic streptolydigin. SlgN1 contains an MbtH-like domain at its N terminus, and our analysis defines the parameters required for an interaction between MbtH-like domains and an adenylating enzyme. Highly conserved tryptophan residues of the MbtH-like domain critically contribute to this interaction. Trp-25 and Trp-35 form a cleft on the surface of the MbtH-like domain, which accommodates the alanine side chain of Ala-433 of the adenylating domain. Mutation of Ala-433 to glutamate abolished the activity of SlgN1. Mutation of Ser-23 of the MbtH-like domain to tyrosine resulted in strongly reduced activity. However, the activity of this S23Y mutant could be completely restored by addition of the intact MbtH-like protein CloY from another organism. This suggests that the interface found in the structure of SlgN1 is the genuine interface between MbtH-like proteins and adenylating enzymes.

THE NATURE OF A GALAXY ALONG THE SIGHT LINE TO PKS 0454+039

International Nuclear Information System (INIS)

Takamiya, Marianne; Chun, Mark; Kulkarni, Varsha P.; Gharanfoli, Soheila

2012-01-01

We report on the properties of a faint blue galaxy (G1) along the line of sight to the QSO PKS 0454+039 from spectroscopic and imaging data. We measured emission lines of Hα, [S II] λλ6716, 6732, and [N II] λ6584 in the spectrum of G1 obtained with the Gemini/GMOS instrument. The spectroscopic redshift of G1 is z = 0.0715 ± 0.0002. From the extinction-corrected Hα flux, we determine a modest star formation rate of SFR = 0.07 M ☉ yr –1 and a specific SFR of log (sSFR) –8.4. Using three different abundance indicators, we determine a nebular abundance 12 + log (O/H) ranging from 7.6 to 8.2. Based on the velocity dispersion inferred from the emission line widths and the observed surface brightness profile, we estimate the virial mass of G1 to be M vir ∼ 6.7 × 10 9 M ☉ with an effective radius of 2.0 kpc. We estimate the stellar mass of G1 using spectral energy distribution fitting to be M * ≈ 1.2 × 10 7 M ☉ and an r'-luminosity of L r' = 1.5x10 8 L ☉ . Overall, G1 is a faint, low-mass, low-metallicity Im/H II galaxy. We also report on the line flux limits of another source (G3) which is the most likely candidate for the absorber system at z = 0.8596. From the spectrum of the QSO itself, we report a previously undetected Mg II λλ2796, 2803 absorption line system at z = 1.245.

Actinobacteria from arid and desert habitats: diversity and biological activity

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Joachim eWink

2016-01-01

Full Text Available Abstract The lack of new antibiotics in the pharmaceutical pipeline guides more and more researchers to leave the classical isolation procedures and to look in special niches and ecosystems. Bioprospecting of extremophilic Actinobacteria through mining untapped strains and avoiding resiolation of known biomolecules is among the most promising strategies for this purpose. With this approach, members of acidtolerant, alkalitolerant, psychrotolerant, thermotolerant, halotolerant and xerotolerant Actinobacteria have been obtained from respective habitats. Among these, little survey exists on the diversity of Actinobacteria in arid areas, which are often adapted to relatively high temperatures, salt concentrations, and radiation. Therefore, arid and desert habitats are special ecosystems which can be recruited for the isolation of uncommon Actinobacteria with new metabolic capability.At the time of this writing, members of Streptomyces, Micromonospora, Saccharothrix, Streptosporangium, Cellulomonas, Amycolatopsis, Geodermatophilus, Lechevalieria, Nocardia and Actinomadura are reported from arid habitats. However, metagenomic data present dominant members of the communities in desiccating condition of areas with limited water availability that are not yet isolated. Furthermore, significant diverse types of polyketide synthase (PKS and nonribosomal peptide synthetase (NRPS genes are detected in xerophilic and xerotolerant Actinobacteria and some bioactive compounds are reported from them. Rather than pharmaceutically active metabolites, molecules with protection activity against drying such as Ectoin and Hydroxyectoin with potential application in industry and agriculture have also been identified from xerophilic Actinobacteria. In addition, numerous biologically active small molecules are expected to be discovered from arid adapted Actinobacteria in the future. In the current survey, the diversity and biotechnological potential of Actinobacteria

Actinobacteria from Arid and Desert Habitats: Diversity and Biological Activity.

Science.gov (United States)

Mohammadipanah, Fatemeh; Wink, Joachim

2015-01-01

The lack of new antibiotics in the pharmaceutical pipeline guides more and more researchers to leave the classical isolation procedures and to look in special niches and ecosystems. Bioprospecting of extremophilic Actinobacteria through mining untapped strains and avoiding resiolation of known biomolecules is among the most promising strategies for this purpose. With this approach, members of acidtolerant, alkalitolerant, psychrotolerant, thermotolerant, halotolerant and xerotolerant Actinobacteria have been obtained from respective habitats. Among these, little survey exists on the diversity of Actinobacteria in arid areas, which are often adapted to relatively high temperatures, salt concentrations, and radiation. Therefore, arid and desert habitats are special ecosystems which can be recruited for the isolation of uncommon Actinobacteria with new metabolic capability. At the time of this writing, members of Streptomyces, Micromonospora, Saccharothrix, Streptosporangium, Cellulomonas, Amycolatopsis, Geodermatophilus, Lechevalieria, Nocardia, and Actinomadura are reported from arid habitats. However, metagenomic data present dominant members of the communities in desiccating condition of areas with limited water availability that are not yet isolated. Furthermore, significant diverse types of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes are detected in xerophilic and xerotolerant Actinobacteria and some bioactive compounds are reported from them. Rather than pharmaceutically active metabolites, molecules with protection activity against drying such as Ectoin and Hydroxyectoin with potential application in industry and agriculture have also been identified from xerophilic Actinobacteria. In addition, numerous biologically active small molecules are expected to be discovered from arid adapted Actinobacteria in the future. In the current survey, the diversity and biotechnological potential of Actinobacteria obtained from arid ecosystems

Actinobacteria from Arid and Desert Habitats: Diversity and Biological Activity

Science.gov (United States)

Mohammadipanah, Fatemeh; Wink, Joachim

2016-01-01

The lack of new antibiotics in the pharmaceutical pipeline guides more and more researchers to leave the classical isolation procedures and to look in special niches and ecosystems. Bioprospecting of extremophilic Actinobacteria through mining untapped strains and avoiding resiolation of known biomolecules is among the most promising strategies for this purpose. With this approach, members of acidtolerant, alkalitolerant, psychrotolerant, thermotolerant, halotolerant and xerotolerant Actinobacteria have been obtained from respective habitats. Among these, little survey exists on the diversity of Actinobacteria in arid areas, which are often adapted to relatively high temperatures, salt concentrations, and radiation. Therefore, arid and desert habitats are special ecosystems which can be recruited for the isolation of uncommon Actinobacteria with new metabolic capability. At the time of this writing, members of Streptomyces, Micromonospora, Saccharothrix, Streptosporangium, Cellulomonas, Amycolatopsis, Geodermatophilus, Lechevalieria, Nocardia, and Actinomadura are reported from arid habitats. However, metagenomic data present dominant members of the communities in desiccating condition of areas with limited water availability that are not yet isolated. Furthermore, significant diverse types of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes are detected in xerophilic and xerotolerant Actinobacteria and some bioactive compounds are reported from them. Rather than pharmaceutically active metabolites, molecules with protection activity against drying such as Ectoin and Hydroxyectoin with potential application in industry and agriculture have also been identified from xerophilic Actinobacteria. In addition, numerous biologically active small molecules are expected to be discovered from arid adapted Actinobacteria in the future. In the current survey, the diversity and biotechnological potential of Actinobacteria obtained from arid ecosystems

Rapid Multiwaveband Polarization Variability in the Quasar PKS 0420-014: Optical Emission from the Compact Radio Jet

Science.gov (United States)

D'Arcangelo, Francesca D.; Marscher, Alan P.; Jorstad, Svetlana G.; Smith, Paul S.; Larionov, Valeri M.; Hagen-Thorn, Vladimir A.; Kopatskaya, Eugenia N.; Williams, G. Grant; Gear, Walter K.

2007-04-01

An 11 day monitoring campaign in late 2005 reveals clear correlation in polarization between the optical emission and the region of the intensity peak (the ``pseudocore'') at the upstream end of the jet in 43 GHz VLBA (Very Long Baseline Array) images in the highly variable quasar PKS 0420-014. The electric-vector position angle (EVPA) of the pseudocore rotated by about 80° in four VLBA observations over a period of 9 days, matching the trend of the optical EVPA. In addition, the 43 GHz EVPAs agree well with the optical values when we correct the former for Faraday rotation. Fluctuations in the polarization at both wave bands are consistent with the variable emission arising from a standing conical shock wave that compresses magnetically turbulent plasma in the ambient jet. The volume of the variable component is the same at both wave bands, although only ~20% of the total 43 GHz emission arises from this site. The remainder of the 43 GHz flux density must originate in a separate region with very low polarization. If 0420-014 is a typical case, the nonthermal optical emission from blazars originates primarily in and near the pseudocore rather than closer to the central engine where the flow collimates and accelerates.

Hydrogen Production from Gasification of Palm Kernel Shell in the Presence of Fe/ CeO_2 Catalysts

International Nuclear Information System (INIS)

Anita Ramli; Mas Fatiha Mohamad; Suzana Yusup; Taufiq, Y.Y.H.

2016-01-01

Bio hydrogen is a renewable source of clean fuel and energy which can be derived from biomass. One of the suitable candidate as a source of biomass is palm kernel shell (PKS). Our initial work shows that bio hydrogen may be produced from PKS in the presence of zeolite supported catalysts. The potential of using cerium oxide (CeO_2) supported catalysts for the production of bio hydrogen from PKS is explored in this work using 2.5 - 10 % Fe loading. The catalysts were prepared by incipient wetness impregnation method and calcined at 500 degree Celsius for 16 h. The physicochemical properties of these catalysts were characterized using BET and XRD. The catalysts were tested in dry and steam gasification of PKS at 700 degree Celsius using PKS feeding rate of 2 g h"-"1 under N_2 atmosphere with biomass to catalyst ratio of 3:1 (wt/ wt). Steam to biomass ratio of 3.5:1 (wt/ wt) was used in steam gasification reaction. The gaseous products were analyzed using an on-line gas chromatography equipped with thermal conductivity detectors (TCD) and fitted with Molsieve 5A and Hayesep Q columns. Result shows that 2.5 % Fe/ CeO_2 gave the highest hydrogen production in both the dry and steam gasification of PKS. (author)

Determination of pyrolysis characteristics and kinetics of palm kernel shell using TGA–FTIR and model-free integral methods

International Nuclear Information System (INIS)

Ma, Zhongqing; Chen, Dengyu; Gu, Jie; Bao, Binfu; Zhang, Qisheng

2015-01-01

Highlights: • Model-free integral kinetics method and analytical TGA–FTIR were conducted on pyrolysis process of PKS. • The pyrolysis mechanism of PKS was elaborated. • Thermal stability was established: lignin > cellulose > xylan. • Detailed compositions in the volatiles of PKS pyrolysis were determinated. • The interaction of biomass three components led to the fluctuation of activation energy in PKS pyrolysis. - Abstract: Palm kernel shell (PKS) from palm oil production is a potential biomass source for bio-energy production. A fundamental understanding of PKS pyrolysis behavior and kinetics is essential to its efficient thermochemical conversion. The thermal degradation profile in derivative thermogravimetry (DTG) analysis shown two significant mass-loss peaks mainly related to the decomposition of hemicellulose and cellulose respectively. This characteristic differentiated with other biomass (e.g. wheat straw and corn stover) presented just one peak or accompanied with an extra “shoulder” peak (e.g. wheat straw). According to the Fourier transform infrared spectrometry (FTIR) analysis, the prominent volatile components generated by the pyrolysis of PKS were CO 2 (2400–2250 cm −1 and 586–726 cm −1 ), aldehydes, ketones, organic acids (1900–1650 cm −1 ), and alkanes, phenols (1475–1000 cm −1 ). The activation energy dependent on the conversion rate was estimated by two model-free integral methods: Flynn–Wall–Ozawa (FWO) and Kissinger–Akahira–Sunose (KAS) method at different heating rates. The fluctuation of activation energy can be interpreted as a result of interactive reactions related to cellulose, hemicellulose and lignin degradation, occurred in the pyrolysis process. Based on TGA–FTIR analysis and model free integral kinetics method, the pyrolysis mechanism of PKS was elaborated in this paper

Genome-wide identification and comprehensive analyses of the kinomes in four pathogenic microsporidia species.

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Zhi Li

Full Text Available Microsporidia have attracted considerable attention because they infect a wide range of hosts, from invertebrates to vertebrates, and cause serious human diseases and major economic losses in the livestock industry. There are no prospective drugs to counteract this pathogen. Eukaryotic protein kinases (ePKs play a central role in regulating many essential cellular processes and are therefore potential drug targets. In this study, a comprehensive summary and comparative analysis of the protein kinases in four microsporidia—Enterocytozoon bieneusi, Encephalitozoon cuniculi, Nosema bombycis and Nosema ceranae—was performed. The results show that there are 34 ePKs and 4 atypical protein kinases (aPKs in E. bieneusi, 29 ePKs and 6 aPKs in E. cuniculi, 41 ePKs and 5 aPKs in N. bombycis, and 27 ePKs and 4 aPKs in N. ceranae. These data support the previous conclusion that the microsporidian kinome is the smallest eukaryotic kinome. Microsporidian kinomes contain only serine-threonine kinases and do not contain receptor-like and tyrosine kinases. Many of the kinases related to nutrient and energy signaling and the stress response have been lost in microsporidian kinomes. However, cell cycle-, development- and growth-related kinases, which are important to parasites, are well conserved. This reduction of the microsporidian kinome is in good agreement with genome compaction, but kinome density is negatively correlated with proteome size. Furthermore, the protein kinases in each microsporidian genome are under strong purifying selection pressure. No remarkable differences in kinase family classification, domain features, gain and/or loss, and selective pressure were observed in these four species. Although microsporidia adapt to different host types, the coevolution of microsporidia and their hosts was not clearly reflected in the protein kinases. Overall, this study enriches and updates the microsporidian protein kinase database and may provide

Multiband Observations of the Quasar PKS 2326–502 during Active and Quiescent Gamma-Ray States in 2010–2012

Energy Technology Data Exchange (ETDEWEB)

Dutka, Michael S. [The Catholic University of America, 620 Michigan Avenue, NE, Washington, DC 20064 (United States); Carpenter, Bryce D.; Gehrels, Neil [NASA Goddard Space Flight Center, Astrophysics Science Division, Code 661, Greenbelt, MD 20771 (United States); Ojha, Roopesh [UMBC/NASA Goddard Space Flight Center, Astrophysics Science Division, Code 661, Greenbelt, MD 20771 (United States); Finke, Justin D. [Naval Research Laboratory, Space Science Division, Code 7653, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States); D’Ammando, Filippo [Università di Bologna Dipartimento di Fisica e Astronomia, INAF-IRA, Bologna (Italy); Kadler, Matthias [Lehrstuhl für Astronomie, Universität Würzburg, Emil -Fischer-Straße 31, D-97074 Würzburg (Germany); Edwards, Philip G. [CSIRO Astronomy and Space Science, P.O. Box 76, Epping NSW 1710 (Australia); Stevens, Jamie [CSIRO Astronomy and Space Science, 1828 Yarrie Lake Road, Narrabri NSW 2390 (Australia); Torresi, Eleonora; Grandi, Paola [Istituto Nazionale di Astrofisica, (National Institute of Astrophysics) INAF-IASFBO, via Gobetti 101, I-40129 Bologna (Italy); Nesci, Roberto [Istituto Nazionale di Astrofisica, (National Institute of Astrophysics) INAF-IAPS, via Fosso del Cavaliere 100, I-00133 Roma (Italy); Krauß, Felicia [GRAPPA and Anton Pannekoek Institute for Astronomy, University of Amsterdam, Science Park 904, 1098 XH Amsterdam (Netherlands); Müller, Cornelia [Department of Astrophysics/IMAPP, Radboud University Nijmegen, P.O. Box 9010, 6500 GL, Nijmegen (Netherlands); Wilms, Joern, E-mail: ditko86@gmail.com, E-mail: carpbr01@gmail.com [Remeis Observatory and ECAP, Sternwartstr. 7, D-96049 Bamberg (Germany)

2017-02-01

Quasi-simultaneous observations of the Flat Spectrum Radio Quasar PKS 2326−502 were carried out in the γ -ray, X-ray, UV, optical, near-infrared, and radio bands. Using these observations, we are able to characterize the spectral energy distribution (SED) of the source during two flaring and one quiescent γ -ray states. These data were used to constrain one-zone leptonic models of the SEDs of each flare and investigate the physical conditions giving rise to them. While modeling one flare required only changes in the electron spectrum compared to the quiescent state, modeling the other flare required changes in both the electron spectrum and the size of the emitting region. These results are consistent with an emerging pattern of two broad classes of flaring states seen in blazars. Type 1 flares are explained by changes solely in the electron distribution, whereas type 2 flares require a change in an additional parameter. This suggests that different flares, even in the same source, may result from different physical conditions or different regions in the jet.

THE NATURE OF A GALAXY ALONG THE SIGHT LINE TO PKS 0454+039

Energy Technology Data Exchange (ETDEWEB)

Takamiya, Marianne [Physics and Astronomy Department, University of Hawaii Hilo, Hilo, HI 96720 (United States); Chun, Mark [Institute for Astronomy, University of Hawaii Manoa, HI 96822 (United States); Kulkarni, Varsha P.; Gharanfoli, Soheila, E-mail: takamiya@hawaii.edu [Department of Physics and Astronomy, University of South Carolina, SC 29208 (United States)

2012-10-01

We report on the properties of a faint blue galaxy (G1) along the line of sight to the QSO PKS 0454+039 from spectroscopic and imaging data. We measured emission lines of H{alpha}, [S II] {lambda}{lambda}6716, 6732, and [N II] {lambda}6584 in the spectrum of G1 obtained with the Gemini/GMOS instrument. The spectroscopic redshift of G1 is z = 0.0715 {+-} 0.0002. From the extinction-corrected H{alpha} flux, we determine a modest star formation rate of SFR = 0.07 M{sub Sun} yr{sup -1} and a specific SFR of log (sSFR) -8.4. Using three different abundance indicators, we determine a nebular abundance 12 + log (O/H) ranging from 7.6 to 8.2. Based on the velocity dispersion inferred from the emission line widths and the observed surface brightness profile, we estimate the virial mass of G1 to be M{sub vir} {approx} 6.7 Multiplication-Sign 10{sup 9} M{sub Sun} with an effective radius of 2.0 kpc. We estimate the stellar mass of G1 using spectral energy distribution fitting to be M{sub *} Almost-Equal-To 1.2 Multiplication-Sign 10{sup 7} M{sub Sun} and an r'-luminosity of L{sub r'} = 1.5x10{sup 8} L{sub Sun }. Overall, G1 is a faint, low-mass, low-metallicity Im/H II galaxy. We also report on the line flux limits of another source (G3) which is the most likely candidate for the absorber system at z = 0.8596. From the spectrum of the QSO itself, we report a previously undetected Mg II {lambda}{lambda}2796, 2803 absorption line system at z = 1.245.

Identification of a polyketide synthase required for alternariol (AOH and alternariol-9-methyl ether (AME formation in Alternaria alternata.

Directory of Open Access Journals (Sweden)

Debjani Saha

Full Text Available Alternaria alternata produces more than 60 secondary metabolites, among which alternariol (AOH and alternariol-9-methyl ether (AME are important mycotoxins. Whereas the toxicology of these two polyketide-based compounds has been studied, nothing is known about the genetics of their biosynthesis. One of the postulated core enzymes in the biosynthesis of AOH and AME is polyketide synthase (PKS. In a draft genome sequence of A. alternata we identified 10 putative PKS-encoding genes. The timing of the expression of two PKS genes, pksJ and pksH, correlated with the production of AOH and AME. The PksJ and PksH proteins are predicted to be 2222 and 2821 amino acids in length, respectively. They are both iterative type I reducing polyketide synthases. PksJ harbors a peroxisomal targeting sequence at the C-terminus, suggesting that the biosynthesis occurs at least partly in these organelles. In the vicinity of pksJ we found a transcriptional regulator, altR, involved in pksJ induction and a putative methyl transferase, possibly responsible for AME formation. Downregulation of pksJ and altR caused a large decrease of alternariol formation, suggesting that PksJ is the polyketide synthase required for the postulated Claisen condensations during the biosynthesis. No other enzymes appeared to be required. PksH downregulation affected pksJ expression and thus caused an indirect effect on AOH production.

Faraday rotation at low frequencies: magnetoionic material of the large FRII radio galaxy PKS J0636-2036

Science.gov (United States)

O'Sullivan, S. P.; Lenc, E.; Anderson, C. S.; Gaensler, B. M.; Murphy, T.

2018-04-01

We present a low-frequency, broad-band polarization study of the FRII radio galaxy PKS J0636-2036 (z = 0.0551), using the Murchison Widefield Array (MWA) from 70 to 230 MHz. The northern and southern hotspots (separated by ˜14.5 arcmin on the sky) are resolved by the MWA (3.3 arcmin resolution) and both are detected in linear polarization across the full frequency range. A combination of Faraday rotation measure (RM) synthesis and broad-band polarization model fitting is used to constrain the Faraday depolarization properties of the source. For the integrated southern hotspot emission, two-RM-component models are strongly favoured over a single RM component, and the best-fitting model requires Faraday dispersions of approximately 0.7 and 1.2 rad m-2 (with a mean RM of ˜50 rad m-2). High-resolution imaging at 5 arcsec with the Australia Telescope Compact Array shows significant sub-structure in the southern hotspot and highlights some of the limitations in the polarization modelling of the MWA data. Based on the observed depolarization, combined with extrapolations of gas density scaling relations for group environments, we estimate magnetic field strengths in the intergalactic medium between ˜0.04 and 0.5 μG. We also comment on future prospects of detecting more polarized sources at low frequencies.

The Feasibility of Palm Kernel Shell as a Replacement for Coarse Aggregate in Lightweight Concrete

Science.gov (United States)

Itam, Zarina; Beddu, Salmia; Liyana Mohd Kamal, Nur; Ashraful Alam, Md; Issa Ayash, Usama

2016-03-01

Implementing sustainable materials into the construction industry is fast becoming a trend nowadays. Palm Kernel Shell is a by-product of Malaysia’s palm oil industry, generating waste as much as 4 million tons per annum. As a means of producing a sustainable, environmental-friendly, and affordable alternative in the lightweight concrete industry, the exploration of the potential of Palm Kernel Shell to be used as an aggregate replacement was conducted which may give a positive impact to the Malaysian construction industry as well as worldwide concrete usage. This research investigates the feasibility of PKS as an aggregate replacement in lightweight concrete in terms of compressive strength, slump test, water absorption, and density. Results indicate that by using PKS for aggregate replacement, it increases the water absorption but decreases the concrete workability and strength. Results however, fall into the range acceptable for lightweight aggregates, hence it can be concluded that there is potential to use PKS as aggregate replacement for lightweight concrete.

Modeling of human prokineticin receptors: interactions with novel small-molecule binders and potential off-target drugs.

Directory of Open Access Journals (Sweden)

Anat Levit

Full Text Available The Prokineticin receptor (PKR 1 and 2 subtypes are novel members of family A GPCRs, which exhibit an unusually high degree of sequence similarity. Prokineticins (PKs, their cognate ligands, are small secreted proteins of ∼80 amino acids; however, non-peptidic low-molecular weight antagonists have also been identified. PKs and their receptors play important roles under various physiological conditions such as maintaining circadian rhythm and pain perception, as well as regulating angiogenesis and modulating immunity. Identifying binding sites for known antagonists and for additional potential binders will facilitate studying and regulating these novel receptors. Blocking PKRs may serve as a therapeutic tool for various diseases, including acute pain, inflammation and cancer.Ligand-based pharmacophore models were derived from known antagonists, and virtual screening performed on the DrugBank dataset identified potential human PKR (hPKR ligands with novel scaffolds. Interestingly, these included several HIV protease inhibitors for which endothelial cell dysfunction is a documented side effect. Our results suggest that the side effects might be due to inhibition of the PKR signaling pathway. Docking of known binders to a 3D homology model of hPKR1 is in agreement with the well-established canonical TM-bundle binding site of family A GPCRs. Furthermore, the docking results highlight residues that may form specific contacts with the ligands. These contacts provide structural explanation for the importance of several chemical features that were obtained from the structure-activity analysis of known binders. With the exception of a single loop residue that might be perused in the future for obtaining subtype-specific regulation, the results suggest an identical TM-bundle binding site for hPKR1 and hPKR2. In addition, analysis of the intracellular regions highlights variable regions that may provide subtype specificity.

PKS’ DEMOCRATIC EXPERIENCES IN RECRUITING MEMBERS AND LEADERS

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Ahmad Ali Nurdin

2011-08-01

Full Text Available This paper focuses on the views of democracy and the implementation of democratic rules in real politics by the Islamic political party that has a democracy platform in Indonesia, Partai Keadilan Sejahtera (PKS. I examine PKS views on the relationship between Islam and democracy and its manner of recruiting members and leaders to show that this Islamic political party is not a threat to democracy at all. PKS believes that democracy goes to the roots of Islam and the Indonesian context in which they exist; and that it is a good political tool for an Islamic party like PKS to achieve its political goals. Taking the process of recruitment of members and leaders of PKS as examples, the paper also shows that the commitment of PKS to strengthening democracy in Indonesia could be seen in their process of recruiting leaders. PKS has practiced democratic rules in their internal party activities, particularly in the way they used to recruit their members who would be nominated as parliamentary members and how they choose their own leaders. However, it is necessary to note that in terms of member recruitment and expanding the cadres of the party, the PKS seems to have a special strategy; that is, encouraging their cadres to have big families. [Artikel mengulas pandangan Partai Keadilan Sejahtera (PKS mengenai demokrasi dan implementasi nilai-nilai demokrasi dalam kehidupan politik. Dalam artikel ini, relasi Islam dan demokrasi serta metode PKS dalam merekrut anggota dan pemimpin partai akan dibahas. PKS sama sekali bukanlah ancaman bagi demokrasi. PKS percaya bahwa prinsip demokrasidapat ditemukan dalam Islam dan konteks Indonesia. Bagi PKS, demokrasi membuka ruang kesempatan bagi partai politik Islam untuk mencapai tujuan politiknya. Selain itu, artikel ini juga mengulas proses rekrutmen anggota dan pemimpin partai. Rekrutmen petinggi PKS memperlihatkan komitmen PKS terhadap penguatan demokrasi di Indonesia. PKS sudah mempraktekkan prinsip demokrasi dalam

The lignin pyrolysis composition and pyrolysis products of palm kernel shell, wheat straw, and pine sawdust

International Nuclear Information System (INIS)

Chang, Guozhang; Huang, Yanqin; Xie, Jianjun; Yang, Huikai; Liu, Huacai; Yin, Xiuli; Wu, Chuangzhi

2016-01-01

Highlights: • The primarily pyrolysis composition of PKS lignin was p-hydroxyphenyl unit. • Higher phenol yield and lower gas energy yield were obtained from PKS pyrolysis. • PKS produced more bio-oil and biochar than WS and PS from pyrolysis at 650–850 °C. • PKS-char had poorer gasification reactivity due to higher ordering carbon degree. - Abstract: The lignin monomer composition of palm kernel shell (PKS) was characterized using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), and the characteristics and distributions of products obtained from PKS pyrolysis were investigated using Py-GC/MS, GC, and a specially designed pyrolysis apparatus. The gasification reactivity of PKS biochar was also characterized using thermogravimetry (TG) and Raman spectroscopy. All the results were compared with those obtained from wheat straw (WS) and pine sawdust (PS). The results showed that PKS lignin is primarily composed of p-hydroxyphenyl structural units, while WS and PS lignins are mainly made up of guaiacyl units. Both the mass and energy yields of non-condensable gases from PKS pyrolysis were lower than those obtained from WS and PS pyrolysis at 650–850 °C, owing to the lower volatile content (75.21%) and lack of methoxy groups in PKS. Compared with WS and PS, higher bio-oil productivity was observed during PKS pyrolysis. Phenols were the main component of PKS bio-oil from pyrolysis at 500 °C, and the phenol content of PKS bio-oil (13.49%) was higher than in WS bio-oil (1.62%) and PS bio-oil (0.55%). A higher yield of biochar (on an ash-free basis) was also obtained from PKS pyrolysis. Because of its greater relative degree of ordered carbon, PKS biochar exhibited lower in situ reactivity during CO_2 or H_2O gasification than WS and PS biochars. A longer residence time and addition of steam were found to be beneficial during PKS biochar gasification.

Preliminary Results on the Evaluation of the Occurrence of Tetrodotoxin Associated to Marine Vibrio spp. in Bivalves from the Galician Rias (Northwest of Spain

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Jose Manuel Leão

2018-03-01

Full Text Available Tetrodotoxins (TTX are a potent group of natural neurotoxins putatively produced by symbiotic microorganisms and affecting the aquatic environment. These neurotoxins have been recently found in some species of bivalves and gastropods along the European Coasts (Greece, UK, and The Netherlands linked to the presence of high concentrations of Vibrio, in particular Vibrio parahaemolyticus. This study is focused on the evaluation of the presence of Vibrio species and TTX in bivalves (mussels, oysters, cockles, clams, scallops, and razor clams from Galician Rias (northwest of Spain. The detection and isolation of the major Vibrio spp. and other enterobacterial populations have been carried out with the aim of screening for the presence of the pathways genes, poliketide synthase (PKS and non-ribosomal peptide synthetase (NRPS possibly involved in the biosynthesis of these toxins. Samples containing Vibrio spp. were analyzed by biochemical (API20E-galery and genetic tests (PCR-RT. These samples were then screened for TTX toxicity by a neuroblastoma cell-based assay (N2a and the presence of TTX was further confirmed by LC-MS/MS. TTX was detected in two infaunal samples. This is the first confirmation of the presence of TTX in bivalve molluscs from the Galician Rias.

Inactivation of the Major Hemolysin Gene Influences Expression of the Nonribosomal Peptide Synthetase Gene swrA in the Insect Pathogen Serratia sp. Strain SCBI.

Science.gov (United States)

Petersen, Lauren M; LaCourse, Kaitlyn; Schöner, Tim A; Bode, Helge; Tisa, Louis S

2017-11-01

Hemolysins are important virulence factors for many bacterial pathogens, including Serratia marcescens The role of the major hemolysin gene in the insect pathogen Serratia sp. strain SCBI was investigated using both forward and reverse-genetics approaches. Introduction of the major hemolysin gene into Escherichia coli resulted in a gain of both virulence and hemolytic activity. Inactivation of this hemolysin in Serratia sp. SCBI resulted in a loss of hemolysis but did not attenuate insecticidal activity. Unexpectedly, inactivation of the hemolysin gene in Serratia sp. SCBI resulted in significantly increased motility and increased antimicrobial activity. Reverse transcription-quantitative PCR (qRT-PCR) analysis of mutants with a disrupted hemolysin gene showed a dramatic increase in mRNA levels of a nonribosomal peptide synthetase gene, swrA , which produces the surfactant serrawettin W2. Mutation of the swrA gene in Serratia sp. SCBI resulted in highly varied antibiotic activity, motility, virulence, and hemolysis phenotypes that were dependent on the site of disruption within this 17.75-kb gene. When introduced into E. coli , swrA increases rates of motility and confers antimicrobial activity. While it is unclear how inactivation of the major hemolysin gene influences the expression of swrA , these results suggest that swrA plays an important role in motility and antimicrobial activity in Serratia sp. SCBI. IMPORTANCE The opportunistic Gram-negative bacteria of the genus Serratia are widespread in the environment and can cause human illness. A comparative genomics analysis between Serratia marcescens and a new Serratia species from South Africa, termed Serratia sp. strain SCBI, shows that these two organisms are closely related but differ in pathogenesis. S. marcescens kills Caenorhabditis nematodes, while Serratia sp. SCBI is not harmful and forms a beneficial association with them. This distinction presented the opportunity to investigate potential differences

Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi

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Ward Pauline N

2005-09-01

Full Text Available Abstract Background The trypanosomatids Leishmania major, Trypanosoma brucei and Trypanosoma cruzi cause some of the most debilitating diseases of humankind: cutaneous leishmaniasis, African sleeping sickness, and Chagas disease. These protozoa possess complex life cycles that involve development in mammalian and insect hosts, and a tightly coordinated cell cycle ensures propagation of the highly polarized cells. However, the ways in which the parasites respond to their environment and coordinate intracellular processes are poorly understood. As a part of an effort to understand parasite signaling functions, we report the results of a genome-wide analysis of protein kinases (PKs of these three trypanosomatids. Results Bioinformatic searches of the trypanosomatid genomes for eukaryotic PKs (ePKs and atypical PKs (aPKs revealed a total of 176 PKs in T. brucei, 190 in T. cruzi and 199 in L. major, most of which are orthologous across the three species. This is approximately 30% of the number in the human host and double that of the malaria parasite, Plasmodium falciparum. The representation of various groups of ePKs differs significantly as compared to humans: trypanosomatids lack receptor-linked tyrosine and tyrosine kinase-like kinases, although they do possess dual-specificity kinases. A relative expansion of the CMGC, STE and NEK groups has occurred. A large number of unique ePKs show no strong affinity to any known group. The trypanosomatids possess few ePKs with predicted transmembrane domains, suggesting that receptor ePKs are rare. Accessory Pfam domains, which are frequently present in human ePKs, are uncommon in trypanosomatid ePKs. Conclusion Trypanosomatids possess a large set of PKs, comprising approximately 2% of each genome, suggesting a key role for phosphorylation in parasite biology. Whilst it was possible to place most of the trypanosomatid ePKs into the seven established groups using bioinformatic analyses, it has not been

Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates

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Stephen A. Jackson

2018-02-01

Full Text Available The genus Streptomyces produces secondary metabolic compounds that are rich in biological activity. Many of these compounds are genetically encoded by large secondary metabolism biosynthetic gene clusters (smBGCs such as polyketide synthases (PKS and non-ribosomal peptide synthetases (NRPS which are modular and can be highly repetitive. Due to the repeats, these gene clusters can be difficult to resolve using short read next generation datasets and are often quite poorly predicted using standard approaches. We have sequenced the genomes of 13 Streptomyces spp. strains isolated from shallow water and deep-sea sponges that display antimicrobial activities against a number of clinically relevant bacterial and yeast species. Draft genomes have been assembled and smBGCs have been identified using the antiSMASH (antibiotics and Secondary Metabolite Analysis Shell web platform. We have compared the smBGCs amongst strains in the search for novel sequences conferring the potential to produce novel bioactive secondary metabolites. The strains in this study recruit to four distinct clades within the genus Streptomyces. The marine strains host abundant smBGCs which encode polyketides, NRPS, siderophores, bacteriocins and lantipeptides. The deep-sea strains appear to be enriched with gene clusters encoding NRPS. Marine adaptations are evident in the sponge-derived strains which are enriched for genes involved in the biosynthesis and transport of compatible solutes and for heat-shock proteins. Streptomyces spp. from marine environments are a promising source of novel bioactive secondary metabolites as the abundance and diversity of smBGCs show high degrees of novelty. Sponge derived Streptomyces spp. isolates appear to display genomic adaptations to marine living when compared to terrestrial strains.

POLARIMETRY AND THE HIGH-ENERGY EMISSION MECHANISMS IN QUASAR JETS: THE CASE OF PKS 1136-135

Energy Technology Data Exchange (ETDEWEB)

Cara, Mihai; Perlman, Eric S. [Department of Physics and Space Sciences, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901 (United States); Uchiyama, Yasunobu [SLAC/KIPAC, Stanford University, 2575 Sand Hill Road, M/S 209, Menlo Park, CA 94025 (United States); Cheung, Chi C. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States); Coppi, Paolo S. [Yale University, Department of Astronomy, P.O. Box 208101, New Haven, CT 06520-8101 (United States); Georganopoulos, Markos [Department of Physics, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 (United States); Worrall, Diana M.; Birkinshaw, Mark [Department of Physics, University of Bristol, Bristol, BS8 1TL (United Kingdom); Sparks, William B. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Marshall, Herman L. [Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Stawarz, Lukasz [Institute of Space Astronautical Science, JAXA, 3-1-1 Yoshinodai, Chuo-Ku, Sagamihara, Kanagawa 252-5210 (Japan); Begelman, Mitchell C. [Department of Astrophysical and Planetary Sciences, UCB 391, University of Colorado, Boulder, CO 80309-0391 (United States); O' Dea, Christopher P. [Laboratory for Multiwavelength Astrophysics, School of Physics and Astronomy, Rochester Institute of Technology, 84 Lomb Memorial Dr., Rochester, NY 14623-5603 (United States); Baum, Stefi A. [Chester F. Carlson Center for Imaging Science, Rochester Institute of Technology, 54 Lomb Memorial Dr., Rochester, NY 14623-5604 (United States)

2013-08-20

Since the discovery of kiloparsec-scale X-ray emission from quasar jets, the physical processes responsible for their high-energy emission have been poorly defined. A number of mechanisms are under active debate, including synchrotron radiation, inverse-Comptonized cosmic microwave background (IC/CMB) emission, and other Comptonization processes. In a number of cases, the optical and X-ray emission of jet regions are inked by a single spectral component, and in those, high-resolution multi-band imaging and polarimetry can be combined to yield a powerful diagnostic of jet emission processes. Here we report on deep imaging photometry of the jet of PKS 1136-135 obtained with the Hubble Space Telescope. We find that several knots are highly polarized in the optical, with fractional polarization {Pi} > 30%. When combined with the broadband spectral shape observed in these regions, this is very difficult to explain via IC/CMB models, unless the scattering particles are at the lowest-energy tip of the electron energy distribution, with Lorentz factor {gamma} {approx} 1, and the jet is also very highly beamed ({delta} {>=} 20) and viewed within a few degrees of the line of sight. We discuss both the IC/CMB and synchrotron interpretation of the X-ray emission in the light of this new evidence, presenting new models of the spectral energy distribution and also the matter content of this jet. The high polarizations do not completely rule out the possibility of IC/CMB optical-to-X-ray emission in this jet, but they do strongly disfavor the model. We discuss the implications of this finding, and also the prospects for future work.

Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

Energy Technology Data Exchange (ETDEWEB)

Sundlov, Jesse A.; Gulick, Andrew M., E-mail: gulick@hwi.buffalo.edu [University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203 (United States)

2013-08-01

The structure of the functional interaction of NRPS adenylation and carrier protein domains, trapped with a mechanism-based inhibitor, is described. Crystals exhibit translational non-crystallographic symmetry, which challenged structure determination and refinement. The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain–carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described.

Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

International Nuclear Information System (INIS)

Sundlov, Jesse A.; Gulick, Andrew M.

2013-01-01

The structure of the functional interaction of NRPS adenylation and carrier protein domains, trapped with a mechanism-based inhibitor, is described. Crystals exhibit translational non-crystallographic symmetry, which challenged structure determination and refinement. The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain–carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described

Comparison of the X-Ray and Radio Light Curves of Quasar PKS 1510--089

Science.gov (United States)

Aller, M. F.; Marscher, A. P.; Marchenko-Jorstad, S. G.; McHardy, I. M.; Aller, H. D.

1998-01-01

We present results for the X-ray-bright superluminal AGN PKS 1510-089 (z=0.36) monitored weekly with the Rossi X-Ray Timing Explorer for the past four years in order to study the origin of X-ray emission from this extremely variable blazer. These RXTE data are compared with weekly cm-band flux and polarization observations from the Michigan Diameter telescope, to identify correlated activity and associated frequency-dependent time delays for constraining X-ray emission models; and bimonthly 7mm VLBA total and linearly polarized intensity imaging to identify temporal associations between X-ray events and the ejection of superluminal components and disturbances in the magnetic field, to test if the X-ray energy release is related to changes in the inner jet flow. Both the X-ray (2-20 keV) and radio flux are highly variable on timescales of weeks. The VLBA mas structure is dominated by a bright core with a weak jet; both the ejection of very fast superluminal knots and changes in the fractional polarization and EVPA of the core on timescales of one to four months are identified. Two outbursts in 1997 are well-resolved in both the centimeter and X-ray bands. Both the strong temporal association and the similar outburst shape support a causal relation, and a discrete cross-correlation analysis identifies that the X-ray lags the radio by 16 days during the bursts. Starting in 1998 the behavior changes: the correlation is weaker with the X-ray possibly leading the radio by six days. During the full time window there is a correlation between bands as expected if the radio photons are upscattered to X-ray energies. The time correlations and difference between the flat X-ray spectral index (0.0 <= alpha <= 0.5 where F(sub v) is proportional to v(exp -alpha)), and the mm-wave synchrotron spectrum (alpha = 0.8) are discussed within the framework of viable SSC models.

Phylogenetic diversity of culturable endophytic fungi in Dongxiang wild rice (Oryza rufipogon Griff), detection of polyketide synthase gene and their antagonistic activity analysis.

Science.gov (United States)

Wang, Ya; Gao, Bo Liang; Li, Xi Xi; Zhang, Zhi Bin; Yan, Ri Ming; Yang, Hui Lin; Zhu, Du

2015-11-01

The biodiversity of plant endophytic fungi is enormous, numerous competent endophytic fungi are capable of providing different forms of fitness benefits to host plants and also could produce a wide array of bioactive natural products, which make them a largely unexplored source of novel compounds with potential bioactivity. In this study, we provided a first insights into revealing the diversity of culturable endophytic fungi in Dongxiang wild rice (Oryza rufipogon Griff.) from China using rDNA-ITS phylogenetic analysis. Here, the potential of fungi in producing bioactive natural products was estimated based on the beta-ketosynthase detected in the polyketide synthase (PKS) gene cluster and on the bioassay of antagonistic activity against two rice phytopathogens Thanatephorus cucumeris and Xanthomonas oryzae. A total of 229 endophytic fungal strains were validated in 19 genera. Among the 24 representative strains, 13 strains displayedantagonistic activity against the phytopathogens. Furthermore, PKS genes were detected in 9 strains, indicating their potential for synthesising PKS compounds. Our study confirms the phylogenetic diversity of endophytic fungi in O. rufipogon G. and highlights that endophytic fungi are not only promising resources of biocontrol agents against phytopathogens of rice plants, but also of bioactive natural products and defensive secondary metabolites. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Distributed Memory Parallel Computing with SEAWAT

Science.gov (United States)

Verkaik, J.; Huizer, S.; van Engelen, J.; Oude Essink, G.; Ram, R.; Vuik, K.

2017-12-01

Fresh groundwater reserves in coastal aquifers are threatened by sea-level rise, extreme weather conditions, increasing urbanization and associated groundwater extraction rates. To counteract these threats, accurate high-resolution numerical models are required to optimize the management of these precious reserves. The major model drawbacks are long run times and large memory requirements, limiting the predictive power of these models. Distributed memory parallel computing is an efficient technique for reducing run times and memory requirements, where the problem is divided over multiple processor cores. A new Parallel Krylov Solver (PKS) for SEAWAT is presented. PKS has recently been applied to MODFLOW and includes Conjugate Gradient (CG) and Biconjugate Gradient Stabilized (BiCGSTAB) linear accelerators. Both accelerators are preconditioned by an overlapping additive Schwarz preconditioner in a way that: a) subdomains are partitioned using Recursive Coordinate Bisection (RCB) load balancing, b) each subdomain uses local memory only and communicates with other subdomains by Message Passing Interface (MPI) within the linear accelerator, c) it is fully integrated in SEAWAT. Within SEAWAT, the PKS-CG solver replaces the Preconditioned Conjugate Gradient (PCG) solver for solving the variable-density groundwater flow equation and the PKS-BiCGSTAB solver replaces the Generalized Conjugate Gradient (GCG) solver for solving the advection-diffusion equation. PKS supports the third-order Total Variation Diminishing (TVD) scheme for computing advection. Benchmarks were performed on the Dutch national supercomputer (https://userinfo.surfsara.nl/systems/cartesius) using up to 128 cores, for a synthetic 3D Henry model (100 million cells) and the real-life Sand Engine model ( 10 million cells). The Sand Engine model was used to investigate the potential effect of the long-term morphological evolution of a large sand replenishment and climate change on fresh groundwater resources

Morphologic, Phylogenetic and Chemical Characterization of a Brackish Colonial Picocyanobacterium (Coelosphaeriaceae with Bioactive Properties

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Kerstin Häggqvist

2016-04-01

Full Text Available Despite their cosmopolitan distribution, knowledge on cyanobacteria in the family Coelosphaeriaceae is limited. In this study, a single species culture of a coelosphaeran cyanobacterium isolated from a brackish rock pool in the Baltic Sea was established. The strain was characterized by morphological features, partial 16S rRNA sequence and nonribosomal oligopeptide profile. The bioactivity of fractionated extracts against several serine proteases, as well as protein-serine/threonine phosphatases was studied. Phylogenetic analyses of the strain suggested a close relationship with Snowella litoralis, but its morphology resembled Woronichinia compacta. The controversial morphologic and phylogenetic results demonstrated remaining uncertainties regarding species division in this cyanobacteria family. Chemical analyses of the strain indicated production of nonribosomal oligopeptides. In fractionated extracts, masses and ion fragmentation spectra of seven possible anabaenopeptins were identified. Additionally, fragmentation spectra of cyanopeptolin-like peptides were collected in several of the fractions. The nonribosomal oligopeptide profile adds another potential identification criterion in future inter- and intraspecies comparisons of coelosphaeran cyanobacteria. The fractionated extracts showed significant activity against carboxypeptidase A and trypsin. Inhibition of these important metabolic enzymes might have impacts at the ecosystem level in aquatic habitats with high cyanobacteria densities.

The partial replacement of palm kernel shell by carbon black and halloysite nanotubes as fillers in natural rubber composites

Science.gov (United States)

Daud, Shuhairiah; Ismail, Hanafi; Bakar, Azhar Abu

2017-07-01

The effect of partial replacement of palm kernel shell powder by carbon black (CB) and halloysite nanotube (HNT) on the tensile properties, rubber-filler interaction, thermal properties and morphological studies of natural rubber (NR) composites were investigated. Four different compositions of NR/PKS/CB and NR/PKS/HNT composites i.e 20/0, 15/5, 10/10,5/15 and 0/20 parts per hundred rubber (phr) were prepared on a two roll mill. The results showed that the tensile strength and modulus at 100% elongation (M100) and 300% elongation (M300) were higher for NR/PKS/CB compared to NR/PKS/HNT composites. NR/PKS/CB composites had the lowest elongation at break (Eb). The effect of commercial fillers in NR/PKS composites on tensile properties was confirmed by the rubber-filler interaction and scanning electron microscopy (SEM) study. The thermal stability of PKS filled NR composites with partially replaced by commercial fillers also determined by Thermo gravimetric Analysis (TGA).

Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products

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Kurt Throckmorton

2015-09-01

Full Text Available Fungal polyketides are a diverse class of natural products, or secondary metabolites (SMs, with a wide range of bioactivities often associated with toxicity. Here, we focus on a group of non-reducing polyketide synthases (NR-PKSs in the fungal phylum Ascomycota that lack a thioesterase domain for product release, group V. Although widespread in ascomycete taxa, this group of NR-PKSs is notably absent in the mycotoxigenic genus Fusarium and, surprisingly, found in genera not known for their secondary metabolite production (e.g., the mycorrhizal genus Oidiodendron, the powdery mildew genus Blumeria, and the causative agent of white-nose syndrome in bats, Pseudogymnoascus destructans. This group of NR-PKSs, in association with the other enzymes encoded by their gene clusters, produces a variety of different chemical classes including naphthacenediones, anthraquinones, benzophenones, grisandienes, and diphenyl ethers. We discuss the modification of and transitions between these chemical classes, the requisite enzymes, and the evolution of the SM gene clusters that encode them. Integrating this information, we predict the likely products of related but uncharacterized SM clusters, and we speculate upon the utility of these classes of SMs as virulence factors or chemical defenses to various plant, animal, and insect pathogens, as well as mutualistic fungi.

SOS2-LIKE PROTEIN KINASE5, an SNF1-RELATED PROTEIN KINASE3-Type Protein Kinase, Is Important for Abscisic Acid Responses in Arabidopsis through Phosphorylation of ABSCISIC ACID-INSENSITIVE51[OPEN

Science.gov (United States)

Zhou, Xiaona; Hao, Hongmei; Zhang, Yuguo; Bai, Yili; Zhu, Wenbo; Qin, Yunxia; Yuan, Feifei; Zhao, Feiyi; Wang, Mengyao; Hu, Jingjiang; Xu, Hong; Guo, Aiguang; Zhao, Huixian; Zhao, Yang; Cao, Cuiling; Yang, Yongqing; Schumaker, Karen S.; Guo, Yan; Xie, Chang Gen

2015-01-01

Abscisic acid (ABA) plays an essential role in seed germination. In this study, we demonstrate that one SNF1-RELATED PROTEIN KINASE3-type protein kinase, SOS2-LIKE PROTEIN KINASE5 (PKS5), is involved in ABA signal transduction via the phosphorylation of an interacting protein, ABSCISIC ACID-INSENSITIVE5 (ABI5). We found that pks5-3 and pks5-4, two previously identified PKS5 superactive kinase mutants with point mutations in the PKS5 FISL/NAF (a conserved peptide that is necessary for interaction with SOS3 or SOS3-LIKE CALCIUM BINDING PROTEINs) motif and the kinase domain, respectively, are hypersensitive to ABA during seed germination. PKS5 was found to interact with ABI5 in yeast (Saccharomyces cerevisiae), and this interaction was further confirmed in planta using bimolecular fluorescence complementation. Genetic studies revealed that ABI5 is epistatic to PKS5. PKS5 phosphorylates a serine (Ser) residue at position 42 in ABI5 and regulates ABA-responsive gene expression. This phosphorylation was induced by ABA in vivo and transactivated ABI5. Expression of ABI5, in which Ser-42 was mutated to alanine, could not fully rescue the ABA-insensitive phenotypes of the abi5-8 and pks5-4abi5-8 mutants. In contrast, mutating Ser-42 to aspartate rescued the ABA insensitivity of these mutants. These data demonstrate that PKS5-mediated phosphorylation of ABI5 at Ser-42 is critical for the ABA regulation of seed germination and gene expression in Arabidopsis (Arabidopsis thaliana). PMID:25858916

POLARIMETRY AND THE HIGH-ENERGY EMISSION MECHANISMS IN QUASAR JETS: THE CASE OF PKS 1136–135

International Nuclear Information System (INIS)

Cara, Mihai; Perlman, Eric S.; Uchiyama, Yasunobu; Cheung, Chi C.; Coppi, Paolo S.; Georganopoulos, Markos; Worrall, Diana M.; Birkinshaw, Mark; Sparks, William B.; Marshall, Herman L.; Stawarz, Lukasz; Begelman, Mitchell C.; O'Dea, Christopher P.; Baum, Stefi A.

2013-01-01

Since the discovery of kiloparsec-scale X-ray emission from quasar jets, the physical processes responsible for their high-energy emission have been poorly defined. A number of mechanisms are under active debate, including synchrotron radiation, inverse-Comptonized cosmic microwave background (IC/CMB) emission, and other Comptonization processes. In a number of cases, the optical and X-ray emission of jet regions are inked by a single spectral component, and in those, high-resolution multi-band imaging and polarimetry can be combined to yield a powerful diagnostic of jet emission processes. Here we report on deep imaging photometry of the jet of PKS 1136–135 obtained with the Hubble Space Telescope. We find that several knots are highly polarized in the optical, with fractional polarization Π > 30%. When combined with the broadband spectral shape observed in these regions, this is very difficult to explain via IC/CMB models, unless the scattering particles are at the lowest-energy tip of the electron energy distribution, with Lorentz factor γ ∼ 1, and the jet is also very highly beamed (δ ≥ 20) and viewed within a few degrees of the line of sight. We discuss both the IC/CMB and synchrotron interpretation of the X-ray emission in the light of this new evidence, presenting new models of the spectral energy distribution and also the matter content of this jet. The high polarizations do not completely rule out the possibility of IC/CMB optical-to-X-ray emission in this jet, but they do strongly disfavor the model. We discuss the implications of this finding, and also the prospects for future work

Cloning and Sequencing of Protein Kinase cDNA from Harbor Seal (Phoca vitulina Lymphocytes

Directory of Open Access Journals (Sweden)

Jennifer C. C. Neale

2004-01-01

Full Text Available Protein kinases (PKs play critical roles in signal transduction and activation of lymphocytes. The identification of PK genes provides a tool for understanding mechanisms of immunotoxic xenobiotics. As part of a larger study investigating persistent organic pollutants in the harbor seal and their possible immunomodulatory actions, we sequenced harbor seal cDNA fragments encoding PKs. The procedure, using degenerate primers based on conserved motifs of human protein tyrosine kinases (PTKs, successfully amplified nine phocid PK gene fragments with high homology to human and rodent orthologs. We identified eight PTKs and one dual (serine/threonine and tyrosine kinase. Among these were several PKs important in early signaling events through the B- and T-cell receptors (FYN, LYN, ITK and SYK and a MAP kinase involved in downstream signal transduction. V-FGR, RET and DDR2 were also expressed. Sequential activation of protein kinases ultimately induces gene transcription leading to the proliferation and differentiation of lymphocytes critical to adaptive immunity. PKs are potential targets of bioactive xenobiotics, including persistent organic pollutants of the marine environment; characterization of these molecules in the harbor seal provides a foundation for further research illuminating mechanisms of action of contaminants speculated to contribute to large-scale die-offs of marine mammals via immunosuppression.

Isolation and expression of two polyketide synthase genes from Trichoderma harzianum 88 during mycoparasitism.

Science.gov (United States)

Yao, Lin; Tan, Chong; Song, Jinzhu; Yang, Qian; Yu, Lijie; Li, Xinling

2016-01-01

Metabolites of mycoparasitic fungal species such as Trichoderma harzianum 88 have important biological roles. In this study, two new ketoacyl synthase (KS) fragments were isolated from cultured Trichoderma harzianum 88 mycelia using degenerate primers and analysed using a phylogenetic tree. The gene fragments were determined to be present as single copies in Trichoderma harzianum 88 through southern blot analysis using digoxigenin-labelled KS gene fragments as probes. The complete sequence analysis in formation of pksT-1 (5669bp) and pksT-2 (7901bp) suggests that pksT-1 exhibited features of a non-reducing type I fungal PKS, whereas pksT-2 exhibited features of a highly reducing type I fungal PKS. Reverse transcription polymerase chain reaction indicated that the isolated genes are differentially regulated in Trichoderma harzianum 88 during challenge with three fungal plant pathogens, which suggests that they participate in the response of Trichoderma harzianum 88 to fungal plant pathogens. Furthermore, disruption of the pksT-2 encoding ketosynthase-acyltransferase domains through Agrobacterium-mediated gene transformation indicated that pksT-2 is a key factor for conidial pigmentation in Trichoderma harzianum 88. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

ORF Alignment: NC_002945 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ... Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis... Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis pdb|1TED|A Chain ... A..., Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis emb|C... pdb|1TED|C Chain ... C, Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculos...is pdb|1TED|B Chain ... B, Crystal Structure Of A

ORF Alignment: NC_002755 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ... Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis... Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis pdb|1TED|A Chain ... A..., Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis emb|C... pdb|1TED|C Chain ... C, Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculos...is pdb|1TED|B Chain ... B, Crystal Structure Of A

ORF Alignment: NC_000962 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ... Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis... Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis pdb|1TED|A Chain ... A..., Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculosis emb|C... pdb|1TED|C Chain ... C, Crystal Structure Of A Type Iii Polyketide Synthase ... Pks18 From Mycobacterium Tuberculos...is pdb|1TED|B Chain ... B, Crystal Structure Of A

Antimicrobial biosynthetic potential and genetic diversity of endophytic actinomycetes associated with medicinal plants.

Science.gov (United States)

Gohain, Anwesha; Gogoi, Animesh; Debnath, Rajal; Yadav, Archana; Singh, Bhim P; Gupta, Vijai K; Sharma, Rajeev; Saikia, Ratul

2015-10-01

Endophytic actinomycetes are one of the primary groups that share symbiotic relationships with medicinal plants and are key reservoir of biologically active compounds. In this study, six selective medicinal plants were targeted for the first time for endophytic actinomycetes isolation from Gibbon Wild Life Sanctuary, Assam, India, during winter and summer and 76 isolates were obtained. The isolates were found to be prevalent in roots followed by stem and leaves. 16S rRNA gene sequence analysis revealed 16 genera, including rare genera, Verrucosispora, Isoptericola and Kytococcus, which have never been previously reported as endophytic. The genus Streptomyces (66%) was dominant in both seasons. Shannon's diversity index showed that Azadirachta indica (1.49), Rauwolfia serpentina (1.43) and Emblica officinalis (1.24) were relatively good habitat for endophytic actinomycetes. Antimicrobial strains showed prevalence of polyketide synthase (PKS) type-II (85%) followed by PKS type-I (14%) encoded in the genomes. Expression studies showed 12-fold upregulation of PKSII gene in seventh day of incubation for Streptomyces antibioticus (EAAG90). Our results emphasize that the actinomycetes assemblages within plant tissue exhibited biosynthetic systems encoding for important biologically active compounds. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The systematic functional analysis of plasmodium protein kinases identifies essential regulators of mosquito transmission

KAUST Repository

Tewari, Rita; Straschil, Ursula; Bateman, Alex; Bö hme, Ulrike; Cherevach, Inna; Gong, Peng; Pain, Arnab; Billker, Oliver

2010-01-01

Although eukaryotic protein kinases (ePKs) contribute to many cellular processes, only three Plasmodium falciparum ePKs have thus far been identified as essential for parasite asexual blood stage development. To identify pathways essential for parasite transmission between their mammalian host and mosquito vector, we undertook a systematic functional analysis of ePKs in the genetically tractable rodent parasite Plasmodium berghei. Modeling domain signatures of conventional ePKs identified 66 putative Plasmodium ePKs. Kinomes are highly conserved between Plasmodium species. Using reverse genetics, we show that 23 ePKs are redundant for asexual erythrocytic parasite development in mice. Phenotyping mutants at four life cycle stages in Anopheles stephensi mosquitoes revealed functional clusters of kinases required for sexual development and sporogony. Roles for a putative SR protein kinase (SRPK) in microgamete formation, a conserved regulator of clathrin uncoating (GAK) in ookinete formation, and a likely regulator of energy metabolism (SNF1/KIN) in sporozoite development were identified. 2010 Elsevier Inc.

The systematic functional analysis of plasmodium protein kinases identifies essential regulators of mosquito transmission

KAUST Repository

Tewari, Rita

2010-10-21

Although eukaryotic protein kinases (ePKs) contribute to many cellular processes, only three Plasmodium falciparum ePKs have thus far been identified as essential for parasite asexual blood stage development. To identify pathways essential for parasite transmission between their mammalian host and mosquito vector, we undertook a systematic functional analysis of ePKs in the genetically tractable rodent parasite Plasmodium berghei. Modeling domain signatures of conventional ePKs identified 66 putative Plasmodium ePKs. Kinomes are highly conserved between Plasmodium species. Using reverse genetics, we show that 23 ePKs are redundant for asexual erythrocytic parasite development in mice. Phenotyping mutants at four life cycle stages in Anopheles stephensi mosquitoes revealed functional clusters of kinases required for sexual development and sporogony. Roles for a putative SR protein kinase (SRPK) in microgamete formation, a conserved regulator of clathrin uncoating (GAK) in ookinete formation, and a likely regulator of energy metabolism (SNF1/KIN) in sporozoite development were identified. 2010 Elsevier Inc.

EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases.

Science.gov (United States)

Wang, Yongbo; Liu, Zexian; Cheng, Han; Gao, Tianshun; Pan, Zhicheng; Yang, Qing; Guo, Anyuan; Xue, Yu

2014-01-01

We present here EKPD (http://ekpd.biocuckoo.org), a hierarchical database of eukaryotic protein kinases (PKs) and protein phosphatases (PPs), the key molecules responsible for the reversible phosphorylation of proteins that are involved in almost all aspects of biological processes. As extensive experimental and computational efforts have been carried out to identify PKs and PPs, an integrative resource with detailed classification and annotation information would be of great value for both experimentalists and computational biologists. In this work, we first collected 1855 PKs and 347 PPs from the scientific literature and various public databases. Based on previously established rationales, we classified all of the known PKs and PPs into a hierarchical structure with three levels, i.e. group, family and individual PK/PP. There are 10 groups with 149 families for the PKs and 10 groups with 33 families for the PPs. We constructed 139 and 27 Hidden Markov Model profiles for PK and PP families, respectively. Then we systematically characterized ∼50,000 PKs and >10,000 PPs in eukaryotes. In addition, >500 PKs and >400 PPs were computationally identified by ortholog search. Finally, the online service of the EKPD database was implemented in PHP + MySQL + JavaScript.

Multiwavelength Variability Study of the Classical BL Lac Object PKS 0735+178 on Timescales Ranging from Decades to Minutes

Energy Technology Data Exchange (ETDEWEB)

Goyal, Arti; Stawarz, Łukasz; Ostrowski, Michał; Soida, Marian [Astronomical Observatory of Jagiellonian University, ul. Orla 171, 30-244 Kraków (Poland); Larionov, Valeri [Astronomical Institute of St. Petersburg State University, Petrodvorets 198504 (Russian Federation); Gopal-Krishna [Centre for Excellence in Basic Sciences (CEBS), University of Mumbai campus (Kalina), Mumbai 400098 (India); Wiita, Paul J. [Department of Physics, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628-0718 (United States); Joshi, Santosh [Aryabhatta Research Institute of Observational Sciences (ARIES), Manora Peak, Nainital 263002 (India); Agudo, Iván, E-mail: arti@oa.uj.edu.pl [Instituto de Astrofísica de Andalucía (CSIC), Apartado 3004, E–18080 Granada (Spain)

2017-03-10

We present the results of our power spectral analysis for the BL Lac object PKS 0735+178, utilizing the Fermi -LAT survey at high-energy γ -rays, several ground-based optical telescopes, and single-dish radio telescopes operating at GHz frequencies. The novelty of our approach is that, by combining long-term and densely sampled intra-night light curves in the optical regime, we were able to construct for the first time the optical power spectrum of the blazar for a time domain extending from 23 years down to minutes. Our analysis reveals that: (1) the optical variability is consistent with a pure red noise, for which the power spectral density can be well approximated by a single power law throughout the entire time domain probed; (2) the slope of power spectral density at high-energy γ -rays (∼1) is significantly flatter than that found at radio and optical frequencies (∼2) within the corresponding time variability range; (3) for the derived power spectra, we did not detect any low-frequency flattening, nor do we see any evidence for cutoffs at the highest frequencies down to the noise floor levels due to measurement uncertainties. We interpret our findings in terms of a model where the blazar variability is generated by the underlying single stochastic process (at radio and optical frequencies), or a linear superposition of such processes (in the γ -ray regime). Along with the detailed PSD analysis, we also present the results of our extended (1998–2015) intra-night optical monitoring program and newly acquired optical photo-polarimetric data for the source.

NCBI nr-aa BLAST: CBRC-DDIS-03-0047 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-DDIS-03-0047 ref|XP_001383670.1| nonribosomal protein of the nucleolus and coi...led bodies [Pichia stipitis CBS 6054] gb|ABN65641.1| nonribosomal protein of the nucleolus and coiled bodies [Pichia stipitis CBS 6054] XP_001383670.1 3e-04 38% ...

Evidence of an Unidentified Extracellular Heat-Stable Factor Produced by Lysobacter enzymogenes (OH11) that Degrade Fusarium graminearum PH1 Hyphae.

Science.gov (United States)

Odhiambo, Benard Omondi; Xu, Gaoge; Qian, Guoliang; Liu, Fengquan

2017-04-01

Lysobacter enzymogenes OH11 produces heat-stable antifungal factor (HSAF) and lytic enzymes possessing antifungal activity. This study bio-prospected for other potential antifungal factors besides those above. The cells and extracellular metabolites of L. enzymogenes OH11 and the mutants ΔchiA, ΔchiB, ΔchiC, Δclp, Δpks, and ΔpilA were examined for antifungal activity against Fusarium graminearum PH1, the causal agent of Fusarium head blight (FHB). Results evidenced that OH11 produces an unidentified extracellular heat-stable degrading metabolite (HSDM) that exhibit degrading activity on F. graminearum PH1 chitinous hyphae. Interestingly, both heat-treated and non-heat-treated extracellular metabolites of OH11 mutants exhibited hyphae-degrading activity against F. graminearum PH1. Enzyme activity detection of heat-treated metabolites ruled out the possibility of enzyme degradation activity. Remarkably, the PKS-NRPS-deficient mutant Δpks cannot produce HSAF or analogues, yet its metabolites exhibited hyphae-degrading activity. HPLC analysis confirmed no HSAF production by Δpks. Δclp lacks hyphae-degrading ability. Therefore, clp regulates HSDM and extracellular lytic enzymes production in L. enzymogenes OH11. ΔpilA had impaired surface cell motility and significantly reduced antagonistic properties. ΔchiA, ΔchiB, and ΔchiC retained hyphae-degrading ability, despite having reduced abilities to produce chitinase enzymes. Ultimately, L. enzymogenes OH11 can produce other unidentified HSDM independent of the PKS-NRPS genes. This suggests HSAF and lytic enzymes production are a fraction of the antifungal mechanisms in OH11. Characterization of HSDM, determination of its biosynthetic gene cluster and understanding its mode of action will provide new leads in the search for effective drugs for FHB management.

Radio and γ -Ray Variability in the BL Lac PKS 0219−164: Detection of Quasi-periodic Oscillations in the Radio Light Curve

Energy Technology Data Exchange (ETDEWEB)

Bhatta, Gopal, E-mail: gopalbhatta716@gmail.com [Astronomical Observatory of the Jagiellonian University, ul. Orla 171, 30-244 Kraków (Poland); Mt. Suhora Observatory, Pedagogical University, ul. Podchorazych 2, 30-084 Kraków (Poland)

2017-09-20

In this work, we explore the long-term variability properties of the blazar PKS 0219−164 in the radio and the γ -ray regime, utilizing the OVRO 15 GHz and the Fermi /LAT observations from the period 2008–2017. We found that γ -ray emission is more variable than the radio emission implying that γ -ray emission possibly originated in more compact regions while the radio emission represented continuum emission from the large-scale jets. Also, in the γ -ray, the source exhibited spectral variability, characterized by the softer-when-brighter trend, a less frequently observed feature in the high-energy emission by BL Lacs. In radio, using Lomb–Scargle periodogram and weighted wavelet z -transform, we detected a strong signal of quasi-periodic oscillation (QPO) with a periodicity of 270 ± 26 days with possible harmonics of 550 ± 42 and 1150 ± 157 day periods. At a time when detections of QPOs in blazars are still under debate, the observed QPO with high statistical significance (∼97%–99% global significance over underlying red-noise processes) and persistent over nearly 10 oscillations could make one of the strongest cases for the detection of QPOs in blazar light curves. We discuss various blazar models that might lead to the γ -ray and radio variability, QPO, and the achromatic behavior seen in the high-energy emission from the source.

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

KAUST Repository

Othoum, Ghofran K; Bougouffa, Salim; Razali, Rozaimi; Bokhari, Ameerah; Alamoudi, Soha; Antunes, André ; Gao, Xin; Hoehndorf, Robert; Arold, Stefan T.; Gojobori, Takashi; Hirt, Heribert; Mijakovic, Ivan; Bajic, Vladimir B.; Lafi, Feras Fawzi; Essack, Magbubah

2018-01-01

are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked

Genome-guided exploration of metabolic features of Streptomyces peucetius ATCC 27952: past, current, and prospect.

Science.gov (United States)

Thuan, Nguyen Huy; Dhakal, Dipesh; Pokhrel, Anaya Raj; Chu, Luan Luong; Van Pham, Thi Thuy; Shrestha, Anil; Sohng, Jae Kyung

2018-05-01

Streptomyces peucetius ATCC 27952 produces two major anthracyclines, doxorubicin (DXR) and daunorubicin (DNR), which are potent chemotherapeutic agents for the treatment of several cancers. In order to gain detailed insight on genetics and biochemistry of the strain, the complete genome was determined and analyzed. The result showed that its complete sequence contains 7187 protein coding genes in a total of 8,023,114 bp, whereas 87% of the genome contributed to the protein coding region. The genomic sequence included 18 rRNA, 66 tRNAs, and 3 non-coding RNAs. In silico studies predicted ~ 68 biosynthetic gene clusters (BCGs) encoding diverse classes of secondary metabolites, including non-ribosomal polyketide synthase (NRPS), polyketide synthase (PKS I, II, and III), terpenes, and others. Detailed analysis of the genome sequence revealed versatile biocatalytic enzymes such as cytochrome P450 (CYP), electron transfer systems (ETS) genes, methyltransferase (MT), glycosyltransferase (GT). In addition, numerous functional genes (transporter gene, SOD, etc.) and regulatory genes (afsR-sp, metK-sp, etc.) involved in the regulation of secondary metabolites were found. This minireview summarizes the genome-based genome mining (GM) of diverse BCGs and genome exploration (GE) of versatile biocatalytic enzymes, and other enzymes involved in maintenance and regulation of metabolism of S. peucetius. The detailed analysis of genome sequence provides critically important knowledge useful in the bioengineering of the strain or harboring catalytically efficient enzymes for biotechnological applications.

Fatty acids from oleaginous yeasts and yeast-like fungi and their potential applications.

Science.gov (United States)

Xue, Si-Jia; Chi, Zhe; Zhang, Yu; Li, Yan-Feng; Liu, Guang-Lei; Jiang, Hong; Hu, Zhong; Chi, Zhen-Ming

2018-02-01

Oleaginous yeasts, fatty acids biosynthesis and regulation in the oleaginous yeasts and the fatty acids from the oleaginous yeasts and their applications are reviewed in this article. Oleaginous yeasts such as Rhodosporidium toruloides, Yarrowia lipolytica, Rhodotorula mucilaginosa, and Aureobasidium melanogenum, which can accumulate over 50% lipid of their cell dry weight, have many advantages over other oleaginous microorganisms. The fatty acids from the oleaginous yeasts have many potential applications. Many oleaginous yeasts have now been genetically modified to over-produce fatty acids and their derivatives. The most important features of the oleaginous yeasts are that they have special enzymatic systems for enhanced biosynthesis and regulation of fatty acids in their lipid particles. Recently, some oleaginous yeasts such as R. toruloides have been found to have a unique fatty acids synthetase and other oleaginous yeasts such as A. melanogenum have a unique highly reducing polyketide synthase (HR-PKS) involved in the biosynthesis of hydroxyl fatty acids. It is necessary to further enhance lipid biosynthesis using metabolic engineering and explore new applications of fatty acids in biotechnology.

Identification of the non-ribosomal peptide synthetase responsible for biosynthesis of the potential anti-cancer drug sansalvamide in Fusarium solani

DEFF Research Database (Denmark)

Romans-Fuertes, Patricia; Sondergaard, Teis Esben; Sandmann, Manuela Ilse Helga

2016-01-01

Sansalvamide is a cyclic pentadepsipeptide produced by Fusarium solani and has shown promising results as potential anti-cancer drug. The biosynthetic pathway has until now remained unidentified, but here we used an Agrobacterium tumefaciens-mediated transformation (ATMT) approach to generate kno...... and Trichoderma virens, which suggests that the ability to produce compounds related to destruxin and sansalvamide is widespread....

New ALMA and Fermi /LAT Observations of the Large-scale Jet of PKS 0637−752 Strengthen the Case Against the IC/CMB Model

Energy Technology Data Exchange (ETDEWEB)

Meyer, Eileen T.; Breiding, Peter; Georganopoulos, Markos [University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 (United States); Oteo, Iván; Ivison, R. J. [Institute for Astronomy, University of Edinburgh, Royal Observatory, Blackford Hill, Edinburgh EH9 3HJ (United Kingdom); Zwaan, Martin A.; Laing, Robert [European Southern Observatory, Karl-Schwarzschild-Str. 2, D-85748 Garching-bei-München (Germany); Godfrey, Leith, E-mail: meyer@umbc.edu [ASTRON, the Netherlands Institute for Radio Astronomy, Postbus 2, 7990 AA Dwingeloo (Netherlands)

2017-02-01

The Chandra X-ray observatory has discovered several dozen anomalously X-ray-bright jets associated with powerful quasars. A popular explanation for the X-ray flux from the knots in these jets is that relativistic synchrotron-emitting electrons inverse-Compton scatter cosmic microwave background (CMB) photons to X-ray energies (the IC/CMB model). This model predicts a high gamma-ray flux that should be detectable by the Fermi /Large Area Telescope (LAT) for many sources. GeV-band upper limits from Fermi /LAT for the well-known anomalous X-ray jet in PKS 0637−752 were previously shown in Meyer et al. to violate the predictions of the IC/CMB model. Previously, measurements of the jet synchrotron spectrum, important for accurately predicting the gamma-ray flux level, were lacking between radio and infrared wavelengths. Here, we present new Atacama Large Millimeter/submillimeter Array (ALMA) observations of the large-scale jet at 100, 233, and 319 GHz, which further constrain the synchrotron spectrum, supporting the previously published empirical model. We also present updated limits from the Fermi /LAT using the new “Pass 8” calibration and approximately 30% more time on source. With these deeper limits, we rule out the IC/CMB model at the 8.7 σ level. Finally, we demonstrate that complete knowledge of the synchrotron SED is critical in evaluating the IC/CMB model.

AcEST: BP913209 [AcEST

Lifescience Database Archive (English)

Full Text Available terized protein OS=Magna... 40 0.10 tr|A3LQY9|A3LQY9_PICST Nonribosomal protein of the nucleolus and... 39 0...AESGKRSA 694 Query: 478 SK 483 SK Sbjct: 695 SK 696 >tr|A3LQY9|A3LQY9_PICST Nonribosomal protein of the nucleolus

Algal carbohydrates affect polyketide synthesis of the lichen-forming fungus Cladonia rangiferina.

Science.gov (United States)

Elshobary, Mostafa E; Osman, Mohamed E; Abo-Shady, Atef M; Komatsu, Emy; Perreault, Hélène; Sorensen, John; Piercey-Normore, Michele D

2016-01-01

Lichen secondary metabolites (polyketides) are produced by the fungal partner, but the role of algal carbohydrates in polyketide biosynthesis is not clear. This study examined whether the type and concentration of algal carbohydrate explained differences in polyketide production and gene transcription by a lichen fungus (Cladonia rangiferina). The carbohydrates identified from a free-living cyanobacterium (Spirulina platensis; glucose), a lichen-forming alga (Diplosphaera chodatii; sorbitol) and the lichen alga that associates with C. rangiferina (Asterochloris sp.; ribitol) were used in each of 1%, 5% and 10% concentrations to enrich malt yeast extract media for culturing the mycobiont. Polyketides were determined by high performance liquid chromatography (HPLC), and polyketide synthase (PKS) gene transcription was measured by quantitative PCR of the ketosynthase domain of four PKS genes. The lower concentrations of carbohydrates induced the PKS gene expression where ribitol up-regulated CrPKS1 and CrPKS16 gene transcription and sorbitol up-regulated CrPKS3 and CrPKS7 gene transcription. The HPLC results revealed that lower concentrations of carbon sources increased polyketide production for three carbohydrates. One polyketide from the natural lichen thallus (fumarprotocetraric acid) also was produced by the fungal culture in ribitol supplemented media only. This study provides a better understanding of the role of the type and concentration of the carbon source in fungal polyketide biosynthesis in the lichen Cladonia rangiferina. © 2016 by The Mycological Society of America.

Functional characterization of O-methyltransferases used to catalyse site-specific methylation in the post-tailoring steps of pradimicin biosynthesis.

Science.gov (United States)

Han, J W; Ng, B G; Sohng, J K; Yoon, Y J; Choi, G J; Kim, B S

2018-01-01

To identify the roles of the two O-methyltransferase homologous genes pdmF and pdmT in the pradimicin biosynthetic gene cluster of Actinomadura hibisca P157-2. Pradimicins are pentangular polyphenol antibiotics synthesized by bacterial type II polyketide synthases (PKSs) and tailoring enzymes. Pradimicins are naturally derivatized by combinatorial O-methylation at two positions (i.e., 7-OH and 11-OH) of the benzo[α]naphthacenequinone structure. PdmF and PdmT null mutants (PFKO and PTKO) were generated. PFKO produced the 11-O-demethyl shunt metabolites 11-O-demethylpradimicinone II (1), 11-O-demethyl-7-methoxypradimicinone II (2), 11-O-demethylpradimicinone I (3) and 11-O-demethylpradimicin A (4), while PTKO generated the 7-O-demethyl derivatives pradimicinone II (5) and 7-hydroxypradimicin A (6). Pradimicinones 1, 2, 3, and 5 were fed to a heterologous host Escherichia coli harbouring expression plasmid pET-22b::pdmF or pET-28a::pdmT. PdmF catalysed 11-O-methylation of pradimicinones 1, 2, and 3 regardless of O-methylation at the C-7 position, while PdmT was unable to catalyse 7-O-methylation when the C-11 hydroxyl group was methylated (5). PdmF and PdmT were involved in 11-O- and 7-O-methylations of the benzo[α]naphthacenequinone moiety of pradimicin, respectively. Methylation of the C-7 hydroxyl group precedes methylation of the C-11 hydroxyl group in pradimicin biosynthesis. This is the first reported demonstration of the functions of PdmF and PdmT for regiospecific O-methylation, which contributes to better understanding of the post-PKS modifications in pradimicin biosynthesis as well as to rational engineering of the pradimicin biosynthetic machinery. © 2017 The Society for Applied Microbiology.

A dual role for a polyketide synthase in dynemicin enediyne and anthraquinone biosynthesis

Science.gov (United States)

Cohen, Douglas R.; Townsend, Craig A.

2018-02-01

Dynemicin A is a member of a subfamily of enediyne antitumour antibiotics characterized by a 10-membered carbocycle fused to an anthraquinone, both of polyketide origin. Sequencing of the dynemicin biosynthetic gene cluster in Micromonospora chersina previously identified an enediyne polyketide synthase (PKS), but no anthraquinone PKS, suggesting gene(s) for biosynthesis of the latter were distant from the core dynemicin cluster. To identify these gene(s), we sequenced and analysed the genome of M. chersina. Sequencing produced a short list of putative PKS candidates, yet CRISPR-Cas9 mutants of each locus retained dynemicin production. Subsequently, deletion of two cytochromes P450 in the dynemicin cluster suggested that the dynemicin enediyne PKS, DynE8, may biosynthesize the anthraquinone. Together with 18O-labelling studies, we now present evidence that DynE8 produces the core scaffolds of both the enediyne and anthraquinone, and provide a working model to account for their formation from the programmed octaketide of the enediyne PKS.

Kernel based machine learning algorithm for the efficient prediction of type III polyketide synthase family of proteins

Directory of Open Access Journals (Sweden)

Mallika V

2010-03-01

Full Text Available Type III Polyketide synthases (PKS are family of proteins considered to have significant role in the biosynthesis of various polyketides in plants, fungi and bacteria. As these proteins show positive effects to human health, more researches are going on regarding this particular protein. Developing a tool to identify the probability of sequence, being a type III polyketide synthase will minimize the time consumption and manpower efforts. In this approach, we have designed and implemented PKSIIIpred, a high performance prediction server for type III PKS where the classifier is Support Vector Machine (SVM. Based on the limited training dataset, the tool efficiently predicts the type III PKS superfamily of proteins with high sensitivity and specificity. PKSIIIpred is available at http://type3pks.in/prediction/. We expect that this tool may serve as a useful resource for type III PKS researchers. Currently work is being progressed for further betterment of prediction accuracy by including more sequence features in the training dataset.

Redirection of pigment biosynthesis to isocoumarins in Fusarium

DEFF Research Database (Denmark)

Sørensen, Jens Laurids; Nielsen, Kristian Fog; Sondergaard, Teis Esben

2012-01-01

Colonies of Fusarium species often appear red due to production of pigments, such as aurofusarin or bikaverin. The primary compounds in these biosynthetic pathways are YWA1 and pre-bikaverin, respectively, catalyzed by two multidomain polyketide synthases (PKSs), which both have a claisen...

Baltic cyanobacteria- A source of biologically active compounds

Digital Repository Service at National Institute of Oceanography (India)

Mazur-Marzec, H.; Błaszczyk, A.; Felczykowska, A.; Hohlfeld, N.; Kobos, J.; Toruńska-Sitarz, A.; PrabhaDevi; Montalva`o, S.; DeSouza, L.; Tammela, P.; Mikosik, A.; Bloch, S.; Nejman-Faleńczyk, B.; Węgrzyn, G.

cyanobacteria, enzyme activity, enzyme inhibitors, immunological activity, natural products, nonribosomal peptides, plant growth regulators 2 INTRODUCTION Cyanobacteria are Gram-negative bacteria which are widely distributed in many water bodies..., immunological, 4 antimicrobial and plant growth tests. The overall aim of the experiments was to identify strains showing the most promising biological activity for potential biotechnological application. MATERIALS AND METHODS Isolation, culture...

Non-ribosomal peptide synthetases

Indian Academy of Sciences (India)

2017-01-19

Jan 19, 2017 ... knowledge of their gene cluster architecture and tailoring enzymes have helped in the in silico genetic ..... The predictive power of the bioinformatics sequence analy- .... identified these motifs manually, though NaPDoS, anti-.

Potensi Lumpur Sawit (SOLID Sebagai Pakan Ruminansia di Kabupaten Pelalawan Provinsi Riau

Directory of Open Access Journals (Sweden)

Kodri Yanto

2008-10-01

Full Text Available Potential of palm oil’s waste (solid as ruminant feed in Pelalawan district of Riau Province ABSTRACT. The objective of this study was to know potential of solid waste in Pelalawan district, Riau province. Research was carried out from December 2007 – January 2008 in Pelalawan district by using 4 factories of Elaeis guineensis (PKS. The four factories that were used for data collection were PT. Multi Palma Sejahtera (MPS, PT. Inti Indo Sawit Subur (IIS, PT. Sinar Agro Raya (SAR and PT. Musim Mas (MM. The results of study showed that solid waste in Pelalawan district of Riau province had a great potential. Production of solid waste in Pelalawan district was around 76.176 tons/year and carrying capacity was 5.132 animals unit. Farmers will use solid waste at large quantity if they raise livestock in commercially, for instance for fattening purpose. The strategies which can be applied to maximize solid waste utilization are through partnership between farmers and factories or local government pihak PKS.

Hybrid polyketide synthases

Energy Technology Data Exchange (ETDEWEB)

Fortman, Jeffrey L.; Hagen, Andrew; Katz, Leonard; Keasling, Jay D.; Poust, Sean; Zhang, Jingwei; Zotchev, Sergey

2016-05-10

The present invention provides for a polyketide synthase (PKS) capable of synthesizing an even-chain or odd-chain diacid or lactam or diamine. The present invention also provides for a host cell comprising the PKS and when cultured produces the even-chain diacid, odd-chain diacid, or KAPA. The present invention also provides for a host cell comprising the PKS capable of synthesizing a pimelic acid or KAPA, and when cultured produces biotin.

Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds

Directory of Open Access Journals (Sweden)

Lynn M. Naughton

2017-08-01

Full Text Available Increased incidences of antimicrobial resistance and the emergence of pan-resistant ‘superbugs’ have provoked an extreme sense of urgency amongst researchers focusing on the discovery of potentially novel antimicrobial compounds. A strategic shift in focus from the terrestrial to the marine environment has resulted in the discovery of a wide variety of structurally and functionally diverse bioactive compounds from numerous marine sources, including sponges. Bacteria found in close association with sponges and other marine invertebrates have recently gained much attention as potential sources of many of these novel bioactive compounds. Members of the genus Pseudovibrio are one such group of organisms. In this study, we interrogate the genomes of 21 Pseudovibrio strains isolated from a variety of marine sources, for the presence, diversity and distribution of biosynthetic gene clusters (BGCs. We expand on results obtained from antiSMASH analysis to demonstrate the similarity between the Pseudovibrio-related BGCs and those characterized in other bacteria and corroborate our findings with phylogenetic analysis. We assess how domain organization of the most abundant type of BGCs present among the isolates (Non-ribosomal peptide synthetases and Polyketide synthases may influence the diversity of compounds produced by these organisms and highlight for the first time the potential for novel compound production from this genus of bacteria, using a genome guided approach.

Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges

DEFF Research Database (Denmark)

Yuzawa, Satoshi; Keasling, Jay D.; Katz, Leonard

2017-01-01

Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containin...... have applications as fuels or industrial chemicals....

[Isolation of actinobacteria with antibiotic associated with soft coral Nephthea sp].

Science.gov (United States)

Ma, Liang; Zhang, Wenjun; Zhu, Yiguang; Wu, Zhengchao; Saurav, Kumar; Hang, Hui; Zhang, Changsheng

2013-10-04

The present study aims to isolate and identify actinobacteria associated with the soft coral Nephthea sp., and to isolate natural products from these actinobacteria under the guidance of PCR screening for polyketides synthase (PKS) genes. Eleven selective media were used to isolate actinobacteria associated with the soft coral Nephthea sp. collected from Yongxin Island. The isolated actinobacteria were classified on the basis of phylogenetic tree analysis of their 16S rRNA genes. Degenerated primers targeted on conserved KS (ketoacyl-synthase) domain of type I PKS genes were used to screen for potential isolates. The positive isolates were cultured in three different media to check their producing profiles. One bioactive strain that is rich in metabolites was subjected to larger scale fermentation for isolating bioactive natural products. A total of 20 strains were isolated from Nephthea sp., and were categorized into 3 genera including Streptomyces, Dietzia and Salinospora, among which 18 strains were positive in screening with type I PKS genes. Two bioactive compounds rifamycin S and rifamycin W were isolated and identified from Salinospora arenicola SH04. This is the first report of isolating indigenous marine actinobacteria Salinospora from the soft coral Nephthea sp. It provides an example of isolating bioactive secondary metabolites from cultivable actinobacteria associated with Nephthea sp. by PCR screening.

Partai Keadilan Sejahtera: A Mawdudian-Meliorist Vision of Islamism in Post-New Order Indonesia

OpenAIRE

Masdar Hilmy

2007-01-01

This article seeks to analyze how one group, that is, the Justice and Welfare Party (PKS), is attempting to clean up politics from within the political party system. This article argues that the existence of PKS has given a new but unique political nuance to the political party system in post-New Order Indonesia. The seemingly sudden rise of PKS has taken many by surprise, and it is for this that the party has become the topic of much discourse amongst scholars of Indonesia.Copyright (c...

Fermi Non-detections of Four X-Ray Jet Sources and Implications for the IC/CMB Mechanism

Science.gov (United States)

Breiding, Peter; Meyer, Eileen T.; Georganopoulos, Markos; Keenan, M. E.; DeNigris, N. S.; Hewitt, Jennifer

2017-11-01

Since its launch in 1999, the Chandra X-ray observatory has discovered several dozen X-ray jets associated with powerful quasars. In many cases, the X-ray spectrum is hard and appears to come from a second spectral component. The most popular explanation for the kpc-scale X-ray emission in these cases has been inverse-Compton (IC) scattering of Cosmic Microwave Background (CMB) photons by relativistic electrons in the jet (the IC/CMB model). Requiring the IC/CMB emission to reproduce the observed X-ray flux density inevitably predicts a high level of gamma-ray emission, which should be detectable with the Fermi Large Area Telescope (LAT). In previous work, we found that gamma-ray upper limits from the large-scale jets of 3C 273 and PKS 0637-752 violate the predictions of the IC/CMB model. Here, we present Fermi/LAT flux density upper limits for the X-ray jets of four additional sources: PKS 1136-135, PKS 1229-021, PKS 1354+195, and PKS 2209+080. We show that these limits violate the IC/CMB predictions at a very high significance level. We also present new Hubble Space Telescope observations of the quasar PKS 2209+080 showing a newly detected optical jet, and Atacama Large Millimeter/submillimeter Array band 3 and 6 observations of all four sources, which provide key constraints on the spectral shape that enable us to rule out the IC/CMB model.

Producing biofuels using polyketide synthases

Science.gov (United States)

Katz, Leonard; Fortman, Jeffrey L; Keasling, Jay D

2013-04-16

The present invention provides for a non-naturally occurring polyketide synthase (PKS) capable of synthesizing a carboxylic acid or a lactone, and a composition such that a carboxylic acid or lactone is included. The carboxylic acid or lactone, or derivative thereof, is useful as a biofuel. The present invention also provides for a recombinant nucleic acid or vector that encodes such a PKS, and host cells which also have such a recombinant nucleic acid or vector. The present invention also provides for a method of producing such carboxylic acids or lactones using such a PKS.

Novel experimental results in human cardiac electrophysiology: measurement of the Purkinje fibre action potential from the undiseased human heart.

Science.gov (United States)

Nagy, Norbert; Szél, Tamás; Jost, Norbert; Tóth, András; Gy Papp, Julius; Varró, András

2015-09-01

Data obtained from canine cardiac electrophysiology studies are often extrapolated to the human heart. However, it has been previously demonstrated that because of the lower density of its K(+) currents, the human ventricular action potential has a less extensive repolarization reserve. Since the relevance of canine data to the human heart has not yet been fully clarified, the aim of the present study was to determine for the first time the action potentials of undiseased human Purkinje fibres (PFs) and to compare them directly with those of dog PFs. All measurements were performed at 37 °C using the conventional microelectrode technique. At a stimulation rate of 1 Hz, the plateau potential of human PFs is more positive (8.0 ± 1.8 vs 8.6 ± 3.4 mV, n = 7), while the amplitude of the spike is less pronounced. The maximal rate of depolarization is significantly lower in human PKs than in canine PFs (406.7 ± 62 vs 643 ± 36 V/s, respectively, n = 7). We assume that the appreciable difference in the protein expression profiles of the 2 species may underlie these important disparities. Therefore, caution is advised when canine PF data are extrapolated to humans, and further experiments are required to investigate the characteristics of human PF repolarization and its possible role in arrhythmogenesis.

On the interaction of the PKS B1358–113 radio galaxy with the A1836 cluster

Energy Technology Data Exchange (ETDEWEB)

Stawarz, Ł.; Simionescu, A.; Hagino, K. [Institute of Space and Astronautical Science, JAXA, 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210 (Japan); Szostek, A.; Kozieł-Wierzbowska, D.; Ostrowski, M. [Astronomical Observatory, Jagiellonian University, ulica Orla 171, 30-244 Kraków (Poland); Cheung, C. C. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States); Siemiginowska, A.; Harris, D. E. [Harvard Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Werner, N. [KIPAC, Stanford University, 452 Lomita Mall, Stanford, CA 94305 (United States); Madejski, G. [W. W. Hansen Experimental Physics Laboratory, Kavli Institute for Particle Astrophysics and Cosmology, Department of Physics and SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305 (United States); Begelman, M. C., E-mail: stawarz@astro.isas.jaxa.jp [JILA, University of Colorado and National Institute of Standards and Technology, 440 UCB, Boulder, CO 80309-0440 (United States)

2014-10-20

Here we present the analysis of multifrequency data gathered for the Fanaroff-Riley type-II (FR II) radio galaxy PKS B1358-113, hosted in the brightest cluster galaxy in the center of A1836. The galaxy harbors one of the most massive black holes known to date, and our analysis of the acquired optical data reveals that this black hole is only weakly active, with a mass accretion rate M-dot {sub acc}∼2×10{sup −4} M-dot {sub Edd}∼0.02 M{sub ⊙} yr{sup –1}. Based on analysis of new Chandra and XMM-Newton X-ray observations and archival radio data, and assuming the well-established model for the evolution of FR II radio galaxies, we derive the preferred range for the jet kinetic luminosity L {sub j} ∼ (1-6) × 10{sup –3} L {sub Edd} ∼ (0.5-3) × 10{sup 45} erg s{sup –1}. This is above the values implied by various scaling relations proposed for radio sources in galaxy clusters, being instead very close to the maximum jet power allowed for the given accretion rate. We also constrain the radio source lifetime as τ{sub j} ∼ 40-70 Myr, meaning the total amount of deposited jet energy E {sub tot} ∼ (2-8) × 10{sup 60} erg. We argue that approximately half of this energy goes into shock heating of the surrounding thermal gas, and the remaining 50% is deposited into the internal energy of the jet cavity. The detailed analysis of the X-ray data provides indication for the presence of a bow shock driven by the expanding radio lobes into the A1836 cluster environment. We derive the corresponding shock Mach number in the range M{sub sh}∼2--4, which is one of the highest claimed for clusters or groups of galaxies. This, together with the recently growing evidence that powerful FR II radio galaxies may not be uncommon in the centers of clusters at higher redshifts, supports the idea that jet-induced shock heating may indeed play an important role in shaping the properties of clusters, galaxy groups, and galaxies in formation. In this context, we speculate on

Crystallization and preliminary crystallographic analysis of an acridone-producing novel multifunctional type III polyketide synthase from Huperzia serrata

Energy Technology Data Exchange (ETDEWEB)

Morita, Hiroyuki [Mitsubishi Kagaku Institute of Life Sciences (MITILS), 11 Minamiooya, Machida, Tokyo 194-8511 (Japan); Kondo, Shin; Kato, Ryohei [Innovation Center Yokohama, Mitsubishi Chemical Corporation, 1000 Kamoshida, Aoba, Yokohama, Kanagawa 227-8502 (Japan); Wanibuchi, Kiyofumi; Noguchi, Hiroshi [School of Pharmaceutical Sciences, University of Shizuoka and the COE21 Program, Shizuoka 422-8526 (Japan); Sugio, Shigetoshi [Innovation Center Yokohama, Mitsubishi Chemical Corporation, 1000 Kamoshida, Aoba, Yokohama, Kanagawa 227-8502 (Japan); Abe, Ikuro [School of Pharmaceutical Sciences, University of Shizuoka and the COE21 Program, Shizuoka 422-8526 (Japan); PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012 (Japan); Kohno, Toshiyuki [Mitsubishi Kagaku Institute of Life Sciences (MITILS), 11 Minamiooya, Machida, Tokyo 194-8511 (Japan)

2007-07-01

An acridone-producing novel type III polyketide synthase from H. serrata has been overexpressed in E. coli, purified and crystallized. Diffraction data have been collected to 2.0 Å. Polyketide synthase 1 (PKS1) from Huperzia serrata is a plant-specific type III polyketide synthase that shows an unusually versatile catalytic potential, producing various aromatic tetraketides, including chalcones, benzophenones, phlorogulucinols and acridones. Recombinant H. serrata PKS1 expressed in Escherichia coli was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group I222 or I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 73.3, b = 85.0, c = 137.7 Å, α = β = γ = 90.0°. Diffraction data were collected to 2.0 Å resolution using synchrotron radiation at BL24XU of SPring-8.

Effect of BaTiO3 Nanopowder Concentration on Rheological Behaviour of Ceramic Inkjet Inks

Science.gov (United States)

Kyrpal, R.; Dulina, I.; Ragulya, A.

2015-04-01

The relationship between rheological properties of ceramic inkjet inks based on BaTiO3 nanopowder and solid phase concentration has been investigated. In the ink volume takes place the formation periodic colloidal structures (PCS). The determining factor of structure formation is powder-dispersant ratio. Structural constitution of in the system with the low pigment concentration represented as PCS2, that contains solid particles in deflocculated that stabilized by the presence of adsorption-solvate layers. Dilatant structure formation for such inks explained by constrained conditions of the interaction. Samples with high BaTiO3 concentration have been classified as PKS1. Dilatant properties of the PKS1 resulted in particles rearrangement under the influence of the flow. In the region of some values powder-dispersant ratio take place conversation PKS2 to PKS1 and ink structure transformation from monodisperse to aggregate state.

Front line defenders of the ecological niche! Screening the structural diversity of peptaibiotics from saprotrophic and fungicolous Trichoderma/Hypocrea species

DEFF Research Database (Denmark)

Röhrich, Christian René; Jaklitsch, Walter Michael; Voglmayr, Hermann

2014-01-01

Approximately 950 individual sequences of nonribosomally biosynthesised peptides are produced by the genus Trichoderma/Hypocreathat belong to a perpetually growing class of mostly linear antibiotic oligopeptides, which are rich in the non-proteinogenic α-aminoisobutyric acid (Aib). Thus, they are......Approximately 950 individual sequences of nonribosomally biosynthesised peptides are produced by the genus Trichoderma/Hypocreathat belong to a perpetually growing class of mostly linear antibiotic oligopeptides, which are rich in the non-proteinogenic α-aminoisobutyric acid (Aib). Thus...

ClusterCAD: a computational platform for type I modular polyketide synthase design

DEFF Research Database (Denmark)

Eng, Clara H.; Backman, Tyler W. H.; Bailey, Constance B.

2018-01-01

barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify...

Urea adsorption by activated carbon prepared from palm kernel shell

Science.gov (United States)

Ooi, Chee-Heong; Sim, Yoke-Leng; Yeoh, Fei-Yee

2017-07-01

Dialysis treatment is crucial for patients suffer from renal failure. The dialysis system removes the uremic toxin to a safe level in a patient's body. One of the major limitations of the current hemodialysis system is the capability to efficiently remove uremic toxins from patient's body. Nanoporous materials can be applied to improve the treatment. Palm kernel shell (PKS) biomass generated from palm oil mills can be utilized to prepare high quality nanoporous activated carbon (AC) and applied for urea adsorption in the dialysis system. In this study, AC was prepared from PKS via different carbonization temperatures and followed by carbon dioxide gas activation processes. The physical and chemical properties of the samples were studied. The results show that the porous AC with BET surface areas ranging from 541 to 622 m2g-1 and with total pore volumes varying from 0.254 to 0.297 cm3g-1, are formed with different carbonization temperatures. The equilibrium constant for urea adsorption by AC samples carbonized at 400, 500 and 600 °C are 0.091, 0.287 and 0.334, respectively. The increase of carbonization temperatures from 400 to 600 °C resulted in the increase in urea adsorption by AC predominantly due to increase in surface area. The present study reveals the feasibility of preparing AC with good porosity from PKS and potentially applied in urea adsorption application.

Devolatilization studies of oil palm biomass for torrefaction process optimization

International Nuclear Information System (INIS)

Daud, D; Rahman, A Abd; Shamsuddin, A H

2013-01-01

Torrefaction of palm biomass, namely Empty Fruit Bunch (EFB) and Palm Kernel Shell (PKS), was conducted using thermogravimetric analyser (TGA). The experiment was conducted in variation of temperatures of 200 °C, 260 °C and 300 °C at a constant residence time of 30 minutes. During the torrefaction process, the sample went through identifiable drying and devolatilization stages from the TGA mass loss. The percentage of volatile gases released was then derived for each condition referring to proximate analysis results for both biomass. It was observed an average of 96.64% and 87.53 % of the total moisture is released for EFB and PKS respectively. In all cases the volatiles released was observed to increase as the torrefaction temperature was increased with significant variation between EFB and PKS. At 300°C EFB lost almost half of its volatiles matter while PKS lost slightly over one third. Results obtained can be used to optimise condition of torrefaction according to different types of oil palm biomass.

Use of Microdosing and Accelerator Mass Spectrometry To Evaluate the Pharmacokinetic Linearity of a Novel Tricyclic GyrB/ParE Inhibitor in Rats

Science.gov (United States)

Lao, Victoria; Ramos, Courtney L.; Ong, Voon S.; Turteltaub, Kenneth W.

2014-01-01

Determining the pharmacokinetics (PKs) of drug candidates is essential for understanding their biological fate. The ability to obtain human PK information early in the drug development process can help determine if future development is warranted. Microdosing was developed to assess human PKs, at ultra-low doses, early in the drug development process. Microdosing has also been used in animals to confirm PK linearity across subpharmacological and pharmacological dose ranges. The current study assessed the PKs of a novel antimicrobial preclinical drug candidate (GP-4) in rats as a step toward human microdosing studies. Dose proportionality was determined at 3 proposed therapeutic doses (3, 10, and 30 mg/kg of body weight), and PK linearity between a microdose and a pharmacological dose was assessed in Sprague-Dawley rats. Plasma PKs over the 3 pharmacological doses were proportional. Over the 10-fold dose range, the maximum concentration in plasma and area under the curve (AUC) increased 9.5- and 15.8-fold, respectively. PKs from rats dosed with a 14C-labeled microdose versus a 14C-labeled pharmacological dose displayed dose linearity. In the animals receiving a microdose and the therapeutically dosed animals, the AUCs from time zero to infinity were 2.6 ng · h/ml and 1,336 ng · h/ml, respectively, and the terminal half-lives were 5.6 h and 1.4 h, respectively. When the AUC values were normalized to a dose of 1.0 mg/kg, the AUC values were 277.5 ng · h/ml for the microdose and 418.2 ng · h/ml for the pharmacological dose. This 1.5-fold difference in AUC following a 300-fold difference in dose is considered linear across the dose range. On the basis of the results, the PKs from the microdosed animals were considered to be predictive of the PKs from the therapeutically dosed animals. PMID:25136019

Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles.

Science.gov (United States)

Liu, Lan; Salam, Nimaichand; Jiao, Jian-Yu; Jiang, Hong-Chen; Zhou, En-Min; Yin, Yi-Rui; Ming, Hong; Li, Wen-Jun

2016-07-01

The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited

Reserve Compensation System Study Supporting Papers. Volume 2. Deferred Compensation and Benefits

Science.gov (United States)

1978-06-01

rtfe REFERENCES &• «•«*■! SOrii CONO.. 2D PKSS.—CH. 70S—JUNK 20,1018 »•ili Midi standards nnd qualifications shall Iw determined perimli...consolidated veterans matters in title 38. In the codification , the expression "six months’ pay" was sub- stituted for "six months’ basic pay (plus

Genome-Wide Identification and Evolutionary Analysis of Sarcocystis neurona Protein Kinases.

Science.gov (United States)

Murungi, Edwin K; Kariithi, Henry M

2017-03-21

The apicomplexan parasite Sarcocystis neurona causes equine protozoal myeloencephalitis (EPM), a degenerative neurological disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions, such as host cell invasion, cell cycle progression and host immune response evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. We identified 97 putative PKs clustering within the various eukaryotic kinase groups. Although containing the universally-conserved PKA (AGC group), S. neurona kinome was devoid of PKB and PKC. Moreover, the kinome contains the six-conserved apicomplexan CDPKs (CAMK group). Several OPK atypical kinases, including ROPKs 19A, 27, 30, 33, 35 and 37 were identified. Notably, S. neurona is devoid of the virulence-associated ROPKs 5, 6, 18 and 38, as well as the Alpha and RIO kinases. Two out of the three S. neurona CK1 enzymes had high sequence similarities to Toxoplasma gondii TgCK1-α and TgCK1-β and the Plasmodium PfCK1. Further experimental studies on the S. neurona putative PKs identified in this study are required to validate the functional roles of the PKs and to understand their involvement in mechanisms that regulate various cellular processes and host-parasite interactions. Given the essentiality of apicomplexan PKs in the survival of apicomplexans, the current study offers a platform for future development of novel therapeutics for EPM, for instance via application of PK inhibitors to block parasite invasion and development in their host.

Genome-Wide Identification and Evolutionary Analysis of Sarcocystis neurona Protein Kinases

Directory of Open Access Journals (Sweden)

Edwin K. Murungi

2017-03-01

Full Text Available The apicomplexan parasite Sarcocystis neurona causes equine protozoal myeloencephalitis (EPM, a degenerative neurological disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs have been implicated in a myriad of critical functions, such as host cell invasion, cell cycle progression and host immune response evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans. We identified 97 putative PKs clustering within the various eukaryotic kinase groups. Although containing the universally-conserved PKA (AGC group, S. neurona kinome was devoid of PKB and PKC. Moreover, the kinome contains the six-conserved apicomplexan CDPKs (CAMK group. Several OPK atypical kinases, including ROPKs 19A, 27, 30, 33, 35 and 37 were identified. Notably, S. neurona is devoid of the virulence-associated ROPKs 5, 6, 18 and 38, as well as the Alpha and RIO kinases. Two out of the three S. neurona CK1 enzymes had high sequence similarities to Toxoplasma gondii TgCK1-α and TgCK1-β and the Plasmodium PfCK1. Further experimental studies on the S. neurona putative PKs identified in this study are required to validate the functional roles of the PKs and to understand their involvement in mechanisms that regulate various cellular processes and host-parasite interactions. Given the essentiality of apicomplexan PKs in the survival of apicomplexans, the current study offers a platform for future development of novel therapeutics for EPM, for instance via application of PK inhibitors to block parasite invasion and development in their host.

Bacterial growth laws reflect the evolutionary importance of energy efficiency.

Science.gov (United States)

Maitra, Arijit; Dill, Ken A

2015-01-13

We are interested in the balance of energy and protein synthesis in bacterial growth. How has evolution optimized this balance? We describe an analytical model that leverages extensive literature data on growth laws to infer the underlying fitness landscape and to draw inferences about what evolution has optimized in Escherichia coli. Is E. coli optimized for growth speed, energy efficiency, or some other property? Experimental data show that at its replication speed limit, E. coli produces about four mass equivalents of nonribosomal proteins for every mass equivalent of ribosomes. This ratio can be explained if the cell's fitness function is the the energy efficiency of cells under fast growth conditions, indicating a tradeoff between the high energy costs of ribosomes under fast growth and the high energy costs of turning over nonribosomal proteins under slow growth. This model gives insight into some of the complex nonlinear relationships between energy utilization and ribosomal and nonribosomal production as a function of cell growth conditions.

Diversity of Micromonospora strains from the deep Mediterranean Sea and their potential to produce bioactive compounds

Directory of Open Access Journals (Sweden)

Andrea Gärtner

2016-06-01

Full Text Available During studies on bacteria from the Eastern Mediterranean deep-sea, incubation under in situ conditions (salinity, temperature and pressure and heat treatment were used to selectively enrich representatives of Micromonospora. From sediments of the Ierapetra Basin (4400 m depth and the Herodotos Plain (2800 m depth, 21 isolates were identified as members of the genus Micromonospora. According to phylogenetic analysis of 16S rRNA gene sequences, the Micromonospora isolates could be assigned to 14 different phylotypes with an exclusion limit of ≥ 99.5% sequence similarity. They formed 7 phylogenetic clusters. Two of these clusters, which contain isolates obtained after enrichment under pressure incubation and phylogenetically are distinct from representative reference organism, could represent bacteria specifically adapted to the conditions in situ and to life in these deep-sea sediments. The majority of the Micromonospora isolates (90% contained at least one gene cluster for biosynthesis of secondary metabolites for non-ribosomal polypeptides and polyketides (polyketide synthases type I and type II. The determination of biological activities of culture extracts revealed that almost half of the strains produced substances inhibitory to the growth of Gram-positive bacteria. Chemical analyses of culture extracts demonstrated the presence of different metabolite profiles also in closely related strains. Therefore, deep-sea Micromonospora isolates are considered to have a large potential for the production of new antibiotic compounds.

Polyketide synthases from poison hemlock (Conium maculatum L.).

Science.gov (United States)

Hotti, Hannu; Seppänen-Laakso, Tuulikki; Arvas, Mikko; Teeri, Teemu H; Rischer, Heiko

2015-11-01

Coniine is a toxic alkaloid, the biosynthesis of which is not well understood. A possible route, supported by evidence from labelling experiments, involves a polyketide formed by the condensation of one acetyl-CoA and three malonyl-CoAs catalysed by a polyketide synthase (PKS). We isolated PKS genes or their fragments from poison hemlock (Conium maculatum L.) by using random amplification of cDNA ends (RACE) and transcriptome analysis, and characterized three full-length enzymes by feeding different starter-CoAs in vitro. On the basis of our in vitro experiments, two of the three characterized PKS genes in poison hemlock encode chalcone synthases (CPKS1 and CPKS2), and one encodes a novel type of PKS (CPKS5). We show that CPKS5 kinetically favours butyryl-CoA as a starter-CoA in vitro. Our results suggest that CPKS5 is responsible for the initiation of coniine biosynthesis by catalysing the synthesis of the carbon backbone from one butyryl-CoA and two malonyl-CoAs. © 2015 FEBS.

A chemical genetic approach to engineer phototropin kinases for substrate labeling.

Science.gov (United States)

Schnabel, Jonathan; Hombach, Peter; Waksman, Thomas; Giuriani, Giovanni; Petersen, Jan; Christie, John M

2018-04-13

Protein kinases (PKs) control many aspects of plant physiology by regulating signaling networks through protein phosphorylation. Phototropins (phots) are plasma membrane-associated serine/threonine PKs that control a range of physiological processes that collectively serve to optimize photosynthetic efficiency in plants. These include phototropism, leaf positioning and flattening, chloroplast movement, and stomatal opening. Despite their identification over two decades ago, only a handful of substrates have been identified for these PKs. Progress in this area has been hampered by the lack of a convenient means to confirm the identity of potential substrate candidates. Here we demonstrate that the kinase domain of Arabidopsis phot1 and phot2 can be successfully engineered to accommodate non-natural ATP analogues by substituting the bulky gatekeeper residue threonine for glycine. This approach circumvents the need for radioactivity to track phot kinase activity and follow light-induced receptor autophosphorylation in vitro by incorporating thiophosphate from N 6 -benzyl-ATPγS. Consequently, thiophosphorylation of phot substrate candidates can be readily monitored when added or co-expressed with phots in vitro Furthermore, gatekeeper-modified phot1 retained its functionality and its ability to accommodate N 6 -benzyl-ATPγS as a phosphodonor when expressed in Arabidopsis We therefore anticipate that this chemical genetic approach will provide new opportunities for labeling and identifying substrates for phots and other related AGC kinases under in vitro and near-native in vivo conditions. © 2018 Schnabel et al.

The importance of mass spectrometric dereplication in fungal secondary metabolite analysis

DEFF Research Database (Denmark)

Nielsen, Kristian Fog; Larsen, Thomas Ostenfeld

2015-01-01

Having entered the Genomic Era, it is now evident that the biosynthetic potential of filamentous fungi is much larger than was thought even a decade ago. Fungi harbor many cryptic gene clusters encoding for the biosynthesis of polyketides, non-ribosomal peptides, and terpenoids - which can all...... the importance of each stage of the process from sample preparation to chromatographic separation and finally toward both manual and more targeted methods for automated dereplication of fungal natural products using state-of-the art MS instrumentation....

Enhancement and prediction of modulus of elasticity of palm kernel shell concrete

International Nuclear Information System (INIS)

Alengaram, U. Johnson; Mahmud, Hilmi; Jumaat, Mohd Zamin

2011-01-01

Research highlights: → Micro-pores of size 16-24 μm were found on the outer surface of palm kernel shell. → Infilling of pores by mineral admixtures was evident. → Sand content influenced both modulus of elasticity and compressive strength. → Proposed equation predicts modulus of elasticity within ±1.5 kN/mm 2 of test results. -- Abstract: This paper presents results of an investigation conducted to enhance and predict the modulus of elasticity (MOE) of palm kernel shell concrete (PKSC). Scanning electron microscopic (SEM) analysis on palm kernel shell (PKS) was conducted. Further, the effect of varying sand and PKS contents and mineral admixtures (silica fume and fly ash) on compressive strength and MOE was investigated. The variables include water-to-binder (w/b) and sand-to-cement (s/c) ratios. Nine concrete mixes were prepared, and tests on static and dynamic moduli of elasticity and compressive strength were conducted. The SEM result showed presence of large number of micro-pores on PKS. The mineral admixtures uniformly filled the micro-pores on the outer surface of PKS. Further, the increase in sand content coupled with reduction in PKS content enhanced the compressive strength and static MOE: The highest MOE recorded in this investigation, 11 kN/mm 2 , was twice that previously published. Moreover, the proposed equation based on CEB/FIP code formula appears to predict the MOE close to the experimental values.

Compressive strength, flexural strength and water absorption of concrete containing palm oil kernel shell

Science.gov (United States)

Noor, Nurazuwa Md; Xiang-ONG, Jun; Noh, Hamidun Mohd; Hamid, Noor Azlina Abdul; Kuzaiman, Salsabila; Ali, Adiwijaya

2017-11-01

Effect of inclusion of palm oil kernel shell (PKS) and palm oil fibre (POF) in concrete was investigated on the compressive strength and flexural strength. In addition, investigation of palm oil kernel shell on concrete water absorption was also conducted. Total of 48 concrete cubes and 24 concrete prisms with the size of 100mm × 100mm × 100mm and 100mm × 100mm × 500mm were prepared, respectively. Four (4) series of concrete mix consists of coarse aggregate was replaced by 0%, 25%, 50% and 75% palm kernel shell and each series were divided into two (2) main group. The first group is without POF, while the second group was mixed with the 5cm length of 0.25% of the POF volume fraction. All specimen were tested after 7 and 28 days of water curing for a compression test, and flexural test at 28 days of curing period. Water absorption test was conducted on concrete cube age 28 days. The results showed that the replacement of PKS achieves lower compressive and flexural strength in comparison with conventional concrete. However, the 25% replacement of PKS concrete showed acceptable compressive strength which within the range of requirement for structural concrete. Meanwhile, the POF which should act as matrix reinforcement showed no enhancement in flexural strength due to the balling effect in concrete. As expected, water absorption was increasing with the increasing of PKS in the concrete cause by the porous characteristics of PKS

Production of Bioactive Secondary Metabolites by Marine Vibrionaceae

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Lone Gram

2011-08-01

Full Text Available Bacteria belonging to the Vibrionaceae family are widespread in the marine environment. Today, 128 species of vibrios are known. Several of them are infamous for their pathogenicity or symbiotic relationships. Despite their ability to interact with eukaryotes, the vibrios are greatly underexplored for their ability to produce bioactive secondary metabolites and studies have been limited to only a few species. Most of the compounds isolated from vibrios so far are non-ribosomal peptides or hybrids thereof, with examples of N-containing compounds produced independent of nonribosomal peptide synthetases (NRPS. Though covering a limited chemical space, vibrios produce compounds with attractive biological activities, including antibacterial, anticancer, and antivirulence activities. This review highlights some of the most interesting structures from this group of bacteria. Many compounds found in vibrios have also been isolated from other distantly related bacteria. This cosmopolitan occurrence of metabolites indicates a high incidence of horizontal gene transfer, which raises interesting questions concerning the ecological function of some of these molecules. This account underlines the pending potential for exploring new bacterial sources of bioactive compounds and the challenges related to their investigation.

Broad Substrate Specificity of the Loading Didomain of the Lipomycin Polyketide Synthase

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Yuzawa, S; Eng, CH; Katz, L; Keasling, JD

2013-06-04

LipPks1, a polyketide synthase subunit of the lipomycin synthase, is believed to catalyze the polyketide chain initiation reaction using isobutyryl-CoA as a substrate, followed by an elongation reaction with methylmalonyl-CoA to start the biosynthesis of antibiotic alpha-lipomycin in Streptomyces aureofaciens Tu117. Recombinant LipPks1, containing the thioesterase domain from the 6-deoxyerythronolide B synthase, was produced in Escherichia coli, and its substrate specificity was investigated in vitro. Surprisingly, several different acyl-CoAs, including isobutyryl-CoA, were accepted as the starter substrates, while no product was observed with acetyl-CoA. These results demonstrate the broad substrate specificity of LipPks1 and may be applied to producing new antibiotics.

Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin

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Li Weijun

2011-01-01

Full Text Available Abstract Background Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS to characterize potential protein-protein interactions in membrane fractions. Results Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins, which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane

Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin.

Science.gov (United States)

Zheng, Jianhua; Wei, Candong; Zhao, Lina; Liu, Liguo; Leng, Wenchuan; Li, Weijun; Jin, Qi

2011-01-18

Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS) to characterize potential protein-protein interactions in membrane fractions. Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins), which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane helixes were identified well in our work. In this

X-ray studies of BL Lacertae objects

International Nuclear Information System (INIS)

Madejski, G.M.

1986-01-01

This thesis presents spectral x-ray data for BL Lac objects observed by the IPC and MPC aboard the Einstein Observatory and interprets that data in a context of their overall radiation spectra using synchrotron and synchrotron self-Compton models. The objects considered are: OJ 287, PKS 0735 + 178, I Zw 186, PKS 0548-322, Mkn 180, BL Lacertae, PKS 2155-304, H 0414-009 and H 0323 + 022. X-ray spectra of BL Lac objects are well described by a power law model with a low energy cutoff due to absorption within the own Galaxy. The best fit values of the energy spectral index α in the IPC (0.2-4.0 keV) band range from 0.73 to 2.35, with a mean of 1.2 and rms spread of 0.51. No single, universal index can fit the spectra of all objects. For all objects except PKS 0735 + 178, the x-ray spectrum is an extrapolation of the infrared/optical UV spectrum; in PKS 0735 + 178, the x-ray spectrum lies significantly below such an extrapolation. The overall electromagnetic distribution in those objects is interpreted as arising due to the synchrotron process in at least two spatial regions, with sizes respectively ∼10 18 cm for the radio component and ∼10 16 cm for the optical component. In objects where the x-ray spectrum lies on the extrapolation of the infrared-optical-ultraviolet spectrum, the x-ray emission is interpreted also to be due to the synchrotron process

Physical Properties of Biomass Fuel Briquette from Oil Palm Residues

African Journals Online (AJOL)

Palm Kernel Shell (PKS) and Mesocarp Fibre (MF) were used for the production of fuel briquettes in this study in order to supplement the energy mix of the nation. PKS was pulverized and then sieved into different grain particles of 350 μm, 250 μm and 150 μm, before mixing with MF in the ratios: 90:10, 80:20 and 70:30 ...

Biosynthesis of fusarielins in Fusarium graminearum

DEFF Research Database (Denmark)

Saei, Wagma; Søndergaard, Teis; Giese, Henriette

Polyketide synthase 9 (PKS9) is one of the 15 identified polyketide synthase (PKS) genes in Fusarium graminearum. The gene is coregulated along with five neighboring genes by a single transcription factor (TF). An overexpression of the transcription factor led to production of three novel...... by this cluster in Fusarium graminearum., deletion mutant of each gene was created in the overexpressed mutant by targeted gene replacemen...

Targeted Disruption of Melanin Biosynthesis Genes in the Human Pathogenic Fungus Lomentospora prolificans and Its Consequences for Pathogen Survival.

Science.gov (United States)

Al-Laaeiby, Ayat; Kershaw, Michael J; Penn, Tina J; Thornton, Christopher R

2016-03-24

The dematiaceous (melanised) fungus Lomentospora (Scedosporium) prolificans is a life-threatening opportunistic pathogen of immunocompromised humans, resistant to anti-fungal drugs. Melanin has been shown to protect human pathogenic fungi against antifungal drugs, oxidative killing and environmental stresses. To determine the protective role of melanin in L. prolificans to oxidative killing (H₂O₂), UV radiation and the polyene anti-fungal drug amphotericin B, targeted gene disruption was used to generate mutants of the pathogen lacking the dihydroxynaphthalene (DHN)-melanin biosynthetic enzymes polyketide synthase (PKS1), tetrahydroxynapthalene reductase (4HNR) and scytalone dehydratase (SCD1). Infectious propagules (spores) of the wild-type strain 3.1 were black/brown, whereas spores of the PKS-deficient mutant ΔLppks1::hph were white. Complementation of the albino mutant ΔLppks1::hph restored the black-brown spore pigmentation, while the 4HNR-deficient mutant ΔLp4hnr::hph and SCD-deficient mutant ΔLpscd1::hph both produced orange-yellow spores. The mutants ΔLppks1::hph and ΔLp4hnr::hph showed significant reductions in spore survival following H₂O₂ treatment, while spores of ΔLpscd1::hph and the ΔLppks1::hph complemented strain ΔLppks1::hph:PKS showed spore survivals similar to strain 3.1. Spores of the mutants ΔLp4hnr::hph and ΔLpscd1::hph and complemented strain ΔLppks1::hph:PKS showed spore survivals similar to 3.1 following exposure to UV radiation, but survival of ΔLppks1::hph spores was significantly reduced compared to the wild-type strain. Strain 3.1 and mutants ΔLp4hnr::hph and ΔLppks1::hph:PKS were resistant to amphotericin B while, paradoxically, the PKS1- and SCD1-deficient mutants showed significant increases in growth in the presence of the antifungal drug. Taken together, these results show that while melanin plays a protective role in the survival of the pathogen to oxidative killing and UV radiation, melanin does not

Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters – Towards Identification of Novel Secondary Metabolisms from Filamentous Fungi -

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Myco eUmemura

2015-05-01

Full Text Available Secondary metabolites are produced mostly by clustered genes that are essential to their biosynthesis. The transcriptional expression of these genes is often cooperatively regulated by a transcription factor located inside or close to a cluster. Most of the secondary metabolism biosynthesis (SMB gene clusters identified to date contain so-called core genes with distinctive sequence features, such as polyketide synthase (PKS and non-ribosomal peptide synthetase (NRPS. Recent efforts in sequencing fungal genomes have revealed far more SMB gene clusters than expected based on the number of core genes in the genomes. Several bioinformatics tools have been developed to survey SMB gene clusters using the sequence motif information of the core genes, including SMURF and antiSMASH.More recently, accompanied by the development of sequencing techniques allowing to obtain large-scale genomic and transcriptomic data, motif-independent prediction methods of SMB gene clusters, including MIDDAS-M, have been developed. Most these methods detect the clusters in which the genes are cooperatively regulated at transcriptional levels, thus allowing the identification of novel SMB gene clusters regardless of the presence of the core genes. Another type of the method, MIPS-CG, uses the characteristics of SMB genes, which are highly enriched in non-syntenic blocks (NSBs, enabling the prediction even without transcriptome data although the results have not been evaluated in detail. Considering that large portion of SMB gene clusters might be sufficiently expressed only in limited uncommon conditions, it seems that prediction of SMB gene clusters by bioinformatics and successive experimental validation is an only way to efficiently uncover hidden SMB gene clusters. Here, we describe and discuss possible novel approaches for the determination of SMB gene clusters that have not been identified using conventional methods.

Cyclopiazonic acid biosynthesis in Aspergillus sp.: characterization of a reductase-like R* domain in cyclopiazonate synthetase that forms and releases cyclo-acetoacetyl-L-tryptophan.

Science.gov (United States)

Liu, Xinyu; Walsh, Christopher T

2009-09-15

The fungal neurotoxin alpha-cyclopiazonic acid (CPA), a nanomolar inhibitor of Ca2+-ATPase, has a pentacyclic indole tetramic acid scaffold that arises from one molecule of tryptophan, acetyl-CoA, malonyl-CoA, and dimethylallyl pyrophosphate by consecutive action of three enzymes, CpaS, CpaD, and CpaO. CpaS is a hybrid, two module polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) that makes and releases cyclo-acetoacetyl-L-tryptophan (cAATrp), the tetramic acid that serves as substrate for subsequent prenylation and oxidative cyclization to the five ring CPA scaffold. The NRPS module in CpaS has a predicted four-domain organization of condensation, adenylation, thiolation, and reductase* (C-A-T-R*), where R* lacks the critical Ser-Tyr-Lys catalytic triad of the short chain dehydrogenase/reductase (SDR) superfamily. By heterologous overproduction in Escherichia coli of the 56 kDa Aspergillus flavus CpaS TR* didomain and the single T and R* domains, we demonstrate that CpaS catalyzes a Dieckmann-type cyclization on the N-acetoacetyl-Trp intermediate bound in thioester linkage to the phosphopantetheinyl arm of the T domain to form and release cAATrp. This occurs without any participation of NAD(P)H, so R* does not function as a canonical SDR family member. Use of the T and R* domains in in trans assays enabled multiple turnovers and evaluation of specific mutants. Mutation of the D3803 residue in the R* domain, conserved in other fungal tetramate synthetases, abolished activity both in in trans and in cis (TR*) activity assays. It is likely that cyclization of beta-ketoacylaminoacyl-S-pantetheinyl intermediates to released tetramates represents a default cyclization/release route for redox-incompetent R* domains embedded in NRPS assembly lines.

Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes.

Science.gov (United States)

Valero-Jiménez, Claudio A; Faino, Luigi; Spring In't Veld, Daphne; Smit, Sandra; Zwaan, Bas J; van Kan, Jan A L

2016-12-01

Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence. A high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to the assemblies of the four other isolates. Whole genome analysis showed a high level of genetic diversity between the five isolates (2.85-16.8 SNPs/kb), which grouped into two distinct phylogenetic clusters. Mating type gene analysis revealed the presence of either the MAT1-1-1 or the MAT1-2-1 gene. Moreover, a putative new MAT gene (MAT1-2-8) was detected in the MAT1-2 locus. Comparative genome analysis revealed that Bb8028 contains 163 genes exclusive for this isolate. These unique genes have a tendency to cluster in the genome and to be often located near the telomeres. Among the genes unique to Bb8028 are a Non-Ribosomal Peptide Synthetase (NRPS) secondary metabolite gene cluster, a polyketide synthase (PKS) gene, and five genes with homology to bacterial toxins. A survey of candidate virulence genes for B. bassiana is presented. Our results indicate several genes and molecular processes that may underpin virulence towards mosquitoes. Thus, the genome sequences of five isolates of B. bassiana provide a better understanding of the natural variation in virulence and will offer a major resource for future research on this important biological control agent.

Genomic and metabolic traits endow Bacillus velezensis CC09 with a potential biocontrol agent in control of wheat powdery mildew disease.

Science.gov (United States)

Cai, Xun-Chao; Liu, Chang-Hong; Wang, Bao-Tong; Xue, Ya-Rong

2017-03-01

Bacillus velezensis CC09, which was isolated from healthy leaves of Cinnamomum camphora and previously identified as Bacillus amyloliquefaciens CC09, shows great potential as a new biocontrol agent, in control of many phytopathogenic diseases. To extend our understanding of the potential antifungal capacities, we did a whole genome analysis of strain CC09. Result shows that strain CC09 has a relatively large genome size (4.17Mb) with an average GC content of 46.1%, and 4021 predicted genes. Thirteen secondary metabolites encoding clusters have been identified within the genome of B. velezensis CC09 using genome mining technique. Data of comparative genomic analysis indicated that 3 of the clusters are conserved by all strains of B. velezensis, B. amyloliquefaciens and B. subtilis 168, 9 by B. velezensis and B. amyloliquefaciens, and 2 by all strains of B. velezensis. Another 2 clusters encoding NRPS (Non-Ribosomal Peptide Synthetases) and NRPS-TransATPKS (NRPS and trans-Acyl Transferase Polyketide Synthetases) respectively are observed only in 15 B. velezensis strains, which might lead to the synthesis of novel bioactive compounds and could be explored as antimicrobial agents in the future. These clusters endow B. velezensis CC09 with strong and broad antimicrobial activities, for example, in control of wheat powdery mildew disease. Moreover, our data further confirmed the taxonomy of strain CC09 is a member of B. velezensis rather than a strain of B. amyloliquefaciens based on core genome sequence analysis using phylogenomic approach. Copyright © 2016 Elsevier GmbH. All rights reserved.

Nonribosomal peptide synthesis in Bacillus subtilis

NARCIS (Netherlands)

Duitman, Erwin Hans

2003-01-01

Numerous microorganisms, both prokaryotes and eukaryotes, have developed various strategies, which enable them to adapt and survive the often adverse circumstances present in their natural environment ... Zie: Summary and general conclusions

A MULTIWAVELENGTH STUDY OF THREE HYBRID BLAZARS

Energy Technology Data Exchange (ETDEWEB)

Stanley, E. C.; Lister, M. L. [Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, IN 47907 (United States); Kharb, P. [Indian Institute of Astrophysics, II Block, Koramangala, Bangalore 560034 (India); Marshall, H. L. [Center for Space Research, Room NE80-6031, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); O’Dea, C.; Baum, S. [Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2 (Canada)

2015-07-01

We present multiwavelength imaging observations of PKS 1045−188, 8C 1849+670, and PKS 2216−038, three radio-loud active galactic nuclei from the MOJAVE-Chandra Sample that straddle the Fanaroff-Riley (FR) boundary between low- and high-power jets. These hybrid sources provide an excellent opportunity to study jet emission mechanisms and the influence of the external environment. We used archival VLA observations, and new Hubble and Chandra observations to identify and study the spectral properties of five knots in PKS 1045−188, two knots in 8C 1849+670, and three knots in PKS 2216−038. For the seven X-ray visible knots, we constructed and fit the broadband spectra using synchrotron and inverse Compton/cosmic microwave background (IC/CMB) emission models. In all cases, we found that the lack of detected optical emission ruled out the X-ray emission from the same electron population that produces radio emission. All three sources have high total extended radio power, similar to that of FR II sources. We find this is in good agreement with previously studied hybrid sources, where high-power hybrid sources emit X-rays via IC/CMB and the low-power hybrid sources emit X-rays via synchrotron emission. This supports the idea that it is total radio power rather than FR morphology that determines the X-ray emission mechanism. We found no significant asymmetries in the diffuse X-ray emission surrounding the host galaxies. Sources PKS 1045−188 and 8C 1849+670 show significant differences in their radio and X-ray termination points, which may result from the deceleration of highly relativistic bulk motion.

Melanisation of Aspergillus terreus—Is Butyrolactone I Involved in the Regulation of Both DOPA and DHN Types of Pigments in Submerged Culture?

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Elina K. Palonen

2017-05-01

Full Text Available Pigments and melanins of fungal spores have been investigated for decades, revealing important roles in the survival of the fungus in hostile environments. The key genes and the encoded enzymes for pigment and melanin biosynthesis have recently been found in Ascomycota, including Aspergillus spp. In Aspergillus terreus, the pigmentation has remained mysterious with only one class of melanin biogenesis being found. In this study, we examined an intriguing, partially annotated gene cluster of A. terreus strain NIH2624, utilizing previously sequenced transcriptome and improved gene expression data of strain MUCL 38669, under the influence of a suggested quorum sensing inducing metabolite, butyrolactone I. The core polyketide synthase (PKS gene of the cluster was predicted to be significantly longer on the basis of the obtained transcriptional data, and the surrounding cluster was positively regulated by butyrolactone I at the late growth phase of submerged culture, presumably during sporulation. Phylogenetic analysis of the extended PKS revealed remarkable similarity with a group of known pigments of Fusarium spp., indicating a similar function for this PKS. We present a hypothesis of this PKS cluster to biosynthesise a 1,8-dihydroxynaphthalene (DHN-type of pigment during sporulation with the influence of butyrolactone I under submerged culture.

Curved Walking Rehabilitation with a Rotating Treadmill in Patients with Parkinson’s Disease: A Proof of Concept

Science.gov (United States)

Godi, Marco; Giardini, Marica; Nardone, Antonio; Turcato, Anna Maria; Caligari, Marco; Pisano, Fabrizio; Schieppati, Marco

2017-01-01

Training subjects to step-in-place eyes open on a rotating platform while maintaining a fixed body orientation in space [podokinetic stimulation (PKS)] produces a posteffect consisting in inadvertent turning around while stepping-in-place eyes closed [podokinetic after-rotation (PKAR)]. Since the rationale for rehabilitation of curved walking in Parkinson’s disease is not fully known, we tested the hypothesis that repeated PKS favors the production of curved walking in these patients, who are uneasy with turning, even when straight walking is little affected. Fifteen patients participated in 10 training sessions distributed in 3 weeks. Both counterclockwise and clockwise PKS were randomly administered in each session. PKS velocity and duration were gradually increased over sessions. The velocity and duration of the following PKAR were assessed. All patients showed PKAR, which increased progressively in peak velocity and duration. In addition, before and at the end of the treatment, all patients walked overground along linear and circular trajectories. Post-training, the velocity of walking bouts increased, more so for the circular than the linear trajectory. Cadence was not affected. This study has shown that parkinsonian patients learn to produce turning while stepping when faced with appropriate training and that this capacity translates into improved overground curved walking. PMID:28293213

Investigation of the Antimicrobial Activity of Bacillus licheniformis Strains Isolated from Retail Powdered Infant Milk Formulae.

Science.gov (United States)

Alvarez-Ordóñez, Avelino; Begley, Máire; Clifford, Tanya; Deasy, Thérèse; Considine, Kiera; O'Connor, Paula; Ross, R Paul; Hill, Colin

2014-03-01

This study investigated the potential antimicrobial activity of ten Bacillus licheniformis strains isolated from retail infant milk formulae against a range of indicator (Lactococcus lactis, Lactobacillus bulgaricus and Listeria innocua) and clinically relevant (Listeria monocytogenes, Staphylococcus aureus, Streptococcus agalactiae, Salmonella Typhimurium and Escherichia coli) microorganisms. Deferred antagonism assays confirmed that all B. licheniformis isolates show antimicrobial activity against the Gram-positive target organisms. PCR and matrix-assisted laser desorption ionization time-of-flight mass spectrometry analyses indicated that four of the B. licheniformis isolates produce the bacteriocin lichenicidin. The remaining six isolates demonstrated a higher antimicrobial potency than lichenicidin-producing strains. Further analyses identified a peptide of ~1,422 Da as the most likely bioactive responsible for the antibacterial activity of these six isolates. N-terminal sequencing of the ~1,422 Da peptide from one strain identified it as ILPEITXIFHD. This peptide shows a high homology to the non-ribosomal peptides bacitracin and subpeptin, known to be produced by Bacillus spp. Subsequent PCR analyses demonstrated that the six B. licheniformis isolates may harbor the genetic machinery needed for the synthesis of a non-ribosomal peptide synthetase similar to those involved in production of subpeptin and bacitracin, which suggests that the ~1,422 Da peptide might be a variant of subpeptin and bacitracin.

Targeted Disruption of Melanin Biosynthesis Genes in the Human Pathogenic Fungus Lomentospora prolificans and Its Consequences for Pathogen Survival

Directory of Open Access Journals (Sweden)

Ayat Al-Laaeiby

2016-03-01

Full Text Available The dematiaceous (melanised fungus Lomentospora (Scedosporium prolificans is a life-threatening opportunistic pathogen of immunocompromised humans, resistant to anti-fungal drugs. Melanin has been shown to protect human pathogenic fungi against antifungal drugs, oxidative killing and environmental stresses. To determine the protective role of melanin in L. prolificans to oxidative killing (H2O2, UV radiation and the polyene anti-fungal drug amphotericin B, targeted gene disruption was used to generate mutants of the pathogen lacking the dihydroxynaphthalene (DHN-melanin biosynthetic enzymes polyketide synthase (PKS1, tetrahydroxynapthalene reductase (4HNR and scytalone dehydratase (SCD1. Infectious propagules (spores of the wild-type strain 3.1 were black/brown, whereas spores of the PKS-deficient mutant ΔLppks1::hph were white. Complementation of the albino mutant ΔLppks1::hph restored the black-brown spore pigmentation, while the 4HNR-deficient mutant ΔLp4hnr::hph and SCD-deficient mutant ΔLpscd1::hph both produced orange-yellow spores. The mutants ΔLppks1::hph and ΔLp4hnr::hph showed significant reductions in spore survival following H2O2 treatment, while spores of ΔLpscd1::hph and the ΔLppks1::hph complemented strain ΔLppks1::hph:PKS showed spore survivals similar to strain 3.1. Spores of the mutants ΔLp4hnr::hph and ΔLpscd1::hph and complemented strain ΔLppks1::hph:PKS showed spore survivals similar to 3.1 following exposure to UV radiation, but survival of ΔLppks1::hph spores was significantly reduced compared to the wild-type strain. Strain 3.1 and mutants ΔLp4hnr::hph and ΔLppks1::hph:PKS were resistant to amphotericin B while, paradoxically, the PKS1- and SCD1-deficient mutants showed significant increases in growth in the presence of the antifungal drug. Taken together, these results show that while melanin plays a protective role in the survival of the pathogen to oxidative killing and UV radiation, melanin does not

Biosynthetic mechanism for sunscreens of the biocontrol agent Lysobacter enzymogenes.

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Yan Wang

Full Text Available Lysobacter are ubiquitous environmental bacteria emerging as novel biocontrol agents and new sources of anti-infectives. So far, very little effort has been invested in the study of the biology of these Gram-negative gliding bacteria. Many Lysobacter species are characterized by their yellow-orange appearance. Using transposon mutagenesis, we identified a stand-alone polyketide synthase (PKS gene cluster required for the pigment production in L. enzymogenes OH11. The yellow pigments were abolished in the "white" mutants generated by target-specific deletions of ketosynthase (KS, acyl carrier protein, or ketoreductase. Spectroscopic data suggested that the pigments belong to xanthomonadin-like aryl polyenes. Polyene-type polyketides are known to be biosynthesized by modular PKS (Type I, not by stand-alone PKS (Type II which always contain the heterodimer KS-CLF (chain-length factor as the key catalytic component. Remarkably, this aryl polyene PKS complex only contains the KS (ORF17, but not the CLF. Instead, a hypothetical protein (ORF16 is located immediately next to ORF17. ORF16-17 homologs are widespread in numerous uncharacterized microbial genomes, in which an ORF17 homolog is always accompanied by an ORF16 homolog. The deletion of ORF16 eliminated pigment production, and homology modeling suggested that ORF16 shares a structural similarity to the N-terminal half of CLF. A point-mutation of glutamine (Q166A that is the conserved active site of known CLF abolished pigment production. The "white" mutants are significantly more sensitive to UV/visible light radiation or H2O2 treatment than the wild type. These results unveil the first example of Type II PKS-synthesized polyene pigments and show that the metabolites serve as Lysobacter "sunscreens" that are important for the survival of these ubiquitous environmental organisms.

Combustion characteristics of Malaysian oil palm biomass, sub-bituminous coal and their respective blends via thermogravimetric analysis (TGA).

Science.gov (United States)

Idris, Siti Shawalliah; Rahman, Norazah Abd; Ismail, Khudzir

2012-11-01

The combustion characteristics of Malaysia oil palm biomass (palm kernel shell (PKS), palm mesocarp fibre (PMF) and empty fruit bunches (EFB)), sub-bituminous coal (Mukah Balingian) and coal/biomass blends via thermogravimetric analysis (TGA) were investigated. Six weight ratios of coal/biomass blends were prepared and oxidised under dynamic conditions from temperature 25 to 1100°C at four heating rates. The thermogravimetric analysis demonstrated that the EFB and PKS evolved additional peak besides drying, devolatilisation and char oxidation steps during combustion. Ignition and burn out temperatures of blends were improved in comparison to coal. No interactions were observed between the coal and biomass during combustion. The apparent activation energy during this process was evaluated using iso-conversional model free kinetics which resulted in highest activation energy during combustion of PKS followed by PMF, EFB and MB coal. Blending oil palm biomass with coal reduces the apparent activation energy value. Copyright © 2012 Elsevier Ltd. All rights reserved.

Modeling of convective drying kinetics of Pistachio kernels in a fixed bed drying system

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Balbay Asım

2013-01-01

Full Text Available Drying kinetics of Pistachio kernels (PKs with initial moisture content of 32.4% (w.b was investigated as a function of drying conditions in a fixed bed drying system. The drying experiments were carried out at different temperatures of drying air (40, 60 and 80°C and air velocities (0.05, 0.075 and 0.1 m/s. Several experiments were performed in terms of mass of PKs (15g and 30g using a constant air velocity of 0.075 m/s. The fit quality of models was evaluated using the determination coefficient (R2, sum square error (SSE and root mean square error (RMSE. Among the selected models, the Midilli et al model was found to be the best models for describing the drying behavior of PKs. The activation energies were calculated as 29.2 kJ/mol and effective diffusivity values were calculated between 1.38 and 4.94x10-10 m2/s depending on air temperatures.

Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent.

Science.gov (United States)

Cochrane, Rachel V K; Sanichar, Randy; Lambkin, Gareth R; Reiz, Béla; Xu, Wei; Tang, Yi; Vederas, John C

2016-01-11

The antimalarial agent cladosporin is a nanomolar inhibitor of the Plasmodium falciparum lysyl-tRNA synthetase, and exhibits activity against both blood- and liver-stage infection. Cladosporin can be isolated from the fungus Cladosporium cladosporioides, where it is biosynthesized by a highly reducing (HR) and a non-reducing (NR) iterative type I polyketide synthase (PKS) pair. Genome sequencing of the host organism and subsequent heterologous expression of these enzymes in Saccharomyces cerevisiae produced cladosporin, confirming the identity of the putative gene cluster. Incorporation of a pentaketide intermediate analogue indicated a 5+3 assembly by the HR PKS Cla2 and the NR PKS Cla3 during cladosporin biosynthesis. Advanced-intermediate analogues were synthesized and incorporated by Cla3 to furnish new cladosporin analogues. A putative lysyl-tRNA synthetase resistance gene was identified in the cladosporin gene cluster. Analysis of the active site emphasizes key structural features thought to be important in resistance to cladosporin. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Actinobacterial diversity in limestone deposit sites in Hundung, Manipur (India and their antimicrobial activities

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Salam eNimaichand

2015-05-01

Full Text Available Studies on actinobacterial diversity in limestone habitats are scarce. This paper reports profiling of actinobacteria isolated from Hundung limestone samples in Manipur, India using ARDRA as the molecular tool for preliminary classification. A total of 137 actinobacteria were clustered into 31 phylotypic groups based on the ARDRA pattern generated and representative of each group was subjected to 16S rRNA gene sequencing. Generic diversity of the limestone isolates consisted of Streptomyces (15 phylotypic groups, Micromonospora (4, Amycolatopsis (3, Arthrobacter (3, Kitasatospora (2, Janibacter (1, Nocardia (1, Pseudonocardia (1 and Rhodococcus (1. Considering the antimicrobial potential of these actinobacteria, 19 showed antimicrobial activities against at least one of the bacterial and candidal test pathogens, while 45 exhibit biocontrol activities against at least one of the rice fungal pathogens. Out of the 137 actinobacterial isolates, 118 were found to have at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, NRPS. The results indicate that 86% of the strains isolated from Hundung limestone deposit sites possessed biosynthetic gene clusters of which 40% exhibited antimicrobial activities. It can, therefore, be concluded that limestone habitat is a promising source for search of novel secondary metabolites.

Identification and functional analysis of gene cluster involvement in biosynthesis of the cyclic lipopeptide antibiotic pelgipeptin produced by Paenibacillus elgii

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Qian Chao-Dong

2012-09-01

Full Text Available Abstract Background Pelgipeptin, a potent antibacterial and antifungal agent, is a non-ribosomally synthesised lipopeptide antibiotic. This compound consists of a β-hydroxy fatty acid and nine amino acids. To date, there is no information about its biosynthetic pathway. Results A potential pelgipeptin synthetase gene cluster (plp was identified from Paenibacillus elgii B69 through genome analysis. The gene cluster spans 40.8 kb with eight open reading frames. Among the genes in this cluster, three large genes, plpD, plpE, and plpF, were shown to encode non-ribosomal peptide synthetases (NRPSs, with one, seven, and one module(s, respectively. Bioinformatic analysis of the substrate specificity of all nine adenylation domains indicated that the sequence of the NRPS modules is well collinear with the order of amino acids in pelgipeptin. Additional biochemical analysis of four recombinant adenylation domains (PlpD A1, PlpE A1, PlpE A3, and PlpF A1 provided further evidence that the plp gene cluster involved in pelgipeptin biosynthesis. Conclusions In this study, a gene cluster (plp responsible for the biosynthesis of pelgipeptin was identified from the genome sequence of Paenibacillus elgii B69. The identification of the plp gene cluster provides an opportunity to develop novel lipopeptide antibiotics by genetic engineering.

How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae.

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Marvin Djukic

Full Text Available Paenibacillus larvae, a Gram positive bacterial pathogen, causes American Foulbrood (AFB, which is the most serious infectious disease of honey bees. In order to investigate the genomic potential of P. larvae, two strains belonging to two different genotypes were sequenced and used for comparative genome analysis. The complete genome sequence of P. larvae strain DSM 25430 (genotype ERIC II consisted of 4,056,006 bp and harbored 3,928 predicted protein-encoding genes. The draft genome sequence of P. larvae strain DSM 25719 (genotype ERIC I comprised 4,579,589 bp and contained 4,868 protein-encoding genes. Both strains harbored a 9.7 kb plasmid and encoded a large number of virulence-associated proteins such as toxins and collagenases. In addition, genes encoding large multimodular enzymes producing nonribosomally peptides or polyketides were identified. In the genome of strain DSM 25719 seven toxin associated loci were identified and analyzed. Five of them encoded putatively functional toxins. The genome of strain DSM 25430 harbored several toxin loci that showed similarity to corresponding loci in the genome of strain DSM 25719, but were non-functional due to point mutations or disruption by transposases. Although both strains cause AFB, significant differences between the genomes were observed including genome size, number and composition of transposases, insertion elements, predicted phage regions, and strain-specific island-like regions. Transposases, integrases and recombinases are important drivers for genome plasticity. A total of 390 and 273 mobile elements were found in strain DSM 25430 and strain DSM 25719, respectively. Comparative genomics of both strains revealed acquisition of virulence factors by horizontal gene transfer and provided insights into evolution and pathogenicity.

How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae.

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Djukic, Marvin; Brzuszkiewicz, Elzbieta; Fünfhaus, Anne; Voss, Jörn; Gollnow, Kathleen; Poppinga, Lena; Liesegang, Heiko; Garcia-Gonzalez, Eva; Genersch, Elke; Daniel, Rolf

2014-01-01

Paenibacillus larvae, a Gram positive bacterial pathogen, causes American Foulbrood (AFB), which is the most serious infectious disease of honey bees. In order to investigate the genomic potential of P. larvae, two strains belonging to two different genotypes were sequenced and used for comparative genome analysis. The complete genome sequence of P. larvae strain DSM 25430 (genotype ERIC II) consisted of 4,056,006 bp and harbored 3,928 predicted protein-encoding genes. The draft genome sequence of P. larvae strain DSM 25719 (genotype ERIC I) comprised 4,579,589 bp and contained 4,868 protein-encoding genes. Both strains harbored a 9.7 kb plasmid and encoded a large number of virulence-associated proteins such as toxins and collagenases. In addition, genes encoding large multimodular enzymes producing nonribosomally peptides or polyketides were identified. In the genome of strain DSM 25719 seven toxin associated loci were identified and analyzed. Five of them encoded putatively functional toxins. The genome of strain DSM 25430 harbored several toxin loci that showed similarity to corresponding loci in the genome of strain DSM 25719, but were non-functional due to point mutations or disruption by transposases. Although both strains cause AFB, significant differences between the genomes were observed including genome size, number and composition of transposases, insertion elements, predicted phage regions, and strain-specific island-like regions. Transposases, integrases and recombinases are important drivers for genome plasticity. A total of 390 and 273 mobile elements were found in strain DSM 25430 and strain DSM 25719, respectively. Comparative genomics of both strains revealed acquisition of virulence factors by horizontal gene transfer and provided insights into evolution and pathogenicity.

Production of novel fusarielins by ectopic activation of the polyketide synthase 9 cluster in Fusarium graminearum

DEFF Research Database (Denmark)

Sørensen, Jens Laurids; Hansen, Frederik Teilfeldt; Sondergaard, Teis Esben

2012-01-01

specific transcription factors. We have developed a system in which an expression cassette containing the transcription factor from the targeted PKS cluster disrupts the production of the red mycelium pigment aurofusarin. This aids with identification of mutants as they appear as white colonies...... and metabolite analyses where aurofusarin and its intermediates are normally among the most abundant compounds. The system was used for constitutive expression of the local transcription factor from the PKS9 cluster (renamed FSL) leading to production of three novel fusarielins, F, G and H. This group...

RADIO-LOUD NARROW-LINE SEYFERT 1 AS A NEW CLASS OF GAMMA-RAY ACTIVE GALACTIC NUCLEI

International Nuclear Information System (INIS)

Abdo, A. A.; Ackermann, M.; Ajello, M.; Bechtol, K.; Berenji, B.; Bloom, E. D.; Borgland, A. W.; Cameron, R. A.; Baldini, L.; Bellazzini, R.; Bregeon, J.; Brez, A.; Ballet, J.; Barbiellini, G.; Bastieri, D.; Bonamente, E.; Brigida, M.; Bruel, P.; Burnett, T. H.; Caliandro, G. A.

2009-01-01

We report the discovery with Fermi/LAT of γ-ray emission from three radio-loud narrow-line Seyfert 1 galaxies: PKS 1502+036 (z = 0.409), 1H 0323+342 (z = 0.061), and PKS 2004 - 447 (z = 0.24). In addition to PMN J0948+0022 (z = 0.585), the first source of this type to be detected in γ rays, they may form an emerging new class of γ-ray active galactic nuclei (AGNs). These findings can have strong implications on our knowledge about relativistic jets and the unified model of the AGN.

Diversity and Impact of Prokaryotic Toxins on Aquatic Environments: A Review

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Rogério Tenreiro

2010-10-01

Full Text Available Microorganisms are ubiquitous in all habitats and are recognized by their metabolic versatility and ability to produce many bioactive compounds, including toxins. Some of the most common toxins present in water are produced by several cyanobacterial species. As a result, their blooms create major threats to animal and human health, tourism, recreation and aquaculture. Quite a few cyanobacterial toxins have been described, including hepatotoxins, neurotoxins, cytotoxins and dermatotoxins. These toxins are secondary metabolites, presenting a vast diversity of structures and variants. Most of cyanobacterial secondary metabolites are peptides or have peptidic substructures and are assumed to be synthesized by non-ribosomal peptide synthesis (NRPS, involving peptide synthetases, or NRPS/PKS, involving peptide synthetases and polyketide synthases hybrid pathways. Besides cyanobacteria, other bacteria associated with aquatic environments are recognized as significant toxin producers, representing important issues in food safety, public health, and human and animal well being. Vibrio species are one of the most representative groups of aquatic toxin producers, commonly associated with seafood-born infections. Some enterotoxins and hemolysins have been identified as fundamental for V. cholerae and V. vulnificus pathogenesis, but there is evidence for the existence of other potential toxins. Campylobacter spp. and Escherichia coli are also water contaminants and are able to produce important toxins after infecting their hosts. Other bacteria associated with aquatic environments are emerging as toxin producers, namely Legionella pneumophila and Aeromonas hydrophila, described as responsible for the synthesis of several exotoxins, enterotoxins and cytotoxins. Furthermore, several Clostridium species can produce potent neurotoxins. Although not considered aquatic microorganisms, they are ubiquitous in the environment and can easily contaminate drinking

Cyclic Lipopeptides of Bacillus amyloliquefaciens subsp. plantarum Colonizing the Lettuce Rhizosphere Enhance Plant Defense Responses Toward the Bottom Rot Pathogen Rhizoctonia solani.

Science.gov (United States)

Chowdhury, Soumitra Paul; Uhl, Jenny; Grosch, Rita; Alquéres, Sylvia; Pittroff, Sabrina; Dietel, Kristin; Schmitt-Kopplin, Philippe; Borriss, Rainer; Hartmann, Anton

2015-09-01

The commercially available inoculant Bacillus amyloliquefaciens FZB42 is able to considerably reduce lettuce bottom rot caused by Rhizoctonia solani. To understand the interaction between FZB42 and R. solani in the rhizosphere of lettuce, we used an axenic system with lettuce bacterized with FZB42 and inoculated with R. solani. Confocal laser scanning microscopy showed that FZB42 could delay the initial establishment of R. solani on the plants. To show which secondary metabolites of FZB42 are produced under these in-situ conditions, we developed an ultra-high performance liquid chromatography coupled to time of flight mass spectrometry-based method and identified surfactin, fengycin, and bacillomycin D in the lettuce rhizosphere. We hypothesized that lipopeptides and polyketides play a role in enhancing the plant defense responses in addition to the direct antagonistic effect toward R. solani and used a quantitative real-time polymerase chain reaction-based assay for marker genes involved in defense signaling pathways in lettuce. A significant higher expression of PDF 1.2 observed in the bacterized plants in response to subsequent pathogen challenge showed that FZB42 could enhance the lettuce defense response toward the fungal pathogen. To identify if surfactin or other nonribosomally synthesized secondary metabolites could elicit the observed enhanced defense gene expression, we examined two mutants of FZB42 deficient in production of surfactin and the lipopetides and polyketides, by expression analysis and pot experiments. In the absence of surfactin and other nonribosomally synthesized secondary metabolites, there was no enhanced PDF 1.2-mediated response to the pathogen challenge. Pot experiment results showed that the mutants failed to reduce disease incidence in lettuce as compared with the FZB42 wild type, indicating, that surfactin as well as other nonribosomally synthesized secondary metabolites play a role in the actual disease suppression and on lettuce

Antagonistic activity of Ocimum sanctum L. essential oil on growth and zearalenone production by Fusarium graminearum in maize grains

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Naveen Kumar eKalagatur

2015-09-01

Full Text Available The present study was aimed to establish the antagonistic effects of Ocimum sanctum L. essential oil (OSEO on growth and zearalenone (ZEA production of Fusarium graminearum. GC-MS chemical profiling of OSEO revealed the existence of 43 compounds and the major compound was found to be eugenol (34.7%. DPPH free radical scavenging activity (IC50 of OSEO was determined to be 8.5µg/mL. Minimum inhibitory concentration (MIC and minimum fungicidal concentration (MFC of OSEO on F. graminearum were recorded as 1250 µg/mL and 1800 µg/mL, respectively. Scanning electron microscope observations showed significant micro morphological damage in OSEO exposed mycelia and spores compared to untreated control culture. Quantitative UHPLC studies revealed that OSEO negatively effected the production of ZEA; the concentration of toxin production was observed to be insignificant at 1500 µg/mL concentration of OSEO. On other hand ZEA concentration was quantified as 3.23 µg/mL in OSEO untreated control culture. Reverse transcriptase qPCR analysis of ZEA metabolic pathway genes (PKS4 and PKS13 revealed that increase in OSEO concentration (250 µg/mL to 1500 µg/mL significantly downregulated the expression of PKS4 and PKS13. These results were in agreement with the artificially contaminated maize grains as well. In conlusion, the antifungal and antimycotoxic effects of OSEO on F. graminearum in the present study reiterated that, the essential oil of O. sanctum could be a promising herbal fungicide in food processing industries as well as grain storage centers.

ORF Alignment: NC_003888 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available tide synthetase [Actinoplanes teichomyceticus] ... Length = 427 ... Query: 12 ... LSPLQEGMLFHNLFDEEELDAYNVQ... NC_003888 gi|32141196 >1l5aA 1 423 12 438 2e-57 ... emb|CAE53352.1| non-ribosomal pep

Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge.

Science.gov (United States)

Martins, Joana; Vasconcelos, Vitor

2015-11-13

Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential.

Study and modeling of the most energetic Active Galactic Nuclei with the Fermi satellite; Etude et modelisation des noyaux actifs de galaxie les plus energetiques avec le satellite Fermi

Energy Technology Data Exchange (ETDEWEB)

Sanchez, D.

2010-06-15

The Fermi satellite was launched in June 2008. The onboard LAT detector is dedicated to the study of galactic and extra-galactic gamma sources with an energy comprised between 200 MeV and 300 GeV. 1451 sources have been detected in less than 11 months. This document is divided into 6 chapters: 1) gamma astronomy, 2) the Fermi satellite, 3) the active galactic nuclei (NAG), 4) the observation of several blazars (PKS-2155-304 and PG-1553+113) and its simulation, 5) the observation of PKS-2155-304 with both RXTE and Fermi, and 6) conclusion

Study and modeling of the most energetic Active Galactic Nuclei with the Fermi satellite

International Nuclear Information System (INIS)

Sanchez, D.

2010-06-01

The Fermi satellite was launched in June 2008. The onboard LAT detector is dedicated to the study of galactic and extra-galactic gamma sources with an energy comprised between 200 MeV and 300 GeV. 1451 sources have been detected in less than 11 months. This document is divided into 6 chapters: 1) gamma astronomy, 2) the Fermi satellite, 3) the active galactic nuclei (NAG), 4) the observation of several blazars (PKS-2155-304 and PG-1553+113) and its simulation, 5) the observation of PKS-2155-304 with both RXTE and Fermi, and 6) conclusion

[Expression of enterotoxigenic Bacteroides fragilis and polyketide synthase gene-expressing Escherichia coli in colorectal adenoma patients].

Science.gov (United States)

Xie, L L; Wu, N; Zhu, Y M; Qiu, X Y; Chen, G D; Zhang, L M; Liu, Y L

2016-03-29

To investigate the distribution of various bacteria in adenoma tissue of colorectal adenoma (T/CRA), normal colonic mucosa tissue adjacent to the adenoma (N/CRA), and healthy colonic mucosa tissue (N/H) by comparing the number of total bacteria, Bacteroides fragilis (BF), enterotoxigenic Bacteroides fragilis (ETBF), polyketide synthase (pks) gene-expressing Escherichia coli(E.coli)(pks(+) E. coli)among the above 3 types of tissues. A total of 36 patients diagnosed with colorectal adenoma by colonoscopy and pathology in Department of Gastroenterology, Peking University People's Hospital from September 2011 to September 2013 were selected into this study. T/CRA and N/CRA tissues from the 36 patients and N/H tissues from 18 healthy controls were collected for DNA extraction. The number of total bacteria, BF, ETBF, pks(+) E. coli was detected by quantitative real time PCR, and their correlation with colorectal adenoma was analyzed. (1) The number of total bacteria decreased gradually from N/H, N/CRA, to T/CRA, with the median values being 3.18×10(8,) 1.57×10(8,) and 7.91×10(7) copies/g, respectively, and with significant difference among the three groups and between each two groups (all PCRA, to T/CRA, the median values being 6.03×10(5,) 4.28×10(4,) and 5.48×10(3) copies/g, respectively, and with significant difference among the three groups and between each two groups (all PCRA, to T/CRA, the relative expression being 1.73±0.30, 6.15±1.52, and 8.54±1.80, respectively. Significant difference was found between the T/CRA and N/H tissue (P=0.003), but not between any other two groups. (4) The expression of clbB in pks(+) E.coli was highest in T/CRA colonic tissue (2.96±0.28), followed by the N/CRA (2.79±0.19) and N/H tissue (1.06±0.08). Significant difference was found between T/CRA and N/H tissues, as well as between N/CRA and N/H tissues (both PCRA and N/CRA tissues. The number of total bacteria is markedly reduced in the colonic mucosa of CRA patients

Growth Promotion and Disease Suppression Ability of a Streptomyces sp. CB-75 from Banana Rhizosphere Soil

Science.gov (United States)

Chen, Yufeng; Zhou, Dengbo; Qi, Dengfeng; Gao, Zhufen; Xie, Jianghui; Luo, Yanping

2018-01-01

An actinomycete strain, CB-75, was isolated from the soil of a diseased banana plantation in Hainan, China. Based on phenotypic and molecular characteristics, and 99.93% sequence similarity with Streptomyces spectabilis NBRC 13424 (AB184393), the strain was identified as Streptomyces sp. This strain exhibited broad-spectrum antifungal activity against 11 plant pathogenic fungi. Type I polyketide synthase (PKS-I) and non-ribosomal peptide synthetase (NRPS) were detected, which were indicative of the antifungal compounds that Streptomyces sp. CB-75 could produce. An ethyl acetate extract from the strain exhibited the lowest minimum inhibitory concentration (MIC) against Colletotrichum musae (ATCC 96167) (0.78 μg/ml) and yielded the highest antifungal activity against Colletotrichum gloeosporioides (ATCC 16330) (50.0 μg/ml). Also, spore germination was significantly inhibited by the crude extract. After treatment with the crude extract of Streptomyces sp. CB-75 at the concentration 2 × MIC, the pathogenic fungi showed deformation, shrinkage, collapse, and tortuosity when observed by scanning electron microscopy (SEM). By gas chromatography-mass spectrometry (GC-MS) of the crude extract, 18 chemical constituents were identified; (Z)-13-docosenamide was the major constituent. Pot experiments showed that the incidence of banana seedlings was reduced after using Streptomyces sp. CB-75 treatment. The disease index was 10.23, and the prevention and control effect was 83.12%. Furthermore, Streptomyces sp. CB-75 had a growth-promoting effect on banana plants. The chlorophyll content showed 88.24% improvement, the leaf area, root length, root diameter, plant height, and stem showed 88.24, 90.49, 136.17, 61.78, and 50.98% improvement, respectively, and the shoot fresh weight, root fresh weight, shoot dry weight, and root dry weight showed 82.38, 72.01, 195.33, and 113.33% improvement, respectively, compared with treatment of fermentation broth without Streptomyces sp. CB-75

The kinome of Phytophthora infestans reveals oomycete-specific innovations and links to other taxonomic groups

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Ah-Fong Audrey MV

2010-12-01

Full Text Available Abstract Background Oomycetes are a large group of economically and ecologically important species. Its most notorious member is Phytophthora infestans, the cause of the devastating potato late blight disease. The life cycle of P. infestans involves hyphae which differentiate into spores used for dispersal and host infection. Protein phosphorylation likely plays crucial roles in these stages, and to help understand this we present here a genome-wide analysis of the protein kinases of P. infestans and several relatives. The study also provides new insight into kinase evolution since oomycetes are taxonomically distant from organisms with well-characterized kinomes. Results Bioinformatic searches of the genomes of P. infestans, P. ramorum, and P. sojae reveal they have similar kinomes, which for P. infestans contains 354 eukaryotic protein kinases (ePKs and 18 atypical kinases (aPKs, equaling 2% of total genes. After refining gene models, most were classifiable into families seen in other eukaryotes. Some ePK families are nevertheless unusual, especially the tyrosine kinase-like (TKL group which includes large oomycete-specific subfamilies. Also identified were two tyrosine kinases, which are rare in non-metazoans. Several ePKs bear accessory domains not identified previously on kinases, such as cyclin-dependent kinases with integral cyclin domains. Most ePKs lack accessory domains, implying that many are regulated transcriptionally. This was confirmed by mRNA expression-profiling studies that showed that two-thirds vary significantly between hyphae, sporangia, and zoospores. Comparisons to neighboring taxa (apicomplexans, ciliates, diatoms revealed both clade-specific and conserved features, and multiple connections to plant kinases were observed. The kinome of Hyaloperonospora arabidopsidis, an oomycete with a simpler life cycle than P. infestans, was found to be one-third smaller. Some differences may be attributable to gene clustering, which

Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone.

Energy Technology Data Exchange (ETDEWEB)

Chiang, Yi Ming; Meyer, Kristen M; Praseuth, Michael; Baker, Scott E; Bruno, Kenneth S; Wang, Clay C

2010-12-06

The genome sequencing of the fungus Aspergillus niger, an industrial workhorse, uncovered a large cache of genes encoding enzymes thought to be involved in the production of secondary metabolites yet to be identified. Identification and structural characterization of many of these predicted secondary metabolites are hampered by their low concentration relative to the known A. niger metabolites such as the naphtho-γ-pyrone family of polyketides. We deleted a nonreducing PKS gene in A. niger strain ATCC 11414, a daughter strain of A. niger ATCC strain 1015 whose genome was sequenced by the DOE Joint Genome Institute. This PKS encoding gene is a predicted ortholog of alb1 from Aspergillus fumigatus which is responsible for production of YWA1, a precursor of fungal DHN melanin. Our results show that the A. niger alb1 PKS is responsible for the production of the polyketide precursor for DHN melanin biosynthesis. Deletion of alb1 elimnates the production of major metabolites, naphtho-γ-pyrones. The generation of an A. niger strain devoid of naphtho-γ-pyrones will greatly facilitate the elucidation of cryptic biosynthetic pathways in this organism.

Effect of Reinforced Hybrid Palm Shells on Mechanical Properties of Polyurethane-Jute Woven/ Vinyl Ester Sandwich Board

International Nuclear Information System (INIS)

Cheng, T.S.; Nurul Ain Nanyan; Lan, D.N.U.; Leng, T.P.

2014-01-01

A natural fiber sandwich was constructed from palm shells/polyurethane core and jute woven/vinyl ester face sheets by the in-situ sandwich process (core and panel prepared simultaneously). The polyurethane sandwich core was reinforced by hybrid shell systems of dried palm shell (DPS) and palm kernel shell (PKS) (50P-50D, 25P-75D), and single shell system of PKS (100P) as well as 20 phr empty fruit bunch (EFB) based on hundred part of polyurethane. The sandwich face sheets are prepared by using two jute woven layers and impregnated by vinyl ester. Interlocking between DPS and polyurethane matrix was formed, which hence enhanced the mechanical properties. The interfacial adhesion between DPS, PKS, and EFB with the polyurethane binder played the important role to achieve high mechanical properties. It was found that hybrid shells exhibited high reinforcement for sandwich's performance resulting better compression (50P-50D) and flexural (25P-75D) properties. The single shell 100P showed only improvement on flexural modulus.The fracture surface morphology of sandwich under mechanical test was performed by using optical microscopy. (author)

ORF Alignment: NC_000964 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available HTH-type ... transcriptional regulator pksA ... Length = 182 ... Query: 8 ... EKRRKQIAEATWRVILERGME...GASARNIAKEAGLSLGALRHYFSTQDELLAFAMKLVQEK 67 ... EKRRKQIAEATWRVILERGMEGASARNIAKEAGLSLGALRHYFSTQDELLAFAM...KLVQEK Sbjct: 1 ... EKRRKQIAEATWRVILERGMEGASARNIAKEAGLSLGALRHYFSTQDELLAFAMKLVQEK 60

Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages.

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Christine N Shulse

Full Text Available Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs, such as eicosapentaenoic acid (EPA, 20:5n-3 and docosahexaenoic acid (DHA, 22:6n-3, is constrained to a narrow subset of marine γ-proteobacteria. The genes responsible for de novo bacterial PUFA biosynthesis, designated pfaEABCD, encode large, multi-domain protein complexes akin to type I iterative fatty acid and polyketide synthases, herein referred to as "Pfa synthases". In addition to the archetypal Pfa synthase gene products from marine bacteria, we have identified homologous type I FAS/PKS gene clusters in diverse microbial lineages spanning 45 genera representing 10 phyla, presumed to be involved in long-chain fatty acid biosynthesis. In total, 20 distinct types of gene clusters were identified. Collectively, we propose the designation of "secondary lipids" to describe these biosynthetic pathways and products, a proposition consistent with the "secondary metabolite" vernacular. Phylogenomic analysis reveals a high degree of functional conservation within distinct biosynthetic pathways. Incongruence between secondary lipid synthase functional clades and taxonomic group membership combined with the lack of orthologous gene clusters in closely related strains suggests horizontal gene transfer has contributed to the dissemination of specialized lipid biosynthetic activities across disparate microbial lineages.

GliZ, a transcriptional regulator of gliotoxin in Aspergillus fumigatus

DEFF Research Database (Denmark)

Bok, J.W.; Chung, D.W.; Balajee, A.

2006-01-01

Gliotoxin is a nonribosomal peptide produced by Aspergillus fumigatus. This compound has been proposed as an A. fumigatus virulence factor due to its cytotoxic, genotoxic, and apoptotic properties. Recent identification of the gliotoxin gene cluster identified several genes (gli genes) likely inv...

Draft Genome Sequence of Pseudomonas sp. Strain In5 Isolated from a Greenlandic Disease Suppressive Soil with Potent Antimicrobial Activity

DEFF Research Database (Denmark)

Hennessy, Rosanna C.; Glaring, Mikkel Andreas; Frydenlund Michelsen, Charlotte

2015-01-01

Pseudomonas sp. In5 is an isolate of disease suppressive soil with potent activity against pathogens. Its antifungal activity has been linked to a gene cluster encoding nonribosomal peptide synthetases producing the peptides nunamycin and nunapeptin. The genome sequence will provide insight into ...

Methyl Effect in Azumamides Provides Insight Into Histone Deacetylase Inhibition by Macrocycles

DEFF Research Database (Denmark)

Maolanon, Alex; Villadsen, Jesper; Christensen, Niels Johan

2014-01-01

Natural, nonribosomal cyclotetrapeptides have traditionally been a rich source of inspiration for design of potent histone deacetylase (HDAC) inhibitors. We recently disclosed the total synthesis and full HDAC pro fi ling of the naturally occurring azumamides ( J. Med. Chem. 2013 , 56 , 6512...

Biosynthesis: Reprogramming assembly lines

Science.gov (United States)

Menon, Binuraj R. K.; Jenner, Matthew

2018-03-01

Rational engineering of biosynthetic assembly lines for production of new compounds is an attractive prospect, yet it presents many challenges. Learning from biology, some of the rules for expanding the chemical diversity of non-ribosomal peptides have been uncovered in two recent studies.

The cyanobacterial metabolite nocuolin A is a natural oxadiazine that triggers apoptosis in human cancer cells

Czech Academy of Sciences Publication Activity Database

Voráčová, K.; Hájek, J.; Mareš, Jan; Urajová, P.; Kuzma, M.; Cheel, J.; Villunger, A.; Kapuscik, A.; Bally, M.; Novák, P.; Kabeláč, M.; Krumschnabel, G.; Lukeš, M.; Voloshko, L.; Kopecký, J.; Hrouzek, P.

2017-01-01

Roč. 12, č. 3 (2017), č. článku e0172850. E-ISSN 1932-6203 Institutional support: RVO:67985939 Keywords : secondary metabolite * cancer * non-ribosomal synthetase Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.806, year: 2016

Evaluating oil palm fresh fruit bunch processing in Nigeria.

Science.gov (United States)

Anyaoha, Kelechi E; Sakrabani, Ruben; Patchigolla, Kumar; Mouazen, Abdul M

2018-03-01

Three routes of oil palm fresh fruit bunch (FFB) processing in Nigeria namely, industrial, small-scale and traditional were compared by means of determining fruit losses associated with each route. The fruits that are not recovered after each process were hand-picked and quantified in terms of crude palm oil (CPO), palm kernel (PK), mesocarp fibre (MF) and palm kernel shell (PKS). The energy value of empty fruit bunch (EFB), MF and PKS were used to determine the value of energy lost for each route. Additionally, the environmental implications of disposal of EFB were estimated, and socio-economics of the industrial and small-scale routes were related. The analysis showed that 29, 18, 75 and 27 kg of CPO, PK, MF and PKS were lost for every 1000 kg of FFB processed with the industrial route, whereas 5.6, 3.2, 1.4 and 5.1 g were lost with the small-scale route, respectively. Approximately 89 kWh and 31 kWh more energy were lost from MF and PKS with the industrial route than the other two routes, respectively. An equivalent of 6670 tonnes carbon dioxide equivalent of methane and nitrogen oxide was released due to the disposal of 29,000 tonnes of EFB from one palm oil mill. The monetary value of lost CPO per 1000 kg of FFB processed in the industrial route is more than the labour cost of processing 1000 kg of FFB in the small-scale route. The advantages of the industrial route are high throughput in terms of FFB processed per hour and high quality of CPO; however, high fruit loss is associated with it and therefore, the poorly threshed EFB is recommended to be fed into the small-scale route.

Elucidation of the biosynthetic pathway for the production of the pigment chrysogine by Penicillium chrysogenum

NARCIS (Netherlands)

Viggiano, Annarita; Salo, Oleksandr; Ali, Hazrat; Szymanski, Wiktor; Lankhorst, Peter P; Nygård, Yvonne; Bovenberg, Roel A L; Driessen, Arnold J M

Chrysogine is a yellow pigment produced by Penicillium chrysogenum and other filamentous fungi. Although it was first isolated in 1973, the biosynthetic pathway has so far not been resolved. Here, we show that the deletion of the highly expressed non-ribosomal peptide synthetase (NRPS) gene

Structure Revision of N-Mercapto-4-formylcarbostyril Produced by Pseudomonas fluorescens G308 to 2-(2-Hydroxyphenyl)thiazole-4-carbaldehyde [aeruginaldehyde

DEFF Research Database (Denmark)

Guillemyn, Karel; Ballet, Steven; Ye, Lumeng

2014-01-01

, displays spectroscopic data identical with those of the alleged carbostyril derivative. In addition, the published H-1 and C-13 NMR data are in agreement with those calculated for aeruginaldehyde. We propose that aeruginaldehyde and aeruginol originate from the non-ribosomal peptide synthetase enzymes...

A gene expression study on strains of Nostoc (Cyanobacteria ...

African Journals Online (AJOL)

Cyanobacteria are well known for their production of a multitude of highly allelopathic compounds. These products have features such as incorporation of non-proteinogenic amino acids which are characteristics of peptides biosynthesized by non-ribosomal peptide synthetases (NRPSs). Some of these peptides have ...

Kin-Driver: a database of driver mutations in protein kinases.

Science.gov (United States)

Simonetti, Franco L; Tornador, Cristian; Nabau-Moretó, Nuria; Molina-Vila, Miguel A; Marino-Buslje, Cristina

2014-01-01

Somatic mutations in protein kinases (PKs) are frequent driver events in many human tumors, while germ-line mutations are associated with hereditary diseases. Here we present Kin-driver, the first database that compiles driver mutations in PKs with experimental evidence demonstrating their functional role. Kin-driver is a manual expert-curated database that pays special attention to activating mutations (AMs) and can serve as a validation set to develop new generation tools focused on the prediction of gain-of-function driver mutations. It also offers an easy and intuitive environment to facilitate the visualization and analysis of mutations in PKs. Because all mutations are mapped onto a multiple sequence alignment, analogue positions between kinases can be identified and tentative new mutations can be proposed for studying by transferring annotation. Finally, our database can also be of use to clinical and translational laboratories, helping them to identify uncommon AMs that can correlate with response to new antitumor drugs. The website was developed using PHP and JavaScript, which are supported by all major browsers; the database was built using MySQL server. Kin-driver is available at: http://kin-driver.leloir.org.ar/ © The Author(s) 2014. Published by Oxford University Press.

Escherichia coli producing colibactin triggers premature and transmissible senescence in mammalian cells.

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Thomas Secher

Full Text Available Cellular senescence is an irreversible state of proliferation arrest evoked by a myriad of stresses including oncogene activation, telomere shortening/dysfunction and genotoxic insults. It has been associated with tumor activation, immune suppression and aging, owing to the secretion of proinflammatory mediators. The bacterial genotoxin colibactin, encoded by the pks genomic island is frequently harboured by Escherichia coli strains of the B2 phylogenetic group. Mammalian cells exposed to live pks+ bacteria exhibit DNA-double strand breaks (DSB and undergo cell-cycle arrest and death. Here we show that cells that survive the acute bacterial infection with pks+ E. coli display hallmarks of cellular senescence: chronic DSB, prolonged cell-cycle arrest, enhanced senescence-associated β-galactosidase (SA-β-Gal activity, expansion of promyelocytic leukemia nuclear foci and senescence-associated heterochromatin foci. This was accompanied by reactive oxygen species production and pro-inflammatory cytokines, chemokines and proteases secretion. These mediators were able to trigger DSB and enhanced SA-β-Gal activity in bystander recipient cells treated with conditioned medium from senescent cells. Furthermore, these senescent cells promoted the growth of human tumor cells. In conclusion, the present data demonstrated that the E. coli genotoxin colibactin induces cellular senescence and subsequently propel bystander genotoxic and oncogenic effects.

Use of Green Mussel Shell as a Desulfurizer in the Blending of Low Rank Coal-Biomass Briquette Combustion

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Mahidin Mahidin

2016-08-01

Full Text Available Calcium oxide-based material is available abundantly and naturally. A potential resource of that material comes from marine mollusk shell such as clams, scallops, mussels, oysters, winkles and nerites. The CaO-based material has exhibited a good performance as the desulfurizer oradsorbent in coal combustion in order to reduce SO2 emission. In this study, pulverized green mussel shell, without calcination, was utilized as the desulfurizer in the briquette produced from a mixture of low rank coal and palm kernel shell (PKS, also known as bio-briquette. The ratio ofcoal to PKS in the briquette was 90:10 (wt/wt. The influence of green mussel shell contents and combustion temperature were examined to prove the possible use of that materialas a desulfurizer. The ratio of Ca to S (Ca = calcium content in desulfurizer; S = sulfur content in briquette werefixed at 1:1, 1.25:1, 1.5:1, 1.75:1, and 2:1 (mole/mole. The burning (or desulfurization temperature range was 300-500 °C; the reaction time was 720 seconds and the air flow rate was 1.2 L/min. The results showed that green mussel shell can be introduced as a desulfurizer in coal briquette or bio-briquette combustions. The desulfurization process using that desulfurizer exhibited the first order reaction and the highest average efficiency of 84.5%.

Improvement of daptomycin yield by overexpression of the ...

African Journals Online (AJOL)

The effects of the accessory genes flanking the non-ribosomal peptide synthetase (NRPS) genes on daptomycin production were investigated by overexpression under the control of ermE* promoter via the integrative Escherichia coli–Streptomyces vector pIB139. The yield of daptomycin was promoted significantly when ...

Engineering the substrate specificity of the DhbE adenylation domain by yeast cell surface display.

Science.gov (United States)

Zhang, Keya; Nelson, Kathryn M; Bhuripanyo, Karan; Grimes, Kimberly D; Zhao, Bo; Aldrich, Courtney C; Yin, Jun

2013-01-24

The adenylation (A) domains of nonribosomal peptide synthetases (NRPSs) activate aryl acids or amino acids to launch their transfer through the NRPS assembly line for the biosynthesis of many medicinally important natural products. In order to expand the substrate pool of NRPSs, we developed a method based on yeast cell surface display to engineer the substrate specificities of the A-domains. We acquired A-domain mutants of DhbE that have 11- and 6-fold increases in k(cat)/K(m) with nonnative substrates 3-hydroxybenzoic acid and 2-aminobenzoic acid, respectively and corresponding 3- and 33-fold decreases in k(cat)/K(m) values with the native substrate 2,3-dihydroxybenzoic acid, resulting in a dramatic switch in substrate specificity of up to 200-fold. Our study demonstrates that yeast display can be used as a high throughput selection platform to reprogram the "nonribosomal code" of A-domains. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sfp-type PPTase inactivation promotes bacterial biofilm formation and ability to enhance wheat drought tolerance

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Salme eTimmusk

2015-05-01

Full Text Available Paenibacillus polymyxa is a common soil bacterium with broad range of practical applications. An important group of secondary metabolites in P. polymyxa are nonribosomal peptide and polyketide derived metabolites (NRP/PK. Modular nonribosomal peptide synthetases catalyse main steps in the biosynthesis of the complex secondary metabolites. Here we report on the inactivation of an A26 sfp-type phosphopantetheinyl transferase. The inactivation of the gene resulted in loss of NRP/PK production. In contrast to the former Bacillus spp. model the mutant strain compared to wild type showed greatly enhanced biofilm formation ability. Its biofilm promotion is directly mediated by NRP/PK, as exogenous addition of the wild type metabolite extracts restores its biofilm formation level. Wheat inoculation with bacteria that had lost their sfp-type PPTase gene resulted in two times higher plant survival and about three times increased biomass under severe drought stress compared to wild type.

Annotating and Interpreting Linear and Cyclic Peptide Tandem Mass Spectra.

Science.gov (United States)

Niedermeyer, Timo Horst Johannes

2016-01-01

Nonribosomal peptides often possess pronounced bioactivity, and thus, they are often interesting hit compounds in natural product-based drug discovery programs. Their mass spectrometric characterization is difficult due to the predominant occurrence of non-proteinogenic monomers and, especially in the case of cyclic peptides, the complex fragmentation patterns observed. This makes nonribosomal peptide tandem mass spectra annotation challenging and time-consuming. To meet this challenge, software tools for this task have been developed. In this chapter, the workflow for using the software mMass for the annotation of experimentally obtained peptide tandem mass spectra is described. mMass is freely available (http://www.mmass.org), open-source, and the most advanced and user-friendly software tool for this purpose. The software enables the analyst to concisely annotate and interpret tandem mass spectra of linear and cyclic peptides. Thus, it is highly useful for accelerating the structure confirmation and elucidation of cyclic as well as linear peptides and depsipeptides.

Genome-Wide Analysis of Secondary Metabolite Gene Clusters in Ophiostoma ulmi and Ophiostoma novo-ulmi Reveals a Fujikurin-Like Gene Cluster with a Putative Role in Infection

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Nicolau Sbaraini

2017-06-01

Full Text Available The emergence of new microbial pathogens can result in destructive outbreaks, since their hosts have limited resistance and pathogens may be excessively aggressive. Described as the major ecological incident of the twentieth century, Dutch elm disease, caused by ascomycete fungi from the Ophiostoma genus, has caused a significant decline in elm tree populations (Ulmus sp. in North America and Europe. Genome sequencing of the two main causative agents of Dutch elm disease (Ophiostoma ulmi and Ophiostoma novo-ulmi, along with closely related species with different lifestyles, allows for unique comparisons to be made to identify how pathogens and virulence determinants have emerged. Among several established virulence determinants, secondary metabolites (SMs have been suggested to play significant roles during phytopathogen infection. Interestingly, the secondary metabolism of Dutch elm pathogens remains almost unexplored, and little is known about how SM biosynthetic genes are organized in these species. To better understand the metabolic potential of O. ulmi and O. novo-ulmi, we performed a deep survey and description of SM biosynthetic gene clusters (BGCs in these species and assessed their conservation among eight species from the Ophiostomataceae family. Among 19 identified BGCs, a fujikurin-like gene cluster (OpPKS8 was unique to Dutch elm pathogens. Phylogenetic analysis revealed that orthologs for this gene cluster are widespread among phytopathogens and plant-associated fungi, suggesting that OpPKS8 may have been horizontally acquired by the Ophiostoma genus. Moreover, the detailed identification of several BGCs paves the way for future in-depth research and supports the potential impact of secondary metabolism on Ophiostoma genus’ lifestyle.

Draft genome sequence and chemical profiling of Fusarium langsethiae, an emerging producer of type A trichothecenes

DEFF Research Database (Denmark)

Lysøe, Erik; Frandsen, Rasmus John Normand; Divon, Hege H.

2016-01-01

. The assembly was fragmented, but reveals a genome of approximately 37.5 Mb, with a GC content around 48%, and 12,232 predicted protein-coding genes. Focusing on secondary metabolism we identified candidate genes for 12 polyketide synthases, 13 non-ribosomal peptide synthetases, and 22 genes for terpene/isoprenoid...

ADSORPTION OF COPPER FROM AQUEOUS SOLUTION BY ELAIS GUINEENSIS KERNEL ACTIVATED CARBON

Directory of Open Access Journals (Sweden)

NAJUA DELAILA TUMIN

2008-08-01

Full Text Available In this study, a series of batch laboratory experiments were conducted in order to investigate the feasibility of Elais Guineensis kernel or known as palm kernel shell (PKS-based activated carbon for the removal of copper from aqueous solution by the adsorption process. Investigation was carried out by studying the influence of initial solution pH, adsorbent dosage and initial concentration of copper. The particle size of PKS used was categorized as PKS–M. All batch experiments were carried out at a constant temperature of 30°C (±2°C using mechanical shaker that operated at 100 rpm. The single component equilibrium data was analyzed using Langmuir, Freundlich, Redlich-Peterson, Temkin and Toth adsorption isotherms.

Strategies in megasynthase engineering – fatty acid synthases (FAS as model proteins

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Manuel Fischer

2017-06-01

Full Text Available Megasynthases are large multienzyme proteins that produce a plethora of important natural compounds by catalyzing the successive condensation and modification of precursor units. Within the class of megasynthases, polyketide synthases (PKS are responsible for the production of a large spectrum of bioactive polyketides (PK, which have frequently found their way into therapeutic applications. Rational engineering approaches have been performed during the last 25 years that seek to employ the “assembly-line synthetic concept” of megasynthases in order to deliver new bioactive compounds. Here, we highlight PKS engineering strategies in the light of the newly emerging structural information on megasynthases, and argue that fatty acid synthases (FAS are and will be valuable objects for further developing this field.

Biosynthesis of Akaeolide and Lorneic Acids and Annotation of Type I Polyketide Synthase Gene Clusters in the Genome of Streptomyces sp. NPS554

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Tao Zhou

2015-01-01

Full Text Available The incorporation pattern of biosynthetic precursors into two structurally unique polyketides, akaeolide and lorneic acid A, was elucidated by feeding experiments with 13C-labeled precursors. In addition, the draft genome sequence of the producer, Streptomyces sp. NPS554, was performed and the biosynthetic gene clusters for these polyketides were identified. The putative gene clusters contain all the polyketide synthase (PKS domains necessary for assembly of the carbon skeletons. Combined with the 13C-labeling results, gene function prediction enabled us to propose biosynthetic pathways involving unusual carbon-carbon bond formation reactions. Genome analysis also indicated the presence of at least ten orphan type I PKS gene clusters that might be responsible for the production of new polyketides.

Construction of an engineering strain which knocked out the gene of thioesterase for Streptomyces parvus HCCB10043 and the reach of metabolites

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YIN Fang

2013-08-01

Full Text Available The major metabolites of Streptomyces parvus HCCB10043 is lipopeptide compounds A21978C,its genome sequence includes the non ribosomal peptide synthetase(NRPS,polyketide synthases(PKS and hybrid NRPS-PKS multi-enzyme system gene clusters,they do have a their common feature in the metabolite biosynthetic cluster,which is called TE domain as well.Thioesterase can synthesized the synthesis of compounds of the chain termination,and with functions to release mature lipopeptide hydrolysis and cyclized peptide chain aliphatic linear.This study,we knockout the TE domain of a gene cluster,which guide the biosynthesis of bipyridine,to obtain engineered bacteria.The fermentation results demonstrates reduced yields for metabolites 2,2′-Bipyridine (2,2′-BP.

Is PKS 2155 an extragalactic source

International Nuclear Information System (INIS)

Maraschi, L.; Treves, A.

1981-01-01

We present here observations in the far ultraviolet (1200-3000 Angstroem) obtained with I.U.E. The presence of weak variable emission features is discussed and the extragalactic nature of the object is questioned. (orig./WL)

Is PKS 2155 an extragalactic source

Energy Technology Data Exchange (ETDEWEB)

Maraschi, L.; Treves, A. (Consiglio Nazionale delle Ricerche, Milan (Italy). Lab. di Fisica Cosmica e Tecnologie Relative; Milan Univ. (Italy). Ist. di Fisica); Tanzi, E.G. (Consiglio Nazionale delle Ricerche, Milan (Italy). Lab. di Fisica Cosmica e Tecnologie Relative); Tarenghi, M. (European Southern Observatory, Garching (Germany, F.R.))

1981-01-01

We present here observations in the far ultraviolet (1200-3000 Angstroem) obtained with I.U.E. The presence of weak variable emission features is discussed and the extragalactic nature of the object is questioned.

Anaerobic bacteria as producers of antibiotics.

Science.gov (United States)

Behnken, Swantje; Hertweck, Christian

2012-10-01

Anaerobic bacteria are the oldest terrestrial creatures. They occur ubiquitously in soil and in the intestine of higher organisms and play a major role in human health, ecology, and industry. However, until lately no antibiotic or any other secondary metabolite has been known from anaerobes. Mining the genome sequences of Clostridium spp. has revealed a high prevalence of putative biosynthesis genes (PKS and NRPS), and only recently the first antibiotic from the anaerobic world, closthioamide, has been isolated from the cellulose degrading bacterium Clostridium cellulolyticum. The successful genetic induction of antibiotic biosynthesis in an anaerobe encourages further investigations of obligate anaerobes to tap their hidden biosynthetic potential.

Continuing professional development: researching non-technical competencies can support cognitive reappraisal and reduced stress in clinicians.

Science.gov (United States)

Kinnison, Tierney; May, Stephen

2017-09-09

Generic professional capabilities (non-technical competencies) are increasingly valued for their links to patient outcomes and clinician well-being. This study explores the emotional change, and practice-related outcomes, of participants of a veterinary professional key skills (PKS) continuing professional development (CPD) module. Reflective summaries produced by participants were analysed. A change in emotion, from 'negative' to 'positive', was the focus of analysis. Sections regarding these emotions were thematically analysed. Analysis was performed on 46 summaries. Three themes were identified: 'the PKS module' (centred on reluctance becoming surprise and stimulation), 'developing non-technical competencies' (unease to confidence) and 'stress and coping through a reflective focus' (anxiety to harmony). The changing emotions were connected to positive cognitive reappraisal and often behaviour changes, benefitting self, practice, clients and patients. The PKS module teaches participants to reflect; a new and challenging concept. The consequences of this enabled participants to understand the importance of professional topics, to be appreciative as well as critical, and to enjoy their job. Importantly, the module stimulated coping responses. Better understanding of roles led to participants having more reasonable expectations of themselves, more appreciation of their work and reduced stress. This research supports more attention to professional skills CPD for health professions. © British Veterinary Association (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Whole genome sequencing for deciphering the resistome of Chryseobacterium indologenes, an emerging multidrug-resistant bacterium isolated from a cystic fibrosis patient in Marseille, France

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T. Cimmino

2016-07-01

Full Text Available We decipher the resistome of Chryseobacterium indologenes MARS15, an emerging multidrug-resistant clinical strain, using the whole genome sequencing strategy. The bacterium was isolated from the sputum of a hospitalized patient with cystic fibrosis in the Timone Hospital in Marseille, France. Genome sequencing was done with Illumina MiSeq using a paired-end strategy. The in silico analysis was done by RAST, the resistome by the ARG-ANNOT database and detection of polyketide synthase (PKS by ANTISMAH. The genome size of C. indologenes MARS15 is 4 972 580 bp with 36.4% GC content. This multidrug-resistant bacterium was resistant to all β-lactams, including imipenem, and also to colistin. The resistome of C. indologenes MARS15 includes Ambler class A and B β-lactams encoding blaCIA and blaIND-2 genes and MBL (metallo-β-lactamase genes, the CAT (chloramphenicol acetyltransferase gene and the multidrug efflux pump AcrB. Specific features include the presence of an urease operon, an intact prophage and a carotenoid biosynthesis pathway. Interestingly, we report for the first time in C. indologenes a PKS cluster that might be responsible for secondary metabolite biosynthesis, similar to erythromycin. The whole genome sequence analysis provides insight into the resistome and the discovery of new details, such as the PKS cluster.

Whole genome sequencing for deciphering the resistome of Chryseobacterium indologenes, an emerging multidrug-resistant bacterium isolated from a cystic fibrosis patient in Marseille, France.

Science.gov (United States)

Cimmino, T; Rolain, J-M

2016-07-01

We decipher the resistome of Chryseobacterium indologenes MARS15, an emerging multidrug-resistant clinical strain, using the whole genome sequencing strategy. The bacterium was isolated from the sputum of a hospitalized patient with cystic fibrosis in the Timone Hospital in Marseille, France. Genome sequencing was done with Illumina MiSeq using a paired-end strategy. The in silico analysis was done by RAST, the resistome by the ARG-ANNOT database and detection of polyketide synthase (PKS) by ANTISMAH. The genome size of C. indologenes MARS15 is 4 972 580 bp with 36.4% GC content. This multidrug-resistant bacterium was resistant to all β-lactams, including imipenem, and also to colistin. The resistome of C. indologenes MARS15 includes Ambler class A and B β-lactams encoding bla CIA and bla IND-2 genes and MBL (metallo-β-lactamase) genes, the CAT (chloramphenicol acetyltransferase) gene and the multidrug efflux pump AcrB. Specific features include the presence of an urease operon, an intact prophage and a carotenoid biosynthesis pathway. Interestingly, we report for the first time in C. indologenes a PKS cluster that might be responsible for secondary metabolite biosynthesis, similar to erythromycin. The whole genome sequence analysis provides insight into the resistome and the discovery of new details, such as the PKS cluster.

The cyanobacterial metabolite nocuolin A is a natural oxadiazine that triggers apoptosis in human cancer cells

Czech Academy of Sciences Publication Activity Database

Voráčová, K.; Hájek, Jan; Mareš, Jan; Urajová, P.; Kuzma, M.; Cheel, J.; Villunger, A.; Kapuscik, A.; Bally, M.; Novák, P.; Kabeláč, M.; Krumschnabel, G.; Lukeš, M.; Voloshko, L.; Kopecký, J.; Hrouzek, P.

2017-01-01

Roč. 12, č. 3 (2017), č. článku e0172850. E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GA14-18067S Institutional support: RVO:60077344 Keywords : secondary metabolite * cancer * non-ribosomal synthetase Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.806, year: 2016

PCR screening reveals considerable unexploited biosynthetic potential of ansamycins and a mysterious family of AHBA-containing natural products in actinomycetes.

Science.gov (United States)

Wang, H-X; Chen, Y-Y; Ge, L; Fang, T-T; Meng, J; Liu, Z; Fang, X-Y; Ni, S; Lin, C; Wu, Y-Y; Wang, M-L; Shi, N-N; He, H-G; Hong, K; Shen, Y-M

2013-07-01

Ansamycins are a family of macrolactams that are synthesized by type I polyketide synthase (PKS) using 3-amino-5-hydroxybenzoic acid (AHBA) as the starter unit. Most members of the family have strong antimicrobial, antifungal, anticancer and/or antiviral activities. We aimed to discover new ansamycins and/or other AHBA-containing natural products from actinobacteria. Through PCR screening of AHBA synthase gene, we identified 26 AHBA synthase gene-positive strains from 206 plant-associated actinomycetes (five positives) and 688 marine-derived actinomycetes (21 positives), representing a positive ratio of 2·4-3·1%. Twenty-five ansamycins, including eight new compounds, were isolated from six AHBA synthase gene-positive strains through TLC-guided fractionations followed by repeated column chromatography. To gain information about those potential ansamycin gene clusters whose products were unknown, seven strains with phylogenetically divergent AHBA synthase genes were subjected to fosmid library construction. Of the seven gene clusters we obtained, three show characteristics for typical ansamycin gene clusters, and other four, from Micromonospora spp., appear to lack the amide synthase gene, which is unusual for ansamycin biosynthesis. The gene composition of these four gene clusters suggests that they are involved in the biosynthesis of a new family of hybrid PK-NRP compounds containing AHBA substructure. PCR screening of AHBA synthase is an efficient approach to discover novel ansamycins and other AHBA-containing natural products. This work demonstrates that the AHBA-based screening method is a useful approach for discovering novel ansamycins and other AHBA-containing natural products from new microbial resources. Journal of Applied Microbiology © 2013 The Society for Applied Microbiology.

HERPES VIRUS CONTAMINATION OF DONOR’S TISSUE AS A POTENTIAL ETIOLOGY OF CORNEAL GRAFT DISEASE AFTER PENETRATING KERATOPLASTY

Directory of Open Access Journals (Sweden)

E. A. Mironkova

2012-01-01

Full Text Available We present the study of outcomes of PCR-diagnostics directed on detection of DNA of herpes-family viruses in donor’s corneal tissues taken during penetrating keratoplasty (PK. In total, there were 46 patients, who under- went PKs. They were followed up from 14 days till 12 months. PCR-research of fragments of a donor cornea re- vealed existence of DNA in 21.7%. The retrospective analysis showed that in the presence of herpes-virus DNA in donor’s cornea is the risk factor of postoperative complications development and increases the rejection rate 2–3 times, reaching 100% – 70%. Thus the high risk of graft failures remains associated not only with the system immunosupressive therapy which is usually considered as the precondition of activization of chronic infections, but also in the absence of that. It gives the ground to conclude that preoperative preparation of a donor material, especially «fresh» corneas, should include expanded PCR-diagnostics on herpes-viruses and its obligatory dis- carding in cases of positive tests. 

Monte Carlo simulation of the ARGO

International Nuclear Information System (INIS)

Depaola, G.O.

1997-01-01

We use GEANT Monte Carlo code to design an outline of the geometry and simulate the performance of the Argentine gamma-ray observer (ARGO), a telescope based on silicon strip detector technlogy. The γ-ray direction is determined by geometrical means and the angular resolution is calculated for small variations of the basic design. The results show that the angular resolutions vary from a few degrees at low energies (∝50 MeV) to 0.2 , approximately, at high energies (>500 MeV). We also made simulations using as incoming γ-ray the energy spectrum of PKS0208-512 and PKS0528+134 quasars. Moreover, a method based on multiple scattering theory is also used to determine the incoming energy. We show that this method is applicable to energy spectrum. (orig.)

Uncovering Nature’s 100 TeV Particle Accelerators in the Large-Scale Jets of Quasars

Science.gov (United States)

Georganopoulos, Markos; Meyer, Eileen; Sparks, William B.; Perlman, Eric S.; Van Der Marel, Roeland P.; Anderson, Jay; Sohn, S. Tony; Biretta, John A.; Norman, Colin Arthur; Chiaberge, Marco

2016-04-01

Since the first jet X-ray detections sixteen years ago the adopted paradigm for the X-ray emission has been the IC/CMB model that requires highly relativistic (Lorentz factors of 10-20), extremely powerful (sometimes super-Eddington) kpc scale jets. R I will discuss recently obtained strong evidence, from two different avenues, IR to optical polarimetry for PKS 1136-135 and gamma-ray observations for 3C 273 and PKS 0637-752, ruling out the EC/CMB model. Our work constrains the jet Lorentz factors to less than ~few, and leaves as the only reasonable alternative synchrotron emission from ~100 TeV jet electrons, accelerated hundreds of kpc away from the central engine. This refutes over a decade of work on the jet X-ray emission mechanism and overall energetics and, if confirmed in more sources, it will constitute a paradigm shift in our understanding of powerful large scale jets and their role in the universe. Two important findings emerging from our work will also discussed be: (i) the solid angle-integrated luminosity of the large scale jet is comparable to that of the jet core, contrary to the current belief that the core is the dominant jet radiative outlet and (ii) the large scale jets are the main source of TeV photon in the universe, something potentially important, as TeV photons have been suggested to heat up the intergalactic medium and reduce the number of dwarf galaxies formed.

Broad spectrum antimicrobial activity of forest-derived soil actinomycete, Nocardia sp. PB-52

Directory of Open Access Journals (Sweden)

Priyanka eSharma

2016-03-01

Full Text Available A mesophilic actinomycete strain designated as PB-52 was isolated from soil samples of Pobitora Wildlife Sanctuary of Assam, India. Based on phenotypic and molecular characteristics, the strain was identified as Nocardia sp. which shares 99.7% sequence similarity with Nocardia niigatensis IFM 0330 (NR_112195. The strain is a Gram-positive filamentous bacterium with rugose spore surface which exhibited a wide range of antimicrobial activity against Gram-positive bacteria including methicillin resistant Staphylococcus aureus (MRSA, Gram-negative bacteria and yeasts. Optimization for the growth and antimicrobial metabolite production of the strain PB-52 was carried out in batch culture under shaking condition. The optimum growth and the antimicrobial metabolite production by the strain PB-52 was recorded in GLM medium at 28ºC, initial pH 7.4 of the medium and incubation period of eight days. Based on polyketide synthases (PKS and nonribosomal peptide synthetases (NRPS gene-targeted PCR amplification, the occurrence of both of these biosynthetic pathways was detected which might be involved in the production of antimicrobial metabolite in PB-52. Extract of the fermented broth culture of PB-52 was prepared with organic solvent extraction method using ethyl acetate. The ethyl acetate extract of PB-52 (EA-PB-52 showed lowest minimum inhibitory concentration (MIC against Staphylococcus aureus MTCC 96 (0.975 μg/ml whereas highest was recorded against Klebsiella pneumoniae ATCC 13883 (62.5 μg/ml. Scanning electron microscopy (SEM revealed that treatment of the test microorganisms with EA-PB-52 destroyed the targeted cells with prominent loss of cell shape and integrity. In order to determine the constituents responsible for its antimicrobial activity, EA-PB-52 was subjected to chemical analysis using gas chromatography-mass spectrometry (GC-MS. GC-MS analysis showed the presence of twelve different chemical constituents in the extract, some of which

The regulation of microcystin biosynthesis pathways and genetic mechanisms

OpenAIRE

Serap YALÇIN

2012-01-01

The cyanobacteria (blue-green algae), as they arecommonly named, comprise a diverse group of oxygenicphotosynthetic bacteria that inhabit a wide rangeof aquatic and terrestrial environments, and displayincredible morphological diversity. Cyanobacteriaproduce bioactive secondary metabolites, includingalkaloids, polyketides and non-ribosomal peptides, someof which are potent toxins. The common occurrenceof toxic cyanobacteria causes problems for health ofanimals and human. Cyanobacterial toxins...

Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase

Directory of Open Access Journals (Sweden)

Nicholas J. Tobias

2016-11-01

Full Text Available Several members of the genus Legionella cause Legionnaires’ disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella. Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella, we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis and secondary metabolism (polyketide and non-ribosomal peptide synthesis. Using conserved active site motifs, we predict some novel compounds that are probably involved in cell-cell communication, differing to known communication systems. We identify several gene clusters, which may represent novel signaling mechanisms and demonstrate the natural product potential of Legionella.

Policing starter unit selection of the enterocin type II polyketide synthase by the type II thioesterase EncL.

Science.gov (United States)

Kalaitzis, John A; Cheng, Qian; Meluzzi, Dario; Xiang, Longkuan; Izumikawa, Miho; Dorrestein, Pieter C; Moore, Bradley S

2011-11-15

Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete 'Streptomyces maritimus'. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here, we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates. Copyright © 2011 Elsevier Ltd. All rights reserved.

Construction of ivermectin producer by domain swaps of avermectin polyketide synthase in Streptomyces avermitilis.

Science.gov (United States)

Zhang, Xiaolin; Chen, Zhi; Li, Meng; Wen, Ying; Song, Yuan; Li, Jilun

2006-10-01

Ivermectin, 22, 23-dihydroavermectin B1, is commercially important in human, veterinary medicine, and pesticides. It is currently synthesized by chemical reduction of the double bond between C22 and C23 of avermectins B1, which are a mixture of B1a (>80%) and B1b (produced by fermentation of Streptomyces avermitilis. The cost of ivermectin is much higher than that of avermectins B1 owing to the necessity of region-specific hydrogenation at C22-C23 of avermectins B1 with rhodium chloride as the catalyst for producing ivermectin. Here we report that ivermectin can be produced directly by fermentation of recombinant strains constructed through targeted genetic engineering of the avermectin polyketide synthase (PKS) in S. avermitilis Olm73-12, which produces only avermectins B and not avermectins A and oligomycin. The DNA region encoding the dehydratase (DH) and ketoreductase (KR) domains of module 2 from the avermectin PKS in S. avermitilis Olm73-12 was replaced by the DNA fragment encoding the DH, enoylreductase, and KR domains from module 4 of the pikromycin PKS of Streptomyces venezuelae ATCC 15439 using a gene replacement vector pXL211. Twenty-seven of mutants were found to produce a small amount of 22, 23-dihydroavermectin B1a and avermectin B1a and B2a by high performance liquid chromatography and liquid chromatography mass spectrometry analysis. This study might provide a route to the low-cost production of ivermectin by fermentation.

Data on the presence or absence of genes encoding essential proteins for ochratoxin and fumonisin biosynthesis in Aspergillus niger and Aspergillus welwitschiae

Directory of Open Access Journals (Sweden)

Fernanda Pelisson Massi

2016-06-01

Full Text Available We present the multiplex PCR data for the presence/absence of genes involved in OTA and FB2 biosynthesis in Aspergillus niger/Aspergillus welwitschiae strains isolated from different food substrates in Brazil. Among the 175 strains analyzed, four mPCR profiles were found: Profile 1 (17% highlights strains harboring in their genome the pks, radH and the fum8 genes. Profile 2 (3.5% highlights strains harboring genes involved in OTA biosynthesis i.e. radH and pks. Profile 3 (51.5% highlights strains harboring the fum8 gene. Profile 4 (28% highlights strains not carrying the genes studied herein. This research content is supplemental to our original research article, “Prospecting for the incidence of genes involved in ochratoxin and fumonisin biosynthesis in Brazilian strains of A. niger and A. welwitschiae” [1].

Reduced clearance of rocuronium and sugammadex in patients with severe to end-stage renal failure: a pharmacokinetic study.

NARCIS (Netherlands)

Staals, L.M.; Snoeck, M.M.J.; Driessen, J.J.; Hamersvelt, H.W. van; Flockton, E.A.; Heuvel, M.W. van den; Hunter, J.M.

2010-01-01

BACKGROUND: Sugammadex is a selective relaxant binding agent designed to encapsulate the neuromuscular blocking agent, rocuronium. The sugammadex-rocuronium complex is eliminated by the kidneys. This trial investigated the pharmacokinetics (PKs) of sugammadex and rocuronium in patients with renal

Models for Very Rapid High-Energy γ-Ray Variability in Blazars G. E. ...

Indian Academy of Sciences (India)

blazar PKS 2155−304 and present synthetic light-curves of the kind that ... radio wavelengths led to a similar situation (see Wagner & Witzel 1995 for a review). Some of the ... If the instabilities grow, the two components will eventually mix.

The effect of malnutrition on the pharmacokinetics and virologic outcomes of lopinavir, efavirenz and nevirapine in food insecure HIV-infected children in Tororo, Uganda

NARCIS (Netherlands)

Bartelink, Imke H.; Savic, Rada M.; Dorsey, Grant; Ruel, Theodore; Gingrich, David; Scherpbier, Henriette J.; Capparelli, Edmund; Jullien, Vincent; Young, Sera L.; Achan, Jane; Plenty, Albert; Charlebois, Edwin; Kamya, Moses; Havlir, Diane; Aweeka, Francesca

2015-01-01

Malnutrition may impact the pharmacokinetics (PKs) of antiretroviral medications and virologic responses in HIV-infected children. The authors therefore evaluated the PK of nevirapine (NVP), efavirenz (EFV) and lopinavir (LPV) in associations with nutritional status in a cohort of HIV-infected

Radiometric well logging instruments

International Nuclear Information System (INIS)

Davydov, A.V.

1975-01-01

The technical properties of well instruments for radioactive logging used in the radiometric logging complexes PKS-1000-1 (''Sond-1'') and PRKS-2 (''Vitok-2'') are described. The main features of the electric circuit of the measuring channels are given

Adaptation of an L-Proline Adenylation Domain to Use 4-Propyl-L-Proline in the Evolution of Lincosamide Biosynthesis

Czech Academy of Sciences Publication Activity Database

Kadlčík, Stanislav; Kučera, Tomáš; Chalupská, Dominika; Gažák, Radek; Koběrská, Markéta; Ulanová, Dana; Kopecký, Jan; Kutejová, Eva; Najmanová, Lucie; Janata, Jiří

2013-01-01

Roč. 8, č. 12 (2013) E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) EE2.3.20.0055; GA MŠk(CZ) EE2.3.30.0003; GA MŠk ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : NONRIBOSOMAL PEPTIDE SYNTHETASES * GENE-CLUSTER * BIOCHEMICAL-CHARACTERIZATION Subject RIV: EE - Microbiology, Virology Impact factor: 3.534, year: 2013

Evolution-guided adaptation of an adenylation domain substrate specificity to an unusual amino acid

Czech Academy of Sciences Publication Activity Database

Vobruba, Šimon; Kadlčík, Stanislav; Gažák, Radek; Janata, Jiří

2017-01-01

Roč. 12, č. 12 (2017), č. článku e0189684. E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GJ17-13436Y; GA MŠk(CZ) LQ1604 Institutional support: RVO:61388971 Keywords : NONRIBOSOMAL PEPTIDE SYNTHETASES * BIOSYNTHETIC GENE-CLUSTER * LINCOSAMIDE ANTIBIOTICS Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.806, year: 2016

Genome Sequence of Vibrio campbellii Strain UMTGB204, a Marine Bacterium Isolated from a Green Barrel Tunicate

Science.gov (United States)

Gan, Huan You; Noor, Mohd Ezhar Mohd; Saari, Nur Azna; Musa, Najiah; Mustapha, Baharim; Usup, Gires

2015-01-01

Vibrio campbellii strain UMTGB204 was isolated from a green barrel tunicate. The genome of this strain comprises 5,652,224 bp with 5,014 open reading frames, 9 rRNAs, and 116 tRNAs. It contains genes related to virulence and environmental tolerance. Gene clusters for the biosynthesis of nonribosomal peptides and bacteriocin were also identified. PMID:25814609

Enabling techniques in the search for new antibiotics: Combinatorial biosynthesis of sugar-containing antibiotics.

Science.gov (United States)

Park, Je Won; Nam, Sang-Jip; Yoon, Yeo Joon

2017-06-15

Nature has a talent for inventing a vast number of natural products, including hybrids generated by blending different scaffolds, resulting in a myriad of bioactive chemical entities. Herein, we review the highlights and recent trends (2010-2016) in the combinatorial biosynthesis of sugar-containing antibiotics where nature's structural diversification capabilities are exploited to enable the creation of new anti-infective and anti-proliferative drugs. In this review, we describe the modern combinatorial biosynthetic approaches for polyketide synthase-derived complex and aromatic polyketides, non-ribosomal peptide synthetase-directed lipo-/glycopeptides, aminoglycosides, nucleoside antibiotics, and alkaloids, along with their therapeutic potential. Finally, we present the feasible nexus between combinatorial biosynthesis, systems biology, and synthetic biology as a toolbox to provide new antibiotics that will be indispensable in the post-antibiotic era. Copyright © 2016 Elsevier Inc. All rights reserved.

Liquid chromatography mass spectrometry for analysis of microbial metabolites

DEFF Research Database (Denmark)

Klitgaard, Andreas

to human health. Because of this, methods for detection and analysis of these compounds are vital. Estimates suggest that there are around 1.5 million different fungal species on Earth, dwarfing the number of plants estimated to 300,000, meaning that there potentially are many more interesting compounds...... is of large commercial interest for production of the bioactive compounds of the future. One part of my study focused on identification and elucidation of the biosynthesis of a nonribosomal peptide (NRP) nidulanin A from Aspergillus nidulans. Although the study was successful several analogs were......Filamentous fungi serve a very important role in Nature where they break down organic matter, releasing nutrients that can be used by other organisms. Fungi and other microorganisms also produce a wide array of bioactive compounds, the secondary metabolites( SMs), used for such diverse roles...

A protein interaction map of the kalimantacin biosynthesis assembly line

Directory of Open Access Journals (Sweden)

Birgit Uytterhoeven

2016-11-01

Full Text Available The antimicrobial secondary metabolite kalimantacin is produced by a hybrid polyketide/ non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein-protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites.This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.

Fatty Acyl Chains of Mycobacterium marinum Lipooligosaccharides

Science.gov (United States)

Rombouts, Yoann; Alibaud, Laeticia; Carrère-Kremer, Séverine; Maes, Emmanuel; Tokarski, Caroline; Elass, Elisabeth; Kremer, Laurent; Guérardel, Yann

2011-01-01

We have recently established the fine structure of the glycan backbone of lipooligosaccharides (LOS-I to LOS-IV) isolated from Mycobacterium marinum, a close relative of Mycobacterium tuberculosis. These studies culminated with the description of an unusual terminal N-acylated monosaccharide that confers important biological functions to LOS-IV, such as macrophage activation, that may be relevant to granuloma formation. It was, however, also suggested that the lipid moiety was required for LOSs to exert their immunomodulatory activity. Herein, using highly purified LOSs from M. marinum, we have determined through a combination of mass spectrometric and NMR techniques, the structure and localization of the fatty acids composing the lipid moiety. The occurrence of two distinct polymethyl-branched fatty acids presenting specific localizations is consistent with the presence of two highly related polyketide synthases (Pks5 and Pks5.1) in M. marinum and presumably involved in the synthesis of these fatty acyl chains. In addition, a bioinformatic search permitted us to identify a set of enzymes potentially involved in the biosynthesis or transfer of these lipids to the LOS trehalose unit. These include MMAR_2343, a member of the Pap (polyketide-associated protein) family, that acylates trehalose-based glycolipids in M. marinum. The participation of MMAR_2343 to LOS assembly was demonstrated using a M. marinum mutant carrying a transposon insertion in the MMAR_2343 gene. Disruption of MMAR_2343 resulted in a severe LOS breakdown, indicating that MMAR_2343, hereafter designated PapA4, fulfills the requirements for LOS acylation and assembly. PMID:21803773

Pharmacokinetic profile of voriconazole in a critically ill patient on therapeutic plasma exchange

NARCIS (Netherlands)

Spriet, I.; Bruggemann, R.J.M.; Annaert, P.; Meersseman, P.; Wijngaerden, E. van; Lagrou, K.; Willems, L.

2013-01-01

BACKGROUND: Extracorporeal removal of drugs during therapeutic plasma exchange (TPE) can lead to decreased efficacy, as shown in several reports discussing altered pharmacokinetics (PKs) of antibiotics during TPE. In particular, drugs with a low volume of distribution or a high protein binding are

Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria

KAUST Repository

Ross, Avena C.

2013-01-23

Thalassospiramides A and B are immunosuppressant cyclic lipopeptides first reported from the marine α-proteobacterium Thalassospira sp. CNJ-328. We describe here the discovery and characterization of an extended family of 14 new analogues from four Tistrella and Thalassospira isolates. These potent calpain 1 protease inhibitors belong to six structure classes in which the length and composition of the acylpeptide side chain varies extensively. Genomic sequence analysis of the thalassospiramide-producing microbes revealed related, genus-specific biosynthetic loci encoding hybrid nonribosomal peptide synthetase/polyketide synthases consistent with thalassospiramide assembly. The bioinformatics analysis of the gene clusters suggests that structural diversity, which ranges from the 803.4 Da thalassospiramide C to the 1291.7 Da thalassospiramide F, results from a complex sequence of reactions involving amino acid substrate channeling and enzymatic multimodule skipping and iteration. Preliminary biochemical analysis of the N-terminal nonribosomal peptide synthetase module from the Thalassospira TtcA megasynthase supports a biosynthetic model in which in cis amino acid activation competes with in trans activation to increase the range of amino acid substrates incorporated at the N terminus. © 2012 American Chemical Society.

Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria

KAUST Repository

Ross, Avena C.; Xü , Ying; Lu, Liang; Kersten, Roland D.; Shao, Zongze; Al-Suwailem, Abdulaziz M.; Dorrestein, Pieter C.; Qian, Peiyuan; Moore, Bradley S.

2013-01-01

Thalassospiramides A and B are immunosuppressant cyclic lipopeptides first reported from the marine α-proteobacterium Thalassospira sp. CNJ-328. We describe here the discovery and characterization of an extended family of 14 new analogues from four Tistrella and Thalassospira isolates. These potent calpain 1 protease inhibitors belong to six structure classes in which the length and composition of the acylpeptide side chain varies extensively. Genomic sequence analysis of the thalassospiramide-producing microbes revealed related, genus-specific biosynthetic loci encoding hybrid nonribosomal peptide synthetase/polyketide synthases consistent with thalassospiramide assembly. The bioinformatics analysis of the gene clusters suggests that structural diversity, which ranges from the 803.4 Da thalassospiramide C to the 1291.7 Da thalassospiramide F, results from a complex sequence of reactions involving amino acid substrate channeling and enzymatic multimodule skipping and iteration. Preliminary biochemical analysis of the N-terminal nonribosomal peptide synthetase module from the Thalassospira TtcA megasynthase supports a biosynthetic model in which in cis amino acid activation competes with in trans activation to increase the range of amino acid substrates incorporated at the N terminus. © 2012 American Chemical Society.

Complete Genome Sequence of the Endophytic Biocontrol Strain Bacillus velezensis CC09

OpenAIRE

Cai, Xunchao; Kang, Xingxing; Xi, Huan; Liu, Changhong; Xue, Yarong

2016-01-01

Bacillus velezensis is a heterotypic synonym of B. methylotrophicus, B. amyloliquefaciens subsp. plantarum, and Bacillus oryzicola, and has been used to control plant fungal diseases. In order to fully understand the genetic basis of antimicrobial capacities, we did a complete genome sequencing of the endophytic B.?velezensis strain CC09. Genes tightly associated with biocontrol ability, including nonribosomal peptide synthetases, polyketide synthetases, iron acquisition, colonization, and vo...

Draft Genome Sequence of Bacillus velezensis B6, a Rhizobacterium That Can Control Plant Diseases.

Science.gov (United States)

Gao, Yu-Han; Guo, Rong-Jun; Li, Shi-Dong

2018-03-22

The draft genome of Bacillus velezensis strain B6, a rhizobacterium with good biocontrol performance isolated from soil in China, was sequenced. The assembly comprises 32 scaffolds with a total size of 3.88 Mb. Gene clusters coding either ribosomally encoded bacteriocins or nonribosomally encoded antimicrobial polyketides and lipopeptides in the genome may contribute to plant disease control. Copyright © 2018 Gao et al.

AcEST: DK947280 [AcEST

Lifescience Database Archive (English)

Full Text Available omal peptide synthetase OS=Actinoplanes teichomyceticus Align length 51 Score (bit) 32.7 E-value 9.4 Report ...ase, module 4-6 OS=Actinop... 33 9.4 >tr|Q70AZ7|Q70AZ7_ACTTI Non-ribosomal peptide synthetase OS=Actinoplanes...VAMMAHQHLGLSEIKQVAGPGAAFDTLVVFENYPRPPR 3362 >tr|Q6ZZJ4|Q6ZZJ4_ACTTI Peptide synthetase, module 4-6 OS=Actinoplanes

Chemical analysis of a genome wide polyketide synthase gene deletion library in Aspergillus nidulans

DEFF Research Database (Denmark)

Larsen, Thomas Ostenfeld; Klejnstrup, Marie Louise; Nielsen, Jakob Blæsbjerg

. This may reflect that many PKs are either produced in small amounts, under special conditions or in developmental stages that are rarely observed under laboratory conditions. In order to trigger expression of “silent” genes we are currently pursuing several approaches; i) stimulation of A. nidulans wild...

Transcriptional factor influence on OTA production and the quelling ...

African Journals Online (AJOL)

This study determined the influence of some transcriptional factors on ochratoxin A production as well as investigates the quelling attributes of some designed siRNA on the OTA producing Aspergillus section Nigri using standard recommended techniques. Results obtained following comparison of the pks gene promoter ...

Antimicrobials of Bacillus species: mining and engineering

NARCIS (Netherlands)

Zhao, Xin

2016-01-01

Bacillus sp. have been successfully used to suppress various bacterial and fungal pathogens. Due to the wide availability of whole genome sequence data and the development of genome mining tools, novel antimicrobials are being discovered and updated,;not only bacteriocins, but also NRPs and PKs. A

Benzalacetone Synthase

Directory of Open Access Journals (Sweden)

Ikuro eAbe

2012-03-01

Full Text Available Benzalacetone synthase, from the medicinal plant Rheum palmatum (Polygonaceae (RpBAS, is a plant-specific chalcone synthase (CHS superfamily of type III polyketide synthase (PKS. RpBAS catalyzes the one-step, decarboxylative condensation of 4-coumaroyl-CoA with malonyl-CoA to produce the C6-C4 benzalacetone scaffold. The X-ray crystal structures of RpBAS confirmed that the diketide-forming activity is attributable to the characteristic substitution of the conserved active-site "gatekeeper" Phe with Leu. Furthermore, the crystal structures suggested that RpBAS employs novel catalytic machinery for the thioester bond cleavage of the enzyme-bound diketide intermediate and the final decarboxylation reaction to produce benzalacetone. Finally, by exploiting the remarkable substrate tolerance and catalytic versatility of RpBAS, precursor-directed biosynthesis efficiently generated chemically and structurally divergent, unnatural novel polyketide scaffolds. These findings provided a structural basis for the functional diversity of the type III PKS enzymes.

Genomic and functional features of the biosurfactant producing Bacillus sp. AM13.

Science.gov (United States)

Shaligram, Shraddha; Kumbhare, Shreyas V; Dhotre, Dhiraj P; Muddeshwar, Manohar G; Kapley, Atya; Joseph, Neetha; Purohit, Hemant P; Shouche, Yogesh S; Pawar, Shrikant P

2016-09-01

Genomic studies provide deeper insights into secondary metabolites produced by diverse bacterial communities, residing in various environmental niches. This study aims to understand the potential of a biosurfactant producing Bacillus sp. AM13, isolated from soil. An integrated approach of genomic and chemical analysis was employed to characterize the antibacterial lipopeptide produced by the strain AM13. Genome analysis revealed that strain AM13 harbors a nonribosomal peptide synthetase (NRPS) cluster; highly similar with known biosynthetic gene clusters from surfactin family: lichenysin (85 %) and surfactin (78 %). These findings were substantiated with supplementary experiments of oil displacement assay and surface tension measurements, confirming the biosurfactant production. Further investigation using LCMS approach exhibited similarity of the biomolecule with biosurfactants of the surfactin family. Our consolidated effort of functional genomics provided chemical as well as genetic leads for understanding the biochemical characteristics of the bioactive compound.

Discovery of antimicrobial lipodepsipeptides produced by a Serratia sp. within mosquito microbiomes.

Science.gov (United States)

Ganley, Jack; Carr, Gavin; Ioerger, Thomas; Sacchettini, James; Clardy, Jon; Derbyshire, Emily

2018-04-26

The Anopheles mosquito that harbors the Plasmodium parasite contains a microbiota that can influence both the vector and parasite. In recent years, insect-associated microbes have highlighted the untapped potential of exploiting interspecies interactions to discover bioactive compounds. In this study, we report the discovery of nonribosomal lipodepsipeptides that are produced by a Serratia sp. within the midgut and salivary glands of A. stephensi mosquitoes. The lipodepsipeptides, stephensiolides A-K, have antibiotic activity and facilitate bacterial surface motility. Bioinformatic analyses indicate that the stephensiolides are ubiquitous in nature and are likely important for Serratia spp. colonization within mosquitoes, humans, and other ecological niches. Our results demonstrate the usefulness of probing insect-microbiome interactions, enhance our understanding of the chemical ecology within Anopheles mosquitoes, and provide a secondary metabolite scaffold to further investigate this complex relationship. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Antibacterial polyketides from Bacillus amyloliquefaciens associated with edible red seaweed Laurenciae papillosa.

Science.gov (United States)

Chakraborty, Kajal; Thilakan, Bini; Raola, Vamshi Krishna; Joy, Minju

2017-03-01

Heterotrophic Bacillus amyloliquefaciens associated with edible red seaweed, Laurenciae papillosa was used to isolate antibacterial polyketide compounds. Antibacterial activity studies integrated with the outcome obtained by polyketide synthetase (pks) coding genes established that seaweed-affiliated bacterial flora had a wide-ranging antibacterial activities and potential natural product diversity, which proved that the bacterium is valuable reservoir of novel bioactive metabolites. Bioactivity-guided isolation of 3-(octahydro-9-isopropyl-2H-benzo[h]chromen-4-yl)-2-methylpropyl benzoate and methyl 8-(2-(benzoyloxy)-ethyl)-hexahydro-4-((E)-pent-2-enyl)-2H-chromene-6-carboxylate of polyketide origin, with activity against human opportunistic food pathogenic microbes, have been isolated from the ethyl acetate extract of B. amyloliquefaciens. Structure-activity relationship analysis revealed that hydrophobic descriptor of the polyketide compounds significantly contribute towards its antibacterial activity. Seaweed-associated microorganisms were shown to represent a potential source of antimicrobial compounds for food and health benefits. The antibacterial polyketide compounds described in the present study may find potential applications in the food industry to reduce food-borne pathogens. Copyright © 2016 Elsevier Ltd. All rights reserved.

Melanin dependent survival of Apergillus fumigatus conidia in lung epithelial cells.

Science.gov (United States)

Amin, Shayista; Thywissen, Andreas; Heinekamp, Thorsten; Saluz, Hans Peter; Brakhage, Axel A

2014-07-01

Aspergillus fumigatus is the most important air-borne pathogenic fungus of humans. Upon inhalation of conidia, the fungus makes close contact with lung epithelial cells, which only possess low phagocytic activity. These cells are in particular interesting to address the question whether there is some form of persistence of conidia of A. fumigatus in the human host. Therefore, by also using uracil-auxotrophic mutant strains, we were able to investigate the interaction of A549 lung epithelial cells and A. fumigatus conidia in detail for long periods. Interestingly, unlike professional phagocytes, our study showed that the presence of conidial dihydroxynaphthalene (DHN) melanin enhanced the uptake of A. fumigatus conidia by epithelial cells when compared with non-pigmented pksP mutant conidia. Furthermore, conidia of A. fumigatus were able to survive within epithelial cells. This was due to the presence of DHN melanin in the cell wall of conidia, because melanised wild-type conidia showed a higher survival rate inside epithelial cells and led to inhibition of acidification of phagolysosomes. Both effects were not observed for white (non-melanised) conidia of the pksP mutant strain. Moreover, in contrast to pksP mutant conidia, melanised wild-type conidia were able to inhibit the extrinsic apoptotic pathway in A549 lung epithelial cells even for longer periods. The anti-apoptotic effect was not restricted to conidia, because both conidia-derived melanin ghosts (cell-free DHN melanin) and a different type of melanin, dihydroxyphenylalanine (DOPA) melanin, acted anti-apoptotically. Taken together, these data indicate the possibility of melanin-dependent persistence of conidia in lung epithelial cells. Copyright © 2014 Elsevier GmbH. All rights reserved.

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota.

Science.gov (United States)

Jami, Mansooreh; Ghanbari, Mahdi; Kneifel, Wolfgang; Domig, Konrad J

2015-06-01

The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated

Draft genome sequence of a human-associated isolate of Haloferax alexandrinus strain Arc-hr, an extremely halophilic archaea.

Science.gov (United States)

Khelaifia, S; Caputo, A; Djossou, F; Raoult, D

2017-01-01

We report the draft genome sequence of Haloferax alexandrinus strain Arc-hr (CSUR P798), isolated from the human gut of a 10-year-old Amazonian individual. Its 3 893 626 bp genome exhibits a 66.00% GC content. The genome of the strain Arc-hr contains 37 genes identified as ORFans, seven genes associated to halocin and 11 genes associated with polyketide synthases or nonribosomal peptide synthetases.

Protein Phosphatase 1-Dependent Transcriptional Programs for Long-Term Memory and Plasticity

Science.gov (United States)

Graff, Johannes; Koshibu, Kyoko; Jouvenceau, Anne; Dutar, Patrick; Mansuy, Isabelle M.

2010-01-01

Gene transcription is essential for the establishment and the maintenance of long-term memory (LTM) and for long-lasting forms of synaptic plasticity. The molecular mechanisms that control gene transcription in neuronal cells are complex and recruit multiple signaling pathways in the cytoplasm and the nucleus. Protein kinases (PKs) and…

Music Pedagogy: The Dissonance between the Taught, the Learned, and the Practiced

Science.gov (United States)

Frady, Rita R.

2011-01-01

The purpose of this mixed methods study was to determine the effectiveness of music teacher preparation programs in Georgia in providing preservice music teachers with the pedagogical knowledge and skills (PKS) required for music instruction in elementary music classrooms. The data-validation variant was utilized for the collection of both…

Characterization of the AN6448 cluster in Aspergillus nidulans

DEFF Research Database (Denmark)

Nielsen, Jakob Blæsbjerg; Klejnstrup, Marie Louise; Khorsand-Jamal, Paiman

2012-01-01

With the aim of mapping the polyketome of A. nidulans we have made a library of strains, which individually overexpress PKS genes from an ectopic locus. A screen of this collection on different media demonstrated that AN6448 leads to production of 3-MOA. An inspection of the DNA sequence surround...

The use of agricultural waste materials for concrete making ...

African Journals Online (AJOL)

This paper presents laterite as fine aggregate and agricultural waste materials such as periwinkle shell, (PS) and palm kernel shell (PKS) as coarse aggregate for making concrete. Saturated surface dry (SSD) bulk density and compressive cube strength tests of concrete made from these were carried at the concrete age of ...

Targeted Gene Disruption of the Cyclo (L-Phe, L-Pro Biosynthetic Pathway in Streptomyces sp. US24 Strain

Directory of Open Access Journals (Sweden)

Samiha Sioud

2007-01-01

Full Text Available We have previously isolated a new actinomycete strain from Tunisian soil called Streptomyces sp. US24, and have shown that it produces two bioactive molecules including a Cyclo (L-Phe, L-Pro diketopiperazine (DKP. To identify the structural genes responsible for the synthesis of this DKP derivative, a PCR amplification (696 bp was carried out using the Streptomyces sp. US24 genomic DNA as template and two degenerate oligonucleotides designed by analogy with genes encoding peptide synthetases (NRPS. The detection of DKP derivative biosynthetic pathway of the Streptomyces sp. US24 strain was then achieved by gene disruption via homologous recombination using a suicide vector derived from the conjugative plasmid pSET152 and containing the PCR product. Chromatography analysis, biological tests and spectroscopic studies of supernatant cultures of the wild-type Streptomyces sp. US24 strain and three mutants obtained by this gene targeting disruption approach showed that the amplified DNA fragment is required for Cyclo (L-Phe, L-Pro biosynthesis in Streptomyces sp. US24 strain. This DKP derivative seems to be produced either directly via a nonribosomal pathway or as a side product in the course of nonribosomal synthesis of a longer peptide.

Measurement of the neutral kaon regeneration amplitude in carbon at momenta below 1 GeV/c

CERN Document Server

Angelopoulos, Angelos; Aslanides, Elie; Backenstoss, Gerhard; Bargassa, P; Behnke, O; Benelli, A; Bertin, V; Blanc, F; Bloch, P; Carlson, P J; Carroll, M; Carvalho, J; Cawley, E; Charalambous, S; Chardin, G; Chertok, M B; Cody, A; Danielsson, M; Dejardin, M; Derré, J; Ealet, A; Eleftheriadis, C; Evangelou, I; Faravel, L; Ferreira-Marques, R; Fetscher, W; Fidecaro, Maria; Filipcic, A; Francis, D; Fry, J; Gabathuler, Erwin; Gamet, R; Garreta, D; Gerber, H J; Go, A; Haselden, A; Hayman, P J; Henry-Coüannier, F; Hollander, R W; Hubert, E; Jon-And, K; Kettle, P R; Kokkas, P; Kreuger, R; Le Gac, R; Leimgruber, F; Liolios, A; Machado, E; Mandic, I; Manthos, N; Marel, Gérard; Mikuz, M; Miller, J; Montanet, François; Müller, A; Nakada, Tatsuya; Pagels, B; Papadopoulos, I M; Pavlopoulos, P; Pinto da Cunha, J; Policarpo, Armando; Polivka, G; Rickenbach, R; Roberts, B L; Ruf, T; Sakelliou, L; Sanders, P; Schäfer, M; Schaller, L A; Schietinger, T; Schopper, A; Soares, A; Tauscher, Ludwig; Thibault, C; Touchard, F; Touramanis, C; Triantis, F A; Van Beveren, E; van Eijk, C W E; Vlachos, S; Weber, P; Wigger, I; Wolter, M; Yéche, C; Zavrtanik, D; Zimmerman, D

1997-01-01

The neutral kaon regeneration amplitude in carbon at momenta between 250 and 750~MeV/$c$ was determined by measuring the interference of inherent and coherently regenerated \\PKS\\ amplitudes. This interference appears in the rates of initially pure (tagged) \\PKz\\ and \\PaKz\\ decaying to \\Pgpp\\Pgpm\\ after crossing a carbon absorber.

Small Private Key PKS on an Embedded Microprocessor

OpenAIRE

Seo, Hwajeong; Kim, Jihyun; Choi, Jongseok; Park, Taehwan; Liu, Zhe; Kim, Howon

2014-01-01

Multivariate quadratic (MQ) cryptography requires the use of long public and private keys to ensure a sufficient security level, but this is not favorable to embedded systems, which have limited system resources. Recently, various approaches to MQ cryptography using reduced public keys have been studied. As a result of this, at CHES2011 (Cryptographic Hardware and Embedded Systems, 2011), a small public key MQ scheme, was proposed, and its feasible implementation on an embedded microprocessor...

Small Private Key PKS on an Embedded Microprocessor

Science.gov (United States)

Seo, Hwajeong; Kim, Jihyun; Choi, Jongseok; Park, Taehwan; Liu, Zhe; Kim, Howon

2014-01-01

Multivariate quadratic ( ) cryptography requires the use of long public and private keys to ensure a sufficient security level, but this is not favorable to embedded systems, which have limited system resources. Recently, various approaches to cryptography using reduced public keys have been studied. As a result of this, at CHES2011 (Cryptographic Hardware and Embedded Systems, 2011), a small public key scheme, was proposed, and its feasible implementation on an embedded microprocessor was reported at CHES2012. However, the implementation of a small private key scheme was not reported. For efficient implementation, random number generators can contribute to reduce the key size, but the cost of using a random number generator is much more complex than computing on modern microprocessors. Therefore, no feasible results have been reported on embedded microprocessors. In this paper, we propose a feasible implementation on embedded microprocessors for a small private key scheme using a pseudo-random number generator and hash function based on a block-cipher exploiting a hardware Advanced Encryption Standard (AES) accelerator. To speed up the performance, we apply various implementation methods, including parallel computation, on-the-fly computation, optimized logarithm representation, vinegar monomials and assembly programming. The proposed method reduces the private key size by about 99.9% and boosts signature generation and verification by 5.78% and 12.19% than previous results in CHES2012. PMID:24651722

Biosynthesis of the antimicrobial cyclic lipopeptides nunamycin and nunapeptin by Pseudomonas fluorescens strain In5 is regulated by the LuxR‐type transcriptional regulator NunF

OpenAIRE

Hennessy, Rosanna C.; Phippen, Christopher B. W.; Nielsen, Kristian F.; Olsson, Stefan; Stougaard, Peter

2017-01-01

Abstract Nunamycin and nunapeptin are two antimicrobial cyclic lipopeptides (CLPs) produced by Pseudomonas fluorescens In5 and synthesized by nonribosomal synthetases (NRPS) located on two gene clusters designated the nun–nup regulon. Organization of the regulon is similar to clusters found in other CLP‐producing pseudomonads except for the border regions where putative LuxR‐type regulators are located. This study focuses on understanding the regulatory role of the LuxR‐type‐encoding gene nun...

The old is new again: asparagine oxidation in calcium-dependent antibiotic biosynthesis.

Science.gov (United States)

Worthington, Andrew S; Burkart, Michael D

2007-03-20

Non-ribosomal peptides are built from both proteinogenic and non-proteinogenic amino acids. The latter resemble amino acids but contain modifications not found in proteins. The recent characterization of a non-heme Fe(2+) and alpha-ketoglutarate-dependent oxygenase that stereospecifically generates beta-hydroxyasparagine, an unnatural amino acid building block for the biosynthesis of calcium-dependent antibiotic, a lipopeptide antibiotic. This work improves our understanding of how these non-proteinogenic amino acids are synthesized.

Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study)

OpenAIRE

OCKY KARNA RADJASA; TORBEN MARTENS; HANS-PETER GROSSART; AGUS SABDONO; MEINHARD SIMON; TONNY BACHTIAR

2005-01-01

A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved s...

Heterologous production of non-ribosomal peptide LLD-ACV in Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Siewers, Verena; Chen, Xiao; Huang, Le

2009-01-01

production of ACV was observed. To improve ACV synthesis, several factors were investigated. Codon optimization of the 5′ end of pcbAB did not significantly increase ACV production. However, a 30-fold enhancement was achieved by lowering the cultivation temperature from 30 to 20 °C. When ACVS and PPTase...... encoding genes were integrated into the yeast genome, a 6-fold decrease in ACV production was observed indicating that gene copy number was one of the rate-limiting factors for ACV production in yeast....

The Presence of Two Cyclase Thioesterases Expands the Conformational Freedom of the Cyclic Peptide Occidiofungin

Science.gov (United States)

Ravichandran, Akshaya; Gu, Ganyu; Escano, Jerome; Lu, Shi-En; Smith, Leif

2014-01-01

Occidiofungin is a cyclic nonribosomally synthesized antifungal peptide with submicromolar activity produced by Gram-negative bacterium Burkholderia contaminans. The biosynthetic gene cluster was confirmed to contain two cyclase thioesterases. NMR analysis revealed that the presence of both thioesterases is used to increase the conformational repertoire of the cyclic peptide. The loss of the OcfN cyclic thioesterase by mutagenesis results in a reduction of conformational variants and an appreciable decrease in bioactivity against Candida species. Presumably, the presence of both asparagine and β-hydroxyasparagine variants coordinate the enzymatic function of both of the cyclase thioesterases. OcfN has presumably evolved to be part of the biosynthetic gene cluster due to its ability to produce structural variants that enhance antifungal activity against some fungi. The enhancement of the antifungal activity from the incorporation of an additional cyclase thioesterase into the biosynthetic gene cluster of occidiofungin supports the need to explore new conformational variants of other therapeutic or potentially therapeutic cyclic peptides. PMID:23394257

Cyanobacteria: photosynthetic factories combining biodiversity, radiation resistance, and genetics to facilitate drug discovery.

Science.gov (United States)

Cassier-Chauvat, Corinne; Dive, Vincent; Chauvat, Franck

2017-02-01

Cyanobacteria are ancient, abundant, and widely diverse photosynthetic prokaryotes, which are viewed as promising cell factories for the ecologically responsible production of chemicals. Natural cyanobacteria synthesize a vast array of biologically active (secondary) metabolites with great potential for human health, while a few genetic models can be engineered for the (low level) production of biofuels. Recently, genome sequencing and mining has revealed that natural cyanobacteria have the capacity to produce many more secondary metabolites than have been characterized. The corresponding panoply of enzymes (polyketide synthases and non-ribosomal peptide synthases) of interest for synthetic biology can still be increased through gene manipulations with the tools available for the few genetically manipulable strains. In this review, we propose to exploit the metabolic diversity and radiation resistance of cyanobacteria, and when required the genetics of model strains, for the production and radioactive ( 14 C) labeling of bioactive products, in order to facilitate the screening for new drugs.

Resveratrol influences platinum pharmacokinetics: A novel mechanism in protection against cisplatin-induced nephrotoxicity.

Science.gov (United States)

Darwish, Mostafa A; Abo-Youssef, Amira M; Khalaf, Marwa M; Abo-Saif, Ali A; Saleh, Ibrahim G; Abdelghany, Tamer M

2018-06-15

Cisplatin (CP) is a widely used drug in treatment of solid tumors. However, the use of CP was hampered by its serious side effects especially nephrotoxicity. This study aims to investigate the effect of resveratrol (RES) on CP-induced nephrotoxicity, particularly, the effect of RES on CP pharmacokinetics (PKs). Male white albino rats were divided to four group's six rats each. The first group received (1%) tween 80 in normal saline and served as control. The second group received RES (30 mg kg -1 ) per day for 14 consecutive day's i.p. The third and fourth groups were given a single i.p. injection of CP (6 mg kg -1 ) with or without pre-treatment of RES (30 mg kg -1 per day for 14 consecutive days), respectively. Following administration of CP, plasma, urine and kidney platinum concentration were monitored to study PKs of CP. Five days after the CP injection, rats were killed; blood samples were collected; kidneys were dissected; and biochemical, immunohistochemical, and histological examinations were performed. Our results revealed that CP treatment significantly deteriorated kidney functions with subsequent alteration in redox balance of the kidney. On the other hand, RES successfully ameliorated CP-induced kidney injury and recovered normal kidney tissue redox status. Importantly, while RES pre-treatment did not significantly alter the plasma CP level, it dramatically decreased the urine concentration of CP and lowered its accumulation into the kidneys. Moreover, it increased CP plasma half-life (t 1/2 ) with subsequent decrease in its elimination rate constant, indicating an important role of PKs modulation in RES protection against CP-induced renal damage. Taken together, RES may protect the kidney tissue from the deleterious effects of CP through constringe of CP renal accumulation and enhancement of CP-induced oxidative stress. Copyright © 2018 Elsevier B.V. All rights reserved.

Pallister–Killian syndrome: Cytogenetics and molecular investigations of mosaic tetrasomy 12p in prenatal chorionic villus and in amniocytes. Strategy of prenatal diagnosis

Directory of Open Access Journals (Sweden)

Francesco Libotte

2016-12-01

Conclusion: New molecular cytogenetic techniques array comparative genomic hybridization and fluorescence in-situ hybridization in association with conventional karyotype are pivotal innovative tools to search for chromosomic anomalies and for a complete prenatal diagnosis, especially in cases such as PKS where array comparative genomic hybridization analysis alone could not show mosaicism of i(12p.

Two novel classes of enzymes are required for the biosynthesis of aurofusarin in Fusarium graminearum

DEFF Research Database (Denmark)

Frandsen, Rasmus John Normand; Schütt, Claes; Lund, Birgitte W.

2011-01-01

genes, aurZ and aurS. Targeted gene replacement of aurZ resulted in the discovery that the compound YWA1, rather than nor-rubrofusarin, is the primary product of F. graminearum polyketide synthase 12 (FgPKS12). AurZ is the first representative of a novel class of dehydratases that act on hydroxylated γ...

Towards Polypharmacokinetics: Pharmacokinetics of Multicomponent Drugs and Herbal Medicines Using a Metabolomics Approach

Directory of Open Access Journals (Sweden)

Ke Lan

2013-01-01

Full Text Available Determination of pharmacokinetics (PKs of multicomponent pharmaceuticals and/or nutraceuticals (polypharmacokinetics, poly-PKs is difficult due to the vast number of compounds present in natural products, their various concentrations across a wide range, complexity of their interactions, as well as their complex degradation dynamics in vivo. Metabolomics coupled with multivariate statistical tools that focus on the comprehensive analysis of small molecules in biofluids is a viable approach to address the challenges of poly-PK. This paper discusses recent advances in the characterization of poly-PK and the metabolism of multicomponent xenobiotic agents, such as compound drugs, dietary supplements, and herbal medicines, using metabolomics strategy. We propose a research framework that integrates the dynamic concentration profile of bioavailable xenobiotic molecules that result from in vivo absorption and hepatic and gut bacterial metabolism, as well as the human metabolic response profile. This framework will address the bottleneck problem in the pharmacological evaluation of multicomponent pharmaceuticals and nutraceuticals, leading to the direct elucidation of the pharmacological and molecular mechanisms of these compounds.

Crystallization and preliminary X-ray analysis of pyruvate kinase from Bacillus stearothermophilus

International Nuclear Information System (INIS)

Suzuki, Kenichiro; Ito, Sohei; Shimizu-Ibuka, Akiko; Sakai, Hiroshi

2005-01-01

This report describes the crystallization and X-ray diffraction data collection of three types (wild-type, W416F/V435W and C9S/C268S) of B. stearothermophilus. Crystals of C9S/C268S belonged to space group P6 2 22 and diffracted to a resolution of 2.4 Å. Pyruvate kinase (PK) from a moderate thermophile, Bacillus stearothermophilus (BstPK), is an allosteric enzyme activated by AMP and ribose 5-phosphate but not by fructose 1,6-bisphosphate (FBP). However, almost all other PKs are activated by FBP. The wild-type and W416F/V435W mutant BstPKs were crystallized by the hanging-drop vapour-diffusion method. However, they were unsuitable for structural analysis because their data sets exhibited low completeness. A crystal suitable for structural analysis was obtained using C9S/C268S enzyme. The crystal belonged to space group P6 2 22, with unit-cell parameters a = b = 145.97, c = 118.03 Å

Synthesis of C-Glucosylated Octaketide Anthraquinones in Nicotiana benthamiana by Using a Multispecies-Based Biosynthetic Pathway.

Science.gov (United States)

Andersen-Ranberg, Johan; Kongstad, Kenneth Thermann; Nafisi, Majse; Staerk, Dan; Okkels, Finn Thyge; Mortensen, Uffe Hasbro; Lindberg Møller, Birger; Frandsen, Rasmus John Normand; Kannangara, Rubini

2017-10-05

Carminic acid is a C-glucosylated octaketide anthraquinone and the main constituent of the natural dye carmine (E120), possessing unique coloring, stability, and solubility properties. Despite being used since ancient times, longstanding efforts to elucidate its route of biosynthesis have been unsuccessful. Herein, a novel combination of enzymes derived from a plant (Aloe arborescens, Aa), a bacterium (Streptomyces sp. R1128, St), and an insect (Dactylopius coccus, Dc) that allows for the biosynthesis of the C-glucosylated anthraquinone, dcII, a precursor for carminic acid, is reported. The pathway, which consists of AaOKS, StZhuI, StZhuJ, and DcUGT2, presents an alternative biosynthetic approach for the production of polyketides by using a type III polyketide synthase (PKS) and tailoring enzymes originating from a type II PKS system. The current study showcases the power of using transient expression in Nicotiana benthamiana for efficient and rapid identification of functional biosynthetic pathways, including both soluble and membrane-bound enzymes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

LaeA and VeA are involved in growth morphology, asexual development, and mycotoxin production in Alternaria alternata.

Science.gov (United States)

Estiarte, N; Lawrence, C B; Sanchis, V; Ramos, A J; Crespo-Sempere, A

2016-12-05

Alternaria alternata is a common filamentous fungus that contaminates various fruits, grains and vegetables causing important economic losses to farmers and the food industry. A. alternata is a mycotoxigenic mould, which may jeopardize human and animal health. Two of the most common A. alternata mycotoxins found in food and feed are alternariol and alternariol monomethyl ether. In this study we examined the role of LaeA and VeA, two regulatory proteins belonging to the velvet family, which have been described to be involved in several functions in many fungi including secondary metabolism. We found that deletion of laeA and veA genes, respectively, greatly reduced sporulation and strongly compromised mycotoxin production, both in vitro or during pathogenesis of tomato fruits. We have also studied how the loss of laeA and veA may affect expression of genes related to alternariol and alternariol monomethyl ether biosynthesis (pksJ and altR), and to melanin biosynthesis (cmrA, pksA). Copyright © 2016 Elsevier B.V. All rights reserved.

Physical Properties of Biomass Fuel Briquette from Oil Palm ...

African Journals Online (AJOL)

ADOWIE PERE

of fuel briquettes in this study in order to supplement the energy mix of the nation. PKS was pulverized ... fossil fuel in the world market is impacting negatively ... useful products that can be applied in many sectors ... at 350 µm, 250 µm and 150 µm with Octagon digital ... formula is one of the models developed to accurately.

Structure, Biosynthesis, and Occurrence of Bacterial Pyrrolizidine Alkaloids.

Science.gov (United States)

Schimming, Olivia; Challinor, Victoria L; Tobias, Nicholas J; Adihou, Hélène; Grün, Peter; Pöschel, Laura; Richter, Christian; Schwalbe, Harald; Bode, Helge B

2015-10-19

Pyrrolizidine alkaloids (PAs) are widespread plant natural products with potent toxicity and bioactivity. Herein, the identification of bacterial PAs from entomopathogenic bacteria using differential analysis by 2D NMR spectroscopy (DANS) and mass spectrometry is described. Their biosynthesis was elucidated to involve a non-ribosomal peptide synthetase. The occurrence of these biosynthesis gene clusters in Gram-negative and Gram-positive bacteria indicates an important biological function in bacteria. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amino Acid Precursor Supply in the Biosynthesis of the RNA Polymerase Inhibitor Streptolydigin by Streptomyces lydicus▿†

OpenAIRE

Gómez, Cristina; Horna, Dina H.; Olano, Carlos; Palomino-Schätzlein, Martina; Pineda-Lucena, Antonio; Carbajo, Rodrigo J.; Braña, Alfredo F.; Méndez, Carmen; Salas, José A.

2011-01-01

Biosynthesis of the hybrid polyketide-nonribosomal peptide antibiotic streptolydigin, 3-methylaspartate, is utilized as precursor of the tetramic acid moiety. The three genes from the Streptomyces lydicus streptolydigin gene cluster slgE1-slgE2-slgE3 are involved in 3-methylaspartate supply. SlgE3, a ferredoxin-dependent glutamate synthase, is responsible for the biosynthesis of glutamate from glutamine and 2-oxoglutarate. In addition to slgE3, housekeeping NADPH- and ferredoxin-dependent glu...

Pentapeptide-repeat proteins that act as topoisomerase poison resistance factors have a common dimer interface

International Nuclear Information System (INIS)

Vetting, Matthew W.; Hegde, Subray S.; Zhang, Yong; Blanchard, John S.

2011-01-01

The pentapeptide repeat protein AlbG, provides self-resistance to the nonribosomally encoded hybrid polyketide-peptide termed albicidin. Analysis of the AlbG three-dimensional structure and the sequences of other pentapeptide repeat proteins that confer resistance to topiosomerase poisons suggests they have a similar dimer interface which may be critical to their interaction with topoisomerases. The protein AlbG is a self-resistance factor against albicidin, a nonribosomally encoded hybrid polyketide-peptide with antibiotic and phytotoxic properties produced by Xanthomonas albilineans. Primary-sequence analysis indicates that AlbG is a member of the pentapeptide-repeat family of proteins (PRP). The structure of AlbG from X. albilineans was determined at 2.0 Å resolution by SAD phasing using data collected from a single trimethyllead acetate derivative on a home source. AlbG folds into a right-handed quadrilateral β-helix composed of approximately eight semi-regular coils. The regularity of the β-helix is blemished by a large loop/deviation in the β-helix between coils 4 and 5. The C-terminus of the β-helix is capped by a dimerization module, yielding a dimer with a 110 Å semi-collinear β-helical axis. This method of dimer formation appears to be common to all PRP proteins that confer resistance to topoisomerase poisons and contrasts with most PRP proteins, which are typically monomeric

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African Journals Online (AJOL)

Ref. Ago Stro Average Average Average Type of failure. Mark No. at test (mm) weight In maximum compressive and remarks. Cube. " TAUmum strength days air (kg) load (kN). (mm). PK, 7 150. 6.75. 126. 5.63 Normal Failure. PKG 7 150 6.36. 119. 5.27 Normal Failure. PKS. 150. 6,39. 108. 4.81 Normal Failure. PK 7 150.

Spectral Evolution of Synchrotron and Inverse Compton Emission in ...

Indian Academy of Sciences (India)

emission peaks in the optical band (e.g., Nieppola et al. 2006). In order to under- stand the evolution of synchrotron and IC spectra of BL Lac objects, the X-ray spectral analysis with XMM–Newton X-ray observations of PKS 2155–304 and. S5 0716+7145 (see Zhang 2008, 2010 for details) was performed. Here, the results.

Polyketide synthase from Fusarium

DEFF Research Database (Denmark)

Kvesel, Kasper; Wimmer, Reinhard; Sørensen, Jens Laurids

described, even fewer from fungi and none from Fusarium species. Multidomain proteins can be quite challenging to work with, which is why the project intends to solve the 3D-structures of single domains of PKS’s. In this project, the plan is to clone, express and purify the Acyl-carrier protein (ACP) domain...... from PKS6 in Fusarium graminearum for structural analysis....

Complete Genome Sequence of the Endophytic Biocontrol Strain Bacillus velezensis CC09.

Science.gov (United States)

Cai, Xunchao; Kang, Xingxing; Xi, Huan; Liu, Changhong; Xue, Yarong

2016-09-29

Bacillus velezensis is a heterotypic synonym of B. methylotrophicus, B. amyloliquefaciens subsp. plantarum, and Bacillus oryzicola, and has been used to control plant fungal diseases. In order to fully understand the genetic basis of antimicrobial capacities, we did a complete genome sequencing of the endophytic B. velezensis strain CC09. Genes tightly associated with biocontrol ability, including nonribosomal peptide synthetases, polyketide synthetases, iron acquisition, colonization, and volatile organic compound synthesis were identified in the genome. Copyright © 2016 Cai et al.

Engineering the Substrate Specificity of the DhbE Adenylation Domain by Yeast Cell Surface Display

OpenAIRE

Zhang, Keya; Nelson, Kathryn M.; Bhuripanyo, Karan; Grimes, Kimberly D.; Zhao, Bo; Aldrich, Courtney C.; Yin, Jun

2013-01-01

The adenylation (A) domains of nonribosomal peptide synthetases (NRPSs) activate aryl acids or amino acids to launch their transfer through the NRPS assembly line for the biosynthesis of many medicinally important natural products. In order to expand the substrate pool of NRPSs, we developed a method based on yeast cell surface display to engineer the substrate specificities of the A-domains. We acquired A-domain mutants of DhbE that have 11- and 6-fold increases in kcat/Km with nonnative sub...

Nunamycin and Nunapeptin: Two novel cyclic peptides are key components of the antimicrobial activity of the Greenlandic isolate Pseudomonas fluorescens In5

DEFF Research Database (Denmark)

Hennessy, Rosanna Catherine; Phippen, Christopher; Nielsen, Kristian F.

Pseudomonas spp. are a rich source of secondary metabolites including bioactive non-ribosomal peptides (NRPs) and polyketides. NRPs are synthesised in large assembly lines by multi-domain modular enzymes known as NRP-synthetases (NRPS). Nunamycin and nunapeptin are two cyclic NRPs synthesised...... by the Greenlandic isolate P. fluorescens In5. Nunamycin shows antifungal activity against the basidiomycete Rhizoctonia solani whereas the only partially structure elucidated nunapeptin appears most active against the ascomycete Fusarium graminearum and the oomycete Pythium aphanidermatum. Originally isolated from...

Chemical Editing of Macrocyclic Natural Products and Kinetic Profiling Reveal Slow, Tight-Binding Histone Deacetylase Inhibitors with Picomolar Affinities

DEFF Research Database (Denmark)

Kitir, Betül; Maolanon, Alex R.; Ohm, Ragnhild G.

2017-01-01

medicines. Therefore, detailed mechanistic information and precise characterization of the chemical probes used to investigate the effects of HDAC enzymes are vital. We interrogated Nature's arsenal of macrocyclic nonribosomal peptide HDAC inhibitors by chemical synthesis and evaluation of more than 30...... natural products and analogues. This furnished surprising trends in binding affinities for the various macrocycles, which were then exploited for the design of highly potent class I and IIb HDAC inhibitors. Furthermore, thorough kinetic investigation revealed unexpected inhibitory mechanisms of important...

Acyl-CoA hydrolysis by the high molecular weight protein 1 subunit of yersiniabactin synthetase: Mutational evidence for a cascade of four acyl-enzyme intermediates during hydrolytic editing

OpenAIRE

Suo, Zucai; Chen, Huawei; Walsh, Christopher T.

2000-01-01

Yersiniabactin (Ybt) synthetase is a three-subunit, 17-domain [7 domains in high molecular weight protein (HMWP)2, 9 in HMWP1, and 1 in YbtE] enzyme producing the virulence-conferring siderophore yersiniabactin in Yersinia pestis. The 350-kDa HMWP1 subunit contains a polyketide synthase module (KS-AT-MT2-KR-ACP) and a nonribosomal peptide synthetase module (Cy3-MT3-PCP3-TE). The full-length HMWP1 was heterologously overexpressed in Escherichia coli and purified...

SeMPI: a genome-based secondary metabolite prediction and identification web server.

Science.gov (United States)

Zierep, Paul F; Padilla, Natàlia; Yonchev, Dimitar G; Telukunta, Kiran K; Klementz, Dennis; Günther, Stefan

2017-07-03

The secondary metabolism of bacteria, fungi and plants yields a vast number of bioactive substances. The constantly increasing amount of published genomic data provides the opportunity for an efficient identification of gene clusters by genome mining. Conversely, for many natural products with resolved structures, the encoding gene clusters have not been identified yet. Even though genome mining tools have become significantly more efficient in the identification of biosynthetic gene clusters, structural elucidation of the actual secondary metabolite is still challenging, especially due to as yet unpredictable post-modifications. Here, we introduce SeMPI, a web server providing a prediction and identification pipeline for natural products synthesized by polyketide synthases of type I modular. In order to limit the possible structures of PKS products and to include putative tailoring reactions, a structural comparison with annotated natural products was introduced. Furthermore, a benchmark was designed based on 40 gene clusters with annotated PKS products. The web server of the pipeline (SeMPI) is freely available at: http://www.pharmaceutical-bioinformatics.de/sempi. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pallister Killian syndrome: unusual significant postnatal overgrowth in a girl with otherwise typical presentation.

Science.gov (United States)

Frković, Sanda Huljev; Durisević, Ivana Tonković; Trcić, Ruzica Lasan; Sarnavka, Vladimir; Gornik, Kristina Crkvenac; Muzinić, Dubravka; Letica, Ljiljana; Barić, Ivo; Begović, Davor

2010-03-01

Pallister Killian syndrome (PKS) is a rare genetic disorder caused by tetrasomy of the short arm of chromosome 12, revealed usually in mosaic distribution of an extra i (12) (p10) chromosome in fibroblasts. The syndrome presents with a recognizable pattern of findings including pigmentary skin changes, coarse face, high forehead, sparse anterior scalp hair, hypertelorism, seizures and progressive psychomotor developmental delay. It was first described independently by Pallister in 1977 and by Killian and Teschler-Nikola in 1981. We report a case of 21 month old girl with PKS and significant overgrowth. Cytogenetic analysis was performed using the GTG banding technique. The karyotype of cultured lymphocytes was normal. The karyotype from skin fibroblasts was established as mosaic tetrasomy of 12p 47,XX,+i (12) (p10)/46,XX. The origin of the extra marker chromosome was determinated by fluorescence in situ hybridization with chromosome 12 specific DNA probes confirming that supernumerary marker is chromosome i (12p) in 68% of cells. Despite the excessive postnatal growth we found low serum growth hormone levels and reduced response to pharmacological stimulation test. This is also the first report of a postnatal patient in our country.

An In Planta-Expressed Polyketide Synthase Produces (R)-Mellein in the Wheat Pathogen Parastagonospora nodorum

Science.gov (United States)

Krill, Christian; Barrow, Russell A.; Chen, Shasha; Trengove, Robert; Oliver, Richard P.; Solomon, Peter S.

2014-01-01

Parastagonospora nodorum is a pathogen of wheat that affects yields globally. Previous transcriptional analysis identified a partially reducing polyketide synthase (PR-PKS) gene, SNOG_00477 (SN477), in P. nodorum that is highly upregulated during infection of wheat leaves. Disruption of the corresponding SN477 gene resulted in the loss of production of two compounds, which we identified as (R)-mellein and (R)-O-methylmellein. Using a Saccharomyces cerevisiae yeast heterologous expression system, we successfully demonstrated that SN477 is the only enzyme required for the production of (R)-mellein. This is the first identification of a fungal PKS that is responsible for the synthesis of (R)-mellein. The P. nodorum ΔSN477 mutant did not show any significant difference from the wild-type strain in its virulence against wheat. However, (R)-mellein at 200 μg/ml inhibited the germination of wheat (Triticum aestivum) and barrel medic (Medicago truncatula) seeds. Comparative sequence analysis identified the presence of mellein synthase (MLNS) homologues in several Dothideomycetes and two sodariomycete genera. Phylogenetic analysis suggests that the MLNSs in fungi and bacteria evolved convergently from fungal and bacterial 6-methylsalicylic acid synthases. PMID:25326302

Potent Nematicidal Activity and New Hybrid Metabolite Production by Disruption of a Cytochrome P450 Gene Involved in the Biosynthesis of Morphological Regulatory Arthrosporols in Nematode-Trapping Fungus Arthrobotrys oligospora.

Science.gov (United States)

Song, Tian-Yang; Xu, Zi-Fei; Chen, Yong-Hong; Ding, Qiu-Yan; Sun, Yu-Rong; Miao, Yang; Zhang, Ke-Qin; Niu, Xue-Mei

2017-05-24

Types of polyketide synthase-terpenoid synthase (PKS-TPS) hybrid metabolites, including arthrosporols with significant morphological regulatory activity, have been elucidated from nematode-trapping fungus Arthrobotrys oligospora. A previous study suggested that the gene cluster AOL_s00215 in A. oligospora was involved in the production of arthrosporols. Here, we report that disruption of one cytochrome P450 monooxygenase gene AOL_s00215g280 in the cluster resulted in significant phenotypic difference and much aerial hyphae. A further bioassay indicated that the mutant showed a dramatic decrease in the conidial formation but developed numerous traps and killed 85% nematodes within 6 h in contact with prey, in sharp contrast to the wild-type strain with no obvious response. Chemical investigation revealed huge accumulation of three new PKS-TPS epoxycyclohexone derivatives with different oxygenated patterns around the epoxycyclohexone moiety and the absence of arthrosporols in the cultural broth of the mutant ΔAOL_s00215g280. These findings suggested that a study on the biosynthetic pathway for morphological regulatory metabolites in nematode-trapping fungus would provide an efficient way to develop new fungal biocontrol agents.

Aspergillus fumigatus melanins: Interference with the host endocytosis pathway and impact on virulence

Directory of Open Access Journals (Sweden)

Thorsten eHeinekamp

2013-01-01

Full Text Available The opportunistic human pathogenic fungus Aspergillus fumigatus produces at least two types of melanin, namely pyomelanin and dihydroxynaphthalene (DHN melanin. Pyomelanin is produced during tyrosine catabolism via accumulation of homogentisic acid. Although pyomelanin protects the fungus against reactive oxygen species and acts as a defense compound in response to cell wall stress, mutants deficient for pyomelanin biosynthesis do not differ in virulence when tested in a murine infection model for invasive pulmonary aspergillosis. DHN melanin is responsible for the characteristic grey-greenish color of A. fumigatus conidia. Mutants lacking a functional polyketide synthase PksP, the enzyme responsible for the initial step in DHN-melanin formation, i.e., the synthesis of naphthopyrone, produce white spores and are attenuated in virulence. The activity of PksP was found to be essential not only for inhibition of apoptosis of phagocytes by interfering with the host PI3K/Akt signaling cascade but also for effective inhibition of acidification of conidia-containing phagolysosomes. These features allow A. fumigatus to survive in phagocytes and thereby to escape from human immune effector cells and to become a successful pathogen.

Regulation of melanin biosynthesis via the dihydroxynaphthalene pathway is dependent on sexual development in the ascomycete Sordaria macrospora.

Science.gov (United States)

Engh, Ines; Nowrousian, Minou; Kück, Ulrich

2007-10-01

The filamentous ascomycete Sordaria macrospora accumulates melanin during sexual development. The four melanin biosynthesis genes pks, teh, sdh and tih were isolated and their homology to genes involved in 1,8 dihydroxynaphthalene (DHN) melanin biosynthesis was shown. The presence of DHN melanin in S. macrospora was further confirmed by disrupting the pks gene encoding a putative polyketide synthase and by RNA interference-mediated silencing of the sdh gene encoding a putative scytalone dehydratase. Because melanin occurs in fruiting bodies that develop through several intermediate stages within 7 days of growth, a Northern analysis of a developmental time-course was conducted. These data revealed a time-dependent regulation of teh and sdh transcript levels. Comparing the transcriptional expression by real-time PCR of melanin biosynthesis genes in the wild type under conditions allowing or repressing sexual development, a significant downregulation during vegetative growth was detected. Quantitative real-time PCR and Northern blot analysis of melanin biosynthesis gene expression in different developmental mutants confirmed that melanin biosynthesis is linked to fruiting body development and is under the control of specific regulatory genes that participate in sexual differentiation.

The grapevine kinome: annotation, classification and expression patterns in developmental processes and stress responses.

Science.gov (United States)

Zhu, Kaikai; Wang, Xiaolong; Liu, Jinyi; Tang, Jun; Cheng, Qunkang; Chen, Jin-Gui; Cheng, Zong-Ming Max

2018-01-01

Protein kinases (PKs) have evolved as the largest family of molecular switches that regulate protein activities associated with almost all essential cellular functions. Only a fraction of plant PKs, however, have been functionally characterized even in model plant species. In the present study, the entire grapevine kinome was identified and annotated using the most recent version of the grapevine genome. A total of 1168 PK-encoding genes were identified and classified into 20 groups and 121 families, with the RLK-Pelle group being the largest, with 872 members. The 1168 kinase genes were unevenly distributed over all 19 chromosomes, and both tandem and segmental duplications contributed to the expansion of the grapevine kinome, especially of the RLK-Pelle group. Ka/Ks values indicated that most of the tandem and segmental duplication events were under purifying selection. The grapevine kinome families exhibited different expression patterns during plant development and in response to various stress treatments, with many being coexpressed. The comprehensive annotation of grapevine kinase genes, their patterns of expression and coexpression, and the related information facilitate a more complete understanding of the roles of various grapevine kinases in growth and development, responses to abiotic stress, and evolutionary history.

Heterologous Expression of Tulip Petal Plasma Membrane Aquaporins in Pichia pastoris for Water Channel Analysis▿

Science.gov (United States)

Azad, Abul Kalam; Sawa, Yoshihiro; Ishikawa, Takahiro; Shibata, Hitoshi

2009-01-01

Water channels formed by aquaporins (AQPs) play an important role in the control of water homeostasis in individual cells and in multicellular organisms. Plasma membrane intrinsic proteins (PIPs) constitute a subclass of plant AQPs. TgPIP2;1 and TgPIP2;2 from tulip petals are members of the PIP family. In this study, we overexpressed TgPIP2;1 and TgPIP2;2 in Pichia pastoris and monitored their water channel activity (WCA) either by an in vivo spheroplast-bursting assay performed after hypo-osmotic shock or by growth assay. Osmolarity, pH, and inhibitors of AQPs, protein kinases (PKs), and protein phosphatases (PPs) affect the WCA of heterologous AQPs in this expression system. The WCA of TgPIP2;2-expressing spheroplasts was affected by inhibitors of PKs and PPs, which indicates that the water channel of this homologue is regulated by phosphorylation in P. pastoris. From the results reported herein, we suggest that P. pastoris can be employed as a heterologous expression system to assay the WCA of PIPs and to monitor the AQP-mediated channel gating mechanism, and it can be developed to screen inhibitors/effectors of PIPs. PMID:19251885

Heterologous expression of tulip petal plasma membrane aquaporins in Pichia pastoris for water channel analysis.

Science.gov (United States)

Azad, Abul Kalam; Sawa, Yoshihiro; Ishikawa, Takahiro; Shibata, Hitoshi

2009-05-01

Water channels formed by aquaporins (AQPs) play an important role in the control of water homeostasis in individual cells and in multicellular organisms. Plasma membrane intrinsic proteins (PIPs) constitute a subclass of plant AQPs. TgPIP2;1 and TgPIP2;2 from tulip petals are members of the PIP family. In this study, we overexpressed TgPIP2;1 and TgPIP2;2 in Pichia pastoris and monitored their water channel activity (WCA) either by an in vivo spheroplast-bursting assay performed after hypo-osmotic shock or by growth assay. Osmolarity, pH, and inhibitors of AQPs, protein kinases (PKs), and protein phosphatases (PPs) affect the WCA of heterologous AQPs in this expression system. The WCA of TgPIP2;2-expressing spheroplasts was affected by inhibitors of PKs and PPs, which indicates that the water channel of this homologue is regulated by phosphorylation in P. pastoris. From the results reported herein, we suggest that P. pastoris can be employed as a heterologous expression system to assay the WCA of PIPs and to monitor the AQP-mediated channel gating mechanism, and it can be developed to screen inhibitors/effectors of PIPs.

Publisher Correction: Resistance to nonribosomal peptide antibiotics mediated by D-stereospecific peptidases.

Science.gov (United States)

Li, Yong-Xin; Zhong, Zheng; Hou, Peng; Zhang, Wei-Peng; Qian, Pei-Yuan

2018-03-07

In the version of this article originally published, the links and files for the Supplementary Information, including Supplementary Tables 1-5, Supplementary Figures 1-25, Supplementary Note, Supplementary Datasets 1-4 and the Life Sciences Reporting Summary, were missing in the HTML. The error has been corrected in the HTML version of this article.

Time Series Analysis of the Quasar PKS 1749+096

Science.gov (United States)

Lam, Michael T.; Balonek, T. J.

2011-01-01

Multiple timescales of variability are observed in quasars at a variety of wavelengths, the nature of which is not fully understood. In 2007 and 2008, the quasar 1749+096 underwent two unprecedented optical outbursts, reaching a brightness never before seen in our twenty years of monitoring. Much lower level activity had been seen prior to these two outbursts. We present an analysis of the timescales of variability over the two regimes using a variety of statistical techniques. An IDL software package developed at Colgate University over the summer of 2010, the Quasar User Interface (QUI), provides effective computation of four time series functions for analyzing underlying trends present in generic, discretely sampled data sets. Using the Autocorrelation Function, Structure Function, and Power Spectrum, we are able to quickly identify possible variability timescales. QUI is also capable of computing the Cross-Correlation Function for comparing variability at different wavelengths. We apply these algorithms to 1749+096 and present our analysis of the timescales for this object. Funding for this project was received from Colgate University, the Justus and Jayne Schlichting Student Research Fund, and the NASA / New York Space Grant.

Fungal NRPS-dependent siderophores: From function to prediction

DEFF Research Database (Denmark)

Sørensen, Jens Laurids; Knudsen, Michael; Hansen, Frederik Teilfeldt

2014-01-01

discuss the function of siderophores in relation to fungal iron uptake mechanisms and their importance for coexistence with host organisms. The chemical nature of the major groups of siderophores and their regulation is described along with the function and architecture of the large multi-domain enzymes...... responsible for siderophore synthesis, namely the non-ribosomal peptide synthetases (NRPSs). Finally, we present the most recent advances in our understanding of the structural biology of fungal NRPSs and discuss opportunities for the development of a fungal NRPS prediction server...

BROAD Lyα EMISSION FROM THREE NEARBY BL LACERTAE OBJECTS

International Nuclear Information System (INIS)

Stocke, John T.; Danforth, Charles W.; Perlman, Eric S.

2011-01-01

We present far-UV HST/COS spectra of four nearby BL Lac objects. BL Lac spectra are dominated by a smooth, power-law continuum which arises in a relativistic jet. However, the spectra are not necessarily featureless; weak, broad- and/or narrow-line emission is sometimes seen in high-quality optical spectra. We present detections of Lyα emission in HST/COS spectra of Mrk 421 (z = 0.030) and PKS 2005-489 (z = 0.071) as well as an archival HST/GHRS observation of Mrk 501 (z = 0.0337). Archival HST/STIS observations of PKS 2155-304 (z = 0.116) show no Lyα emission to a very low upper limit. Using the assumption that the broad-line region (BLR) clouds are symmetrically placed around the active galactic nucleus (AGN), we use these measured Lyα emission features to constrain either the relativistic Γ values for the ionizing continuum produced by the jet (in the ionization-bounded case) or the mass of warm gas (in the density-bounded case). While realistic Γ values can be obtained for all four cases, the values for Mrk 421 and PKS 2155-304 are high enough to suggest that covering factors of BLR clouds of ∼1%-2% might be required to provide consistency with earlier values of Doppler boosting and viewing angles suggested for this class of BL Lacs. This discrepancy also exists in the case of M 87, where the amount of Doppler boosting in our direction is expected to be minimal, again suggestive of a small covering factor of BLR clouds. If, as these small covering factors might suggest, the assumptions of a density-bounded model could be more correct, then the observed Lyα luminosities require that BL Lac/FR 1 nuclei possess very little warm gas (10 -4 to 10 -5 M sun ) as suggested by Guilbert et al. If these clouds are in pressure balance with a hotter (∼10 6 K) gas, the BLR contains too little mass to power the AGN by accretion alone.

A Survey on the Usage of Biomass Wastes from Palm Oil Mills on Sustainable Development of Oil Palm Plantations in Sarawak

Science.gov (United States)

Phang, K. Y.; Lau, S. W.

2017-06-01

As one of the world’s largest palm oil producers and exporters, Malaysia is committed to sustainable management of this industry to address the emerging environmental challenges. This descriptive study aims to evaluate the oil palm planters’ opinions regarding the usage of biomass wastes from palm oil mills and its impact on sustainable development of oil palm plantations in Sarawak. 253 planters across Sarawak were approached for their opinions about the usage of empty fruit bunch (EFB), palm oil mill effluent (POME), mesocarp fibre (MF), and palm kernel shell (PKS). This study revealed that the planters had generally higher agreement on the beneficial application of EFB and POME in oil palm plantations. This could be seen from the higher means of agreement rating of 3.64 - 4.22 for EFB and POME, compared with the rating of 3.19 - 3.41 for MF and PKS in the 5-point Likert scale (with 5 being the strongest agreement). Besides, 94.7 percent of the planters’ companies were found to comply with the Environmental Impact Assessment (EIA) requirements where nearly 38 percent carried out the EIA practice twice a year. Therefore high means of agreement were correlated to the compliance of environmental regulations, recording a Likert rating of 3.89 to 4.31. Lastly, the usage of EFB and POME also gained higher Likert scale point of 3.76 to 4.17 against MF and PKS of 3.34 to 3.49 in the evaluation of the impact of sustainability in oil palm plantations. The planters agreed that the usage of EFB and POME has reduced the environmental impact and improved the sustainable development, and its application has been improved and increased by research and development. However the planters were uncertain of the impact of usage of biomass wastes with respect to the contribution to social responsibility and company image in terms of transparency in waste management.

Identification of cellular targets involved in cardiac failure caused by PKI in oncology: an approach combining pharmacovigilance and pharmacodynamics.

Science.gov (United States)

Patras de Campaigno, Emilie; Bondon-Guitton, Emmanuelle; Laurent, Guy; Montastruc, Francois; Montastruc, Jean-Louis; Lapeyre-Mestre, Maryse; Despas, Fabien

2017-07-01

The aims of the present study were to evaluate the risk of cardiac failure (CF) associated with 15 anticancer protein kinase inhibitors (PKIs) through a case/noncase analysis and to identify which PK(s) and pathways are involved in PKI-induced CF. In order to evaluate the risk of CF, adjusted reporting odds ratios (aRORs) were calculated for the 15 anticancer PKIs in the World Health Organization safety report database (VigiBase®). We realised a literature review to identify 21 protein kinases (PKs) that were possibly involved in CF caused by PKIs. Pearson correlation coefficients (r) between aRORs and affinity data of the 15 PKIs for the 21 PKs were calculated to identify the cellular target most likely to be involved in PKI-induced CF. A total of 141 601 individual case safety reports (ICSRs) were extracted from VigiBase® for the following PKIs: afatinib, axitinib, bosutinib, crizotinib, dasatinib, erlotinib, gefitinib, imatinib, lapatinib, nilotinib, pazopanib, ruxolitinib, sorafenib, sunitinib and vandetanib. Among them, 2594 ICSRs concerned CF. The disproportionality analysis revealed that, for dasatinib, imatinib, bosutinib, sunitinib and nilotinib, disproportionality for CF was significantly higher than for other PKIs, with aRORs of 2.52 [95% CI 2.26, 2.82], 1.79 (95% CI 1.57, 2.03), 1.73 (95% CI 1.18, 2.54), 1.67 (95% CI 1.51, 1.84) and 1.38 (95% CI 1.18, 1.61), respectively. Significant values for correlation coefficients between the product of dissociation constant (pKd) and aROR were observed for two non-receptor protein kinases: ABL1 (non-phosphorylated and phosphorylated forms) and ABL2 protein kinases, with values of r = 0.83 (P = 0.0001), r = 0.75 (P = 0.0014) and r = 0.78 (P = 0.0006), respectively. We observed a higher disproportionality for CF with dasatinib, imatinib, bosutinib, sunitinib and nilotinib than with other PKIs. In addition, the study highlighted the role of ABL tyrosine kinases in CF caused by anticancer PKIs. © 2017 The British

Proteomics of Aspergillus fumigatus Conidia-containing Phagolysosomes Identifies Processes Governing Immune Evasion.

Science.gov (United States)

Schmidt, Hella; Vlaic, Sebastian; Krüger, Thomas; Schmidt, Franziska; Balkenhol, Johannes; Dandekar, Thomas; Guthke, Reinhard; Kniemeyer, Olaf; Heinekamp, Thorsten; Brakhage, Axel A

2018-06-01

Invasive infections by the human pathogenic fungus Aspergillus fumigatus start with the outgrowth of asexual, airborne spores (conidia) into the lung tissue of immunocompromised patients. The resident alveolar macrophages phagocytose conidia, which end up in phagolysosomes. However, A. fumigatus conidia resist phagocytic degradation to a certain degree. This is mainly attributable to the pigment 1,8-dihydroxynaphthalene (DHN) melanin located in the cell wall of conidia, which manipulates the phagolysosomal maturation and prevents their intracellular killing. To get insight in the underlying molecular mechanisms, we comparatively analyzed proteins of mouse macrophage phagolysosomes containing melanized wild-type (wt) or nonmelanized pksP mutant conidia. For this purpose, a protocol to isolate conidia-containing phagolysosomes was established and a reference protein map of phagolysosomes was generated. We identified 637 host and 22 A. fumigatus proteins that were differentially abundant in the phagolysosome. 472 of the host proteins were overrepresented in the pksP mutant and 165 in the wt conidia-containing phagolysosome. Eight of the fungal proteins were produced only in pksP mutant and 14 proteins in wt conidia-containing phagolysosomes. Bioinformatical analysis compiled a regulatory module, which indicates host processes affected by the fungus. These processes include vATPase-driven phagolysosomal acidification, Rab5 and Vamp8-dependent endocytic trafficking, signaling pathways, as well as recruitment of the Lamp1 phagolysosomal maturation marker and the lysosomal cysteine protease cathepsin Z. Western blotting and immunofluorescence analyses confirmed the proteome data and moreover showed differential abundance of the major metabolic regulator mTOR. Taken together, with the help of a protocol optimized to isolate A. fumigatus conidia-containing phagolysosomes and a potent bioinformatics algorithm, we were able to confirm A. fumigatus conidia

A Survey of occurrence of toxogenic fungi and mycotoxins in pig feed samples-Use in evaluation of risk assessment

Directory of Open Access Journals (Sweden)

Dragan Milicevic

Full Text Available In order to assess of risk assessment, the aim of this paper was to provide good and detailed insight into the level of contamination of complete feedmixes intended for fattening swine from mycotoxin-producing fungi and mycotoxins (n=18. Isolation and quantitative enumeration of fungal propagules were done on solid media using the standard microbiological procedure. These plates were incubated the number of colonies was determined and thent on the basis of characteristic colonies and microscopic analysis was performed to identify genera and species of moulds. Isolates identified as Aspergillus and Penicillium species were subjected to molecular characterization of the presence of genes responsible for the synthesis of OTA (polyketide synthase gene-PKS. Total fungal counts (CFU/g ranged from 0,5x105 do 4x106. From a total samples analysed, seven samples had fungal counts higher than the limit established by Serbian regulations (3x105. During a mycological analysis of complete feedmixes intended for fattening swine, a total of six genera and 14 species of moulds were identified of which the most frequent one was of the genus Penicillium (94,4% while the moulds from Fusarium genere isolated in 55,5% and Paecilomyces in 44,4% of the samples from investigated localities. Other fungi from the genera Aspergillus (22%, Mycor (11,1% and Alternaria (5,5% were represented in a less amount. Polymerase chain reaction (PCR is a set of 18 isolates of the DNA belonging to families Penicillium and Aspergillus. The sequences of PCR reaction products in three samples were compared with nucleotide sequences of genes for poliketid synthase (PKS from Penicillium species and found that the samples possess PKS sequence. The traditional methods for identification of ochratoxin-producing fungi are time-consuming and labor-intensive. Rapid and specific detection of ochratoxinproducing fungi is important for ensuring microbiological quality and safety of feed and food

Brevibacillus laterosporus, a Pathogen of Invertebrates and a Broad-Spectrum Antimicrobial Species

Directory of Open Access Journals (Sweden)

Luca Ruiu

2013-09-01

Full Text Available Brevibacillus laterosporus, a bacterium characterized by the production of a unique canoe-shaped lamellar body attached to one side of the spore, is a natural inhabitant of water, soil and insects. Its biopesticidal potential has been reported against insects in different orders including Coleoptera, Lepidoptera, Diptera and against nematodes and mollusks. In addition to its pathogenicity against invertebrates, different B. laterosporus strains show a broad-spectrum antimicrobial activity including activity against phytopathogenic bacteria and fungi. A wide variety of molecules, including proteins and antibiotics, have been associated with the observed pathogenicity and mode of action. Before being considered as a biological control agent against plant pathogens, the antifungal and antibacterial properties of certain B. laterosporus strains have found medical interest, associated with the production of antibiotics with therapeutic effects. The recent whole genome sequencing of this species revealed its potential to produce polyketides, nonribosomal peptides, and toxins. Another field of growing interest is the use of this bacterium for bioremediation of contaminated sites by exploiting its biodegradation properties. The aim of the present review is to gather and discuss all recent findings on this emerging entomopathogen, giving a wider picture of its complex and broad-spectrum biocontrol activity.

Heterologous Production and Yield Improvement of Epothilones in Burkholderiales Strain DSM 7029.

Science.gov (United States)

Bian, Xiaoying; Tang, Biao; Yu, Yucong; Tu, Qiang; Gross, Frank; Wang, Hailong; Li, Aiying; Fu, Jun; Shen, Yuemao; Li, Yue-Zhong; Stewart, A Francis; Zhao, Guoping; Ding, Xiaoming; Müller, Rolf; Zhang, Youming

2017-07-21

The cloning of microbial natural product biosynthetic gene clusters and their heterologous expression in a suitable host have proven to be a feasible approach to improve the yield of valuable natural products and to begin mining cryptic natural products in microorganisms. Myxobacteria are a prolific source of novel bioactive natural products with only limited choices of heterologous hosts that have been exploited. Here, we describe the use of Burkholderiales strain DSM 7029 as a potential heterologous host for the functional expression of myxobacterial secondary metabolites. Using a newly established electroporation procedure, the 56 kb epothilone biosynthetic gene cluster from the myxobacterium Sorangium cellulosum was introduced into the chromosome of strain DSM 7029 by transposition. Production of epothilones A, B, C, and D was detected despite their yields being low. Optimization of the medium, introduction of the exogenous methylmalonyl-CoA biosynthetic pathway, and overexpression of rare tRNA genes resulted in an approximately 75-fold increase in the total yields of epothilones to 307 μg L -1 . These results show that strain DSM 7029 has the potential to produce epothilones with reasonable titers and might be a broadly applicable host for the heterologous expression of other myxobacterial polyketide synthases and nonribosomal peptide synthetases, expediting the process of genome mining.

Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from Irish waters.

Science.gov (United States)

Kennedy, Jonathan; Baker, Paul; Piper, Clare; Cotter, Paul D; Walsh, Marcella; Mooij, Marlies J; Bourke, Marie B; Rea, Mary C; O'Connor, Paula M; Ross, R Paul; Hill, Colin; O'Gara, Fergal; Marchesi, Julian R; Dobson, Alan D W

2009-01-01

Samples of the marine sponge Haliclona simulans were collected from Irish coastal waters, and bacteria were isolated from these samples. Phylogenetic analyses of the cultured isolates showed that four different bacterial phyla were represented; Bacteriodetes, Actinobacteria, Proteobacteria, and Firmicutes. The sponge bacterial isolates were assayed for the production of antimicrobial substances, and biological activities against Gram-positive and Gram-negative bacteria and fungi were demonstrated, with 50% of isolates showing antimicrobial activity against at least one of the test strains. Further testing showed that the antimicrobial activities extended to the important pathogens Pseudomonas aeruginosa, Clostridium difficile, multi-drug-resistant Staphylococcus aureus, and pathogenic yeast strains. The Actinomycetes were numerically the most abundant producers of antimicrobial activities, although activities were also noted from Bacilli and Pseudovibrio isolates. Surveys for the presence of potential antibiotic encoding polyketide synthase and nonribosomal peptide synthetase genes also revealed that genes for the biosynthesis of these secondary metabolites were present in most bacterial phyla but were particularly prevalent among the Actinobacteria and Proteobacteria. This study demonstrates that the culturable fraction of bacteria from the sponge H. simulans is diverse and appears to possess much potential as a source for the discovery of new medically relevant biological active agents.

Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by 'Entotheonella'.

Science.gov (United States)

Nakashima, Yu; Egami, Yoko; Kimura, Miki; Wakimoto, Toshiyuki; Abe, Ikuro

2016-01-01

Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an 'Entotheonella' sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.

Diversity Profile and Dynamics of Peptaibols Produced by Green Mould Trichoderma Species in Interactions with Their Hosts Agaricus bisporus and Pleurotus ostreatus.

Science.gov (United States)

Marik, Tamás; Urbán, Péter; Tyagi, Chetna; Szekeres, András; Leitgeb, Balázs; Vágvölgyi, Máté; Manczinger, László; Druzhinina, Irina S; Vágvölgyi, Csaba; Kredics, László

2017-06-01

Certain Trichoderma species are causing serious losses in mushroom production worldwide. Trichoderma aggressivum and Trichoderma pleuroti are among the major causal agents of the green mould diseases affecting Agaricus bisporus and Pleurotus ostreatus, respectively. The genus Trichoderma is well-known for the production of bioactive secondary metabolites, including peptaibols, which are short, linear peptides containing unusual amino acid residues and being synthesised via non-ribosomal peptide synthetases (NRPSs). The aim of this study was to get more insight into the peptaibol production of T. aggressivum and T. pleuroti. HPLC/MS-based methods revealed the production of peptaibols closely related to hypomurocins B by T. aggressivum, while tripleurins representing a new group of 18-residue peptaibols were identified in T. pleuroti. Putative NRPS genes enabling the biosynthesis of the detected peptaibols could be found in the genomes of both Trichoderma species. In vitro experiments revealed that peptaibols are potential growth inhibitors of mushroom mycelia, and that the host mushrooms may have an influence on the peptaibol profiles of green mould agents. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.

Directory of Open Access Journals (Sweden)

Augix Guohua Xu

Full Text Available Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20-28% of non-ribosomal transcripts correspond to annotated exons and 20-23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40-48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20% represents 3'UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits.

Identification of Four New agr Quorum Sensing-Interfering Cyclodepsipeptides from a Marine Photobacterium

DEFF Research Database (Denmark)

Kjærulff, Louise; Nielsen, Anita; Månsson, Maria

2013-01-01

During our search for new natural products from the marine environment, we discovered a wide range of cyclic peptides from a marine Photobacterium, closely related to P. halotolerans. The chemical fingerprint of the bacterium showed primarily non-ribosomal peptide synthetase (NRPS)-like compounds......, including the known pyrrothine antibiotic holomycin and a wide range of peptides, from diketopiperazines to cyclodepsipeptides of 500–900 Da. Purification of components from the pellet fraction led to the isolation and structure elucidation of four new cyclodepsipeptides, ngercheumicin F, G, H, and I...

Metabollic Engineering of Saccharomyces Cereviae a,omi acid metabolism for production of products of industrial interest

DEFF Research Database (Denmark)

Chen, Xiao

-based processes. This study has focused on metabolic engineering of the amino acid metabolism in S. cerevisiae for production of two types of chemicals of industrial interest. The first chemical is δ-(L-α-aminoadipyl)–L-cysteinyl–D-valine (LLD-ACV). ACV belongs to non-ribosomal peptides (NRPs), which......Saccharomyces cerevisiae is widely used in microbial production of chemicals, metabolites and proteins, mainly because genetic manipulation of S. cerevisiae is relatively easy and experiences from its wide application in the existing industrial fermentations directly benefit new S. cerevisiae...

Harnessing natural product assembly lines: structure, promiscuity, and engineering.

Science.gov (United States)

Ladner, Christopher C; Williams, Gavin J

2016-03-01

Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.

LHCb: Measuring $CP$ Violation in $\\Lambda_{c}^{+}$ Decays at LHCb

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Pearce, A

2013-01-01

An ongoing analysis of a measurement of CP violation in decays of the charmed baryon $\\Lambda_{c}^{+}$, using the full $3\\mathrm{fb}^{-1}$ of data collected by LHCb in 2011 and 2012, is presented. The detection asymmetry of the final states is considered, leading to the use of the narrow $p\\phi$ and $pK_{s}^{0}$ resonances in the $pK^{+}K^{-}$ and $p\\pi^{+}\\pi^{-}$ phase spaces, respectively.

Phosphagen kinase in Schistosoma japonicum: characterization of its enzymatic properties and determination of its gene structure.

Science.gov (United States)

Tokuhiro, Shinji; Uda, Kouji; Yano, Hiroko; Nagataki, Mitsuru; Jarilla, Blanca R; Suzuki, Tomohiko; Agatsuma, Takeshi

2013-04-01

Phosphagen kinases (PKs) play a major role in the regulation of energy metabolism in animals. Creatine kinase (CK) is the sole PK in vertebrates, whereas several PKs are present in invertebrates. Here, we report the enzymatic properties and gene structure of PK in the trematode Schistosoma japonicum (Sj). SjPK has a unique contiguous dimeric structure comprising domain 1 (D1) and domain 2 (D2). The three states of the recombinant SjPK (D1, D2, and D1D2) show a specific activity for the substrate taurocyamine. The comparison of the two domains of SjPK revealed that D1 had a high turnover rate (kcat=52.91) and D2 exhibited a high affinity for taurocyamine (Km(Tauro) =0.53±0.06). The full-length protein exhibited higher affinity for taurocyamine (Km(Tauro) =0.47±0.03) than the truncated domains (D1=1.30±0.10, D2=0.53±0.06). D1D2 also exhibited higher catalytic efficiency (kcat/Km(Tauro) =82.98) than D1 (40.70) and D2 (29.04). These results demonstrated that both domains of SjTKD1D2 interacted efficiently and remained functional. The three-dimensional structure of SjPKD1 was constructed by the homology modeling based on the transition state analog complex state of Limulus AK. This protein model of SjPKD1 suggests that the overall structure is almost conserve between SjPKD1 and Limulus AK except for the flexible loops, that is, particularly guanidino-specificity (GS) region, which is associated with the recognition of the corresponding guanidino substrate. The constructed NJ tree and the comparison of exon/intron organization suggest that SjTK has evolved from an arginine kinase (AK) gene. SjTK has potential as a novel antihelminthic drug target as it is absent in mammals and its strong activity may imply a significant role for this protein in the energy metabolism of the parasite. Copyright © 2013 Elsevier B.V. All rights reserved.

THE SEARCH FOR BLAZARS AMONG THE UNIDENTIFIED EGRET gamma-RAY SOURCES

Directory of Open Access Journals (Sweden)

Pieter J. Meintjes

2013-12-01

Full Text Available In this paper we report the results of a multi-wavelength follow-up study of selected flat spectrum extragalactic radio-optical counterparts within the error boxes of 13 unidentified EGRET sources. Two of these previously unidentified counterparts have been selected for optical photometric and spectroscopic follow-up studies. Spectroscopic observations made with the 4.1m SOAR telescope at Cerro Pachón, Chile, showed that the spectra of the optical counterparts of 3EG J0821−5814 (PKS J0820−5705 and 3EG J0706−3837 (PMN J0710−3835 correspond to a flat spectrum radio quasar (FSRQ and LINER-Seyfert I galaxy respectively. Optical photometry of these sources, performed with the 1.0m telescope at Sutherland (South-Africa shows noticeable intranight variability for PKS J0820−5705, as well as a 5 sigma variation of the mean brightness in the R-filter over a timescale of three nights. Significant variability has been detected in the B-band for PMN J0710−3835 as well. The gamma-ray spectral indices of all 13 candidates range between 2–3, correlating well with the BL Lacs and FSRQs detected with Fermi-LAT in the first 11 months of operation.

MATE transport of the E. coli-derived genotoxin colibactin

Science.gov (United States)

Mousa, Jarrod J.; Yang, Ye; Tomkovich, Sarah; Shima, Ayaka; Newsome, Rachel C.; Tripathi, Prabhanshu; Oswald, Eric; Bruner, Steven D.; Jobin, Christian

2017-01-01

Various forms of cancer have been linked to the carcinogenic activities of microorganisms1–3. The virulent gene island polyketide synthase (pks) produces the secondary metabolite colibactin, a genotoxic molecule(s) causing double-stranded DNA breaks4 and enhanced colorectal cancer development5,6. Colibactin biosynthesis involves a prodrug resistance strategy where an N-terminal prodrug scaffold (precolibactin) is assembled, transported into the periplasm and cleaved to release the mature product7–10. Here, we show that ClbM, a multidrug and toxic compound extrusion (MATE) transporter, is a key component involved in colibactin activity and transport. Disruption of clbM attenuated pks+ E. coli-induced DNA damage in vitro and significantly decreased the DNA damage response in gnotobiotic Il10−/− mice. Colonization experiments performed in mice or zebrafish animal models indicate that clbM is not implicated in E. coli niche establishment. The X-ray structure of ClbM shows a structural motif common to the recently described MATE family. The 12-transmembrane ClbM is characterized as a cation-coupled antiporter, and residues important to the cation-binding site are identified. Our data identify ClbM as a precolibactin transporter and provide the first structure of a MATE transporter with a defined and specific biological function. PMID:27571755

Effective potential for non-convex potentials

International Nuclear Information System (INIS)

Fujimoto, Y.; O'Raifeartaigh, L.; Parravicini, G.

1983-01-01

It is shown that the well-known relationship between the effective potential GAMMA and the vacuum graphs μ of scalar QFT follows directly from the translational invariance of the measure, and that it holds for all values of the fields phi if, and only if, the classical potential is convex. In the non-convex case μ appears to become complex for some values of phi, but it is shown that the complexity is only apparent and is due to the failure of the loop expansion. The effective potential actually remains real and well-defined for all phi, and reduces to μ in the neighbourhood of the classical minima. A number of examples are considered, notably potentials which are spontaneously broken. In particular the mechanism by which a spontaneous breakdown may be generated by radiative corrections is re-investigated and some new insights obtained. Finally, it is shown that the renormalization group equations for the parameters may be obtained by inspection from the effective potential, and among the examples considered are SU(n) fields and supermultiplets. In particular, it is shown that for supermultiplets the effective potential is not only real but positive. (orig.)

Use of octaketide synthases to produce kermesic acid and flavokermesic acid

DEFF Research Database (Denmark)

2017-01-01

A method for producing an octaketide derived aromatic compound of interest (e.g. carminic acid), wherein the method comprises (I): heterologous expression of a recombinantly introduced Type III polyketide synthase (PKS) gene encoding an octaketide synthase (OKS) to obtain non-reduced octaketide...... in vivo within the recombinant host cell and (II): converting in vivo the non-reduced octaketide of step (I) into a C14-C34 aromatic compound of interest (e.g. carminic acid)....

Use of octaketide synthases to produce kermesic acid and flavokermesic acid

DEFF Research Database (Denmark)

2016-01-01

A method for producing an octaketide derived aromatic compound of interest (e.g. carminic acid), wherein the method comprises (I): heterologous expression of a recombinantly introduced Type III polyketide synthase (PKS) gene encoding an octaketide synthase (OKS) to obtain non-reduced octaketide...... in vivo within the recombinant host cell and (II): converting in vivo the non-reduced octaketide of step (I) into a C14-C34 aromatic compound of interest (e.g. carminic acid)....

Identification and reconstitution of the polyketide synthases responsible for biosynthesis of the anti-malarial agent, cladosporin

OpenAIRE

Cochrane, Rachel V. K.; Sanichar, Randy; Lambkin, Gareth R.; Reiz, Béla; Xu, Wei; Tang, Yi; Vederas, John C.

2015-01-01

The anti-malarial agent cladosporin is a nanomolar inhibitor of Plasmodium falciparum lysyl-tRNA synthetase, and exhibits activity against both blood and liver stage infection. Cladosporin can be isolated from the fungus Cladosporium cladosporioides, where it was believed to be biosynthesized by a highly reducing (HR) and non-reducing (NR) iterative type I polyketide synthase (PKS) pair. Genome sequencing of the host organism, and subsequent heterologous expression of these enzymes in Sacchar...

Revelation and cloning of valinomycin synthetase genes in Streptomyces lavendulae ACR-DA1 and their expression analysis under different fermentation and elicitation conditions.

Science.gov (United States)

Sharma, Richa; Jamwal, Vijaylakshmi; Singh, Varun P; Wazir, Priya; Awasthi, Praveen; Singh, Deepika; Vishwakarma, Ram A; Gandhi, Sumit G; Chaubey, Asha

2017-07-10

Streptomyces species are amongst the most exploited microorganisms due to their ability to produce a plethora of secondary metabolites with bioactive potential, including several well known drugs. They are endowed with immense unexplored potential and substantial efforts are required for their isolation as well as characterization for their bioactive potential. Unexplored niches and extreme environments are host to diverse microbial species. In this study, we report Streptomyces lavendulae ACR-DA1, isolated from extreme cold deserts of the North Western Himalayas, which produces a macrolactone antibiotic, valinomycin. Valinomycin is a K + ionophoric non-ribosomal cyclodepsipeptide with a broad range of bioactivities including antibacterial, antifungal, antiviral and cytotoxic/anticancer activities. Production of valinomycin by the strain S. lavendulae ACR-DA1 was studied under different fermentation conditions like fermentation medium, temperature and addition of biosynthetic precursors. Synthetic medium at 10°C in the presence of precursors i.e. valine and pyruvate showed enhanced valinomycin production. In order to assess the impact of various elicitors, expression of the two genes viz. vlm1 and vlm2 that encode components of heterodimeric valinomycin synthetase, was analyzed using RT-PCR and correlated with quantity of valinomycin using LC-MS/MS. Annelid, bacterial and yeast elicitors increased valinomycin production whereas addition of fungal and plant elicitors down regulated the biosynthetic genes and reduced valinomycin production. This study is also the first report of valinomycin biosynthesis by Streptomyces lavendulae. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection techniques for the H.E.S.S. II telescope, data modeling of gravitational lensing and emission of blazars in HE-VHE astronomy

International Nuclear Information System (INIS)

Barnacka, Anna

2013-01-01

This thesis presents the study of four aspects of high energy astronomy. The first part of my thesis is dedicated to an aspect of instrument development for imaging atmospheric Cherenkov telescopes, namely the Level 2 trigger system of the High Energy Stereoscopic System (H.E.S.S.). My work on the project focused on the algorithm development and the Monte Carlo simulations of the trigger system and overall instrument. The hardware implementation of the system is described and its expected performances are then evaluated. The H.E.S.S. array has been used to observe the blazar PKS 1510-089. The second part of my thesis deals with the data analysis and modeling of broad-band emission of this particular blazar. In part II of my thesis, I am presenting the analysis of the H.E.S.S. data: the light curve and spectrum of PKS 1510-089, together with the FERMI data and a collection of multi-wavelength data obtained with various instruments. I am presenting the model of PKS 1510-089 observations carried out during a flare recorded by H.E.S.S.. The model is based on a single zone internal shock scenario. The third part of my thesis deals with blazars observed by the FERMI-LAT, but from the point of view of other phenomena: a strong gravitational lensing. This part of my thesis shows the first evidence for gravitational lensing phenomena in high energy gamma-rays. This evidence comes from the observation of a gravitational lens system induced echo in the light curve of the distant blazar PKS 1830-211. Traditional methods for the estimation of time delays in gravitational lensing systems rely on the cross-correlation of the light curves from individual images. In my thesis, I used 300 MeV-30 GeV photons detected by the Fermi-LAT instrument. The FERMI-LAT instrument cannot separate the images of known lenses. The observed light curve is thus the superposition of individual image light curves. The FERMI-LAT instrument has the advantage of providing long, evenly spaced, time series

Pseudo potentials and model potentials in atomic collisions

International Nuclear Information System (INIS)

Reyes, O.; Jouin, H.; Fuentealba, P.

1988-01-01

In this work, it is discussed the main differences between the use of pseudo-potentials and model potentials in collision problems . It is shown the potential energy curves for distinct systems obtained with both kinds of potentials. (A.C.A.S.) [pt

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes.

Science.gov (United States)

Boivin, Vincent; Deschamps-Francoeur, Gabrielle; Couture, Sonia; Nottingham, Ryan M; Bouchard-Bourelle, Philia; Lambowitz, Alan M; Scott, Michelle S; Abou-Elela, Sherif

2018-07-01

Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. S tructured n on c oding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing. © 2018 Boivin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Role of MbtH-like Proteins in the Adenylation of Tyrosine during Aminocoumarin and Vancomycin Biosynthesis*

Science.gov (United States)

Boll, Björn; Taubitz, Tatjana; Heide, Lutz

2011-01-01

MbtH-like proteins consist of ∼70 amino acids and are encoded in the biosynthetic gene clusters of non-ribosomally formed peptides and other secondary metabolites derived from amino acids. Recently, several MbtH-like proteins have been shown to be required for the adenylation of amino acid in non-ribosomal peptide synthesis. We now investigated the role of MbtH-like proteins in the biosynthesis of the aminocoumarin antibiotics novobiocin, clorobiocin, and simocyclinone D8 and of the glycopeptide antibiotic vancomycin. The tyrosine-adenylating enzymes CloH, SimH, and Pcza361.18, involved in the biosynthesis of clorobiocin, simocyclinone D8, and vancomycin, respectively, required the presence of MbtH-like proteins in a 1:1 molar ratio, forming heterotetrameric complexes. In contrast, NovH, involved in novobiocin biosynthesis, showed activity in the absence of MbtH-like proteins. Comparison of the active centers of CloH and NovH showed only one amino acid to be different, i.e. Leu-383 versus Met-383. Mutation of this amino acid in CloH (L383M) indeed led to MbtH-independent adenylating activity. All investigated tyrosine-adenylating enzymes exhibited remarkable promiscuity for MbtH-like proteins from different pathways and organisms. YbdZ, the MbtH-like protein from the expression host Escherichia coli, was found to bind to adenylating enzymes during expression and to influence their biochemical properties markedly. Therefore, the use of ybdZ-deficient expression hosts is important in biochemical studies of adenylating enzymes. PMID:21890635

An engineered yeast efficiently secreting penicillin.

Directory of Open Access Journals (Sweden)

Loknath Gidijala

Full Text Available This study aimed at developing an alternative host for the production of penicillin (PEN. As yet, the industrial production of this beta-lactam antibiotic is confined to the filamentous fungus Penicillium chrysogenum. As such, the yeast Hansenula polymorpha, a recognized producer of pharmaceuticals, represents an attractive alternative. Introduction of the P. chrysogenum gene encoding the non-ribosomal peptide synthetase (NRPS delta-(L-alpha-aminoadipyl-L-cysteinyl-D-valine synthetase (ACVS in H. polymorpha, resulted in the production of active ACVS enzyme, when co-expressed with the Bacillus subtilis sfp gene encoding a phosphopantetheinyl transferase that activated ACVS. This represents the first example of the functional expression of a non-ribosomal peptide synthetase in yeast. Co-expression with the P. chrysogenum genes encoding the cytosolic enzyme isopenicillin N synthase as well as the two peroxisomal enzymes isopenicillin N acyl transferase (IAT and phenylacetyl CoA ligase (PCL resulted in production of biologically active PEN, which was efficiently secreted. The amount of secreted PEN was similar to that produced by the original P. chrysogenum NRRL1951 strain (approx. 1 mg/L. PEN production was decreased over two-fold in a yeast strain lacking peroxisomes, indicating that the peroxisomal localization of IAT and PCL is important for efficient PEN production. The breakthroughs of this work enable exploration of new yeast-based cell factories for the production of (novel beta-lactam antibiotics as well as other natural and semi-synthetic peptides (e.g. immunosuppressive and cytostatic agents, whose production involves NRPS's.

Establishing a high yielding streptomyces-based cell-free protein synthesis system.

Science.gov (United States)

Li, Jian; Wang, He; Kwon, Yong-Chan; Jewett, Michael C

2017-06-01

Cell-free protein synthesis (CFPS) has emerged as a powerful platform for applied biotechnology and synthetic biology, with a range of applications in synthesizing proteins, evolving proteins, and prototyping genetic circuits. To expand the current CFPS repertoire, we report here the development and optimization of a Streptomyces-based CFPS system for the expression of GC-rich genes. By developing a streamlined crude extract preparation protocol and optimizing reaction conditions, we were able to achieve active enhanced green fluorescent protein (EGFP) yields of greater than 50 μg/mL with batch reactions lasting up to 3 h. By adopting a semi-continuous reaction format, the EGFP yield could be increased to 282 ± 8 μg/mL and the reaction time was extended to 48 h. Notably, our extract preparation procedures were robust to multiple Streptomyces lividans and Streptomyces coelicolor strains, although expression yields varied. We show that our optimized Streptomyces lividans system provides benefits when compared to an Escherichia coli-based CFPS system for increasing percent soluble protein expression for four Streptomyces-originated high GC-content genes that are involved in biosynthesis of the nonribosomal peptides tambromycin and valinomycin. Looking forward, we believe that our Streptomyces-based CFPS system will contribute significantly towards efforts to express complex natural product gene clusters (e.g., nonribosomal peptides and polyketides), providing a new avenue for obtaining and studying natural product biosynthesis pathways. Biotechnol. Bioeng. 2017;114: 1343-1353. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Chain elongation and cyclization in type III PKS DpgA.

Science.gov (United States)

Wu, Hai-Chen; Li, Yi-San; Liu, Yu-Chen; Lyu, Syue-Yi; Wu, Chang-Jer; Li, Tsung-Lin

2012-04-16

Chain elongation and cyclization of precursors of dihydroxyphenylacetyl-CoA (DPA-CoA) catalyzed by the bacterial type III polyketide synthase DpgA were studied. Two labile intermediates, di- and tri-ketidyl-CoA (DK- and TK-CoA), were proposed and chemically synthesized. In the presence of DpgABD, each of these with [(13)C(3)]malonyl-CoA (MA-CoA) was able to form partially (13)C-enriched DPA-CoA. By NMR and MS analysis, the distribution of (13)C atoms in the partially (13)C-enriched DPA-CoA shed light on how the polyketide chain elongates and cyclizes in the DpgA-catalyzed reaction. Polyketone intermediates elongate in a manner different from that which had been believed: two molecules of DK-CoA, or one DK-CoA plus one acetoacetyl-CoA (AA-CoA), but not two molecules of AA-CoA can form one molecule of DPA-CoA. As a result, polyketidyl-CoA serves as both the starter and extender, whereas polyketone-CoA without the terminal carboxyl group can only act as an extender. The terminal carboxyl group is crucial for the cyclization that likely takes place on CoA. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Potential of yeasts isolated from dry-cured ham to control ochratoxin A production in meat models.

Science.gov (United States)

Peromingo, Belén; Núñez, Félix; Rodríguez, Alicia; Alía, Alberto; Andrade, María J

2018-03-02

The environmental conditions reached during the ripening of dry-cured meat products favour the proliferation of moulds on their surface. Some of these moulds are hazardous to consumers because of their ability to produce ochratoxin A (OTA). Biocontrol using Debaryomyces hansenii could be a suitable strategy to prevent the growth of ochratoxigenic moulds and OTA accumulation in dry-cured meat products. The aim of this work was to evaluate the ability of two strains of D. hansenii to control the growth and OTA production of Penicillium verrucosum in a meat model under water activities (a w ) values commonly reached during the dry-cured meat product ripening. The presence of D. hansenii strains triggered a lengthening of the lag phase and a decrease of the growth rate of P. verrucosum in meat-based media at 0.97 and 0.92 a w . Both D. hansenii strains significantly reduced OTA production (between 85.16 and 92.63%) by P. verrucosum in the meat-based medium at 0.92 a w . Neither absorption nor detoxification of OTA by D. hansenii strains seems to be involved. However, a repression of the expression of the non-ribosomal peptide synthetase (otanpsPN) gene linked to the OTA biosynthetic pathway was observed in the presence of D. hansenii. To confirm the protective role of D. hansenii strains, they were inoculated together with P. verrucosum Pv45 in dry-fermented sausage and dry-cured ham slices. Although P. verrucosum Pv45 counts were not affected by the presence of D. hansenii in both meat matrices, a reduction of OTA amount was observed. Therefore, the effect of D. hansenii strains on OTA accumulation should be attributed to a reduction at transcriptional level. Consequently, native D. hansenii can be useful as biocontrol agent in dry-cured meat products for preventing the hazard associated with the presence of OTA. Copyright © 2018 Elsevier B.V. All rights reserved.

The global land-potential knowledge system (LandPKS): Supporting evidence-based, site-specific land use and management through cloud computing, mobile applications and crowdsourcing

Science.gov (United States)

Agricultural production must increase significantly to meet the needs of a growing global population with increasing per capita consumption of food, fiber, building materials, and fuel. Consumption already exceeds net primary production in many parts of the world. In addition to reducing consumptio...

Activation of the pacidamycin PacL adenylation domain by MbtH-like proteins.

Science.gov (United States)

Zhang, Wenjun; Heemstra, John R; Walsh, Christopher T; Imker, Heidi J

2010-11-23

Nonribosomal peptide synthetase (NRPS) assembly lines are major avenues for the biosynthesis of a vast array of peptidyl natural products. Several hundred bacterial NRPS gene clusters contain a small (∼70-residue) protein belonging to the MbtH family for which no function has been defined. Here we show that two strictly conserved Trp residues in MbtH-like proteins contribute to stimulation of amino acid adenylation in some NRPS modules. We also demonstrate that adenylation can be stimulated not only by cognate MbtH-like proteins but also by homologues from disparate natural product pathways.