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Glutamate 2,3-aminomutase: a new member of the radical SAM superfamily of enzymes

BackgroundThe genus Vibrio is a diverse group of Gram-negative bacteria comprised of 74 species. Furthermore, the genus has and is expected to continue expanding...Full Text Available

Regulation of human ribosomal RNA transcription.

SUMMARYA gene eam in Clostridium difficile encodes a protein that is homologous to lysine 2,3-aminomutase (LAM) in many other species but does...Full Text Available

2007-02-01

Rapid in situ hybridization technique using 16S rRNA segments for detecting and differentiating the closely related gram-positive organisms Bacillus polymyxa and Bacillus macerans

We have used a cell-free polymerase I transcription system derived from HeLa cells to study the regulation of human rRNA synthesis. Analysis of deletion mutants spanning the start site of transcription at nucleotide +1 indicates that the control region affecting initiation of human rRNA synthesis is contained within sequences from nucleotides -158 to +18. This promoter region can be subdivided into (i) a central segment of approximately 40 base pair that is required for transcription and (ii) flanking sequences that influence the efficiency of transcription in vitro. We have examined the in vitro transcriptional activity of the human extract under various conditions that are thought to modulate rRNA synthesis in vivo. Cell-free extracts prepared from HeLa cells infected with adenovirus 2 synthesize human rRNA at levels greatly decreased relative to uninfected cell extracts. By contrast, in vitro ...

1983-06-01

Emergence of Klebsiella pneumoniae Coproducing KPC-2 and 16S rRNA Methylase ArmA in Poland ?

A rapid, sensitive, inexpensive in situ hybridization technique, using 30-mer 16S rRNA probes, can

1992-01-01

Nucleotide sequence of a Euglena gracilis chloroplast gene coding for the 16S rRNA: homologies to E. coli and Zea mays chloroplast 16S rRNA.

A Klebsiella pneumoniae epidemic strain that coproduced carbapenemase KPC-2 (K. pneumoniae carbapenemase 2) and 16S rRNA methylase ArmA has emerged in Poland. Four...Full Text Available

2011-01-01

The nucleotide sequence and organization of nuclear 5S rRNA genes in yellow lupine

The nucleotide sequence of 16S rDNA from Euglena gracilis chloroplasts has been determined representing the first complete sequence of an algal chloroplast rRNA gene. The structural part of the 16S...Full Text Available

1982-10-25

Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity

We have isolated a genomic clone containing 'Lupinus luteus' 5S ribosomal RNA genes by screening with 5S rDNA probe clones that were hybridized previously with the initiator methionine tRNA preparation (contaminated) with traces of rRNA or its degradation products). The clone isolated contains ten repeat units of 342 bp with 119 bp fragment showing 100% homology to the 5S rRNA from yellow lupine. Sequence analysis indicates only point heterogeneities among the flanking regions of the genes. (author). 6 refs, 3 figs.

1993-01-01

Norwegian Open Research Archives (NORA)

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Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits.

Identification of pork derivatives in food products by species-specific polymerase chain reaction (PCR) for halal verification

Ribosomal protein L1 from Saccharomyces cerevisiae binds 5S rRNA and can be released from intact 60S ribosomal subunits as an L1-5S ribonucleoprotein (RNP) particle. To understand the nature of the...Full Text Available

1993-05-01

British Library Electronic Table of Contents (United Kingdom)

Pork identification in four types of food products, which are sausages and the casings, bread and biscuits, using species-specific polymerase chain reaction (PCR) detection of a conserved region in the mitochondrial (mt) 12S ribosomal RNA (rRNA) gene was developed. Genomic DNA of the food products were successfully extracted except for the casing samples, where no genomic DNA was detected. The extracted genomic DNA was then subjected to PCR amplification targeting the specific regions of the 12S rRNA gene. The genomic DNA from the food products were found to be of good quality and produced clear PCR products on the amplification of 12S rRNA gene of 387 base pairs (bp) from pork species. The species-specific PCR identification yielded excellent results for identification of pork derivatives...

2007-01-01

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Worlds within worlds: evolution of the vertebrate gut microbiota

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Use of synthetic oligonucleotide DNA probes for identification and direct detection of Bacteroides forsythus in plaque samples.

Here we use published 16S rRNA gene sequences to compare the bacterial assemblages associated with humans, other mammals, other metazoa, and free-living microbial communities spanning a range...Full Text Available

2008-10-01

Seasonal and Spatial Variability of Bacterial and Archaeal Assemblages in the Coastal Waters near Anvers Island, Antarctica

Oligonucleotide DNA probes complementary to the hypervariable region of the 16S rRNA of Bacteroides forsythus were tested for their specificity and sensitivity against reference and clinical isolates...Full Text Available

1991-10-01

Scintillation proximity assay for measurement of RNA methylation

A previous report of high levels of members of the domain Archaea in Antarctic coastal waters prompted us to investigate the ecology of Antarctic planktonic prokaryotes. rRNA hybridization...Full Text Available

1998-07-01

Improved Understanding of the Bacterial Vaginal Microbiota of Women before and after Probiotic Instillation

Methylation of RNA by methyltransferases is a phylogenetically ubiquitous post-transcriptional modification that occurs most extensively in transfer RNA (tRNA) and ribosomal RNA (rRNA). Biochemical...Full Text Available

2009-03-01

Detection of Atopobium vaginae in Postmenopausal Women by Cultivation-Independent Methods Warrants Further Investigation

The vaginal bacterial microbiota of 19 premenopausal women was examined by PCR-denaturing gradient gel electrophoresis (DGGE) and sequencing of the V2-V3 region of the 16S rRNA gene. Ten of the women...Full Text Available

2003-01-01

Association of Unique, Isolated Treponemes with Bovine Digital Dermatitis Lesions?

2004-04-01

The Morphology, Ontogeny, and Small Subunit rRNA Gene Sequence Analysis of Diophrys parappendiculata n. sp. (Protozoa, Ciliophora, Euplotida), a New Marine Ciliate from Coastal Waters of Southern China

This study used a PCR-based approach targeting 16S rRNA gene fragments to determine the occurrence and association of the three bovine digital dermatitis (BDD) treponeme phylogroups within lesions found...Full Text Available

2009-03-01

British Library Electronic Table of Contents (United Kingdom)

ABSTRACT. The morphology, morphogenesis, and phylogeny of Diophrys parappendiculata n. sp., a large marine ciliate isolated from the coastal waters of Daya Bay, southern China, were investigated. This new species is characterized by a combination of its large size, appendiculata-pattern of ciliature, and bipartite adoral zone of membranelles. The main stages of morphogenesis during binary fission were also recorded and described. Comparisons of morphological characteristics with similar congeners support the validity of the new species. The small subunit rRNA gene sequence of D. parappendiculata is 96.3-99.94% similar to those of four other congeners; it differs in four nucleotides from that of Diophrys appendiculata (i.e. structural similarity was 99.94%). Phylogenetic analysis indicates ...

2011-01-01

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Oxidation of Elemental Sulfur by Fusarium solani Strain THIF01 Harboring Endobacterium Bradyrhizobium sp.

British Library Electronic Table of Contents (United Kingdom)

Nineteen fungal strains having an ability to oxidize elemental sulfur in mineral salts medium were isolated from deteriorated sandstones of Angkor monuments. These fungi formed clearing zone on agar medium supplemented with powder sulfur due to the dissolution of sulfur. Representative of the isolates, strain THIF01, was identified as Fusarium solani on the basis of morphological characteristics and phylogenetic analyses. PCR amplification targeting 16S rRNA gene and analyses of full 16S rRNA gene sequence indicated strain THIF01 harbors an endobacterium Bradyrhizobium sp.; however, involvement of the bacterium in the sulfur oxidation is still unclear. Strain THIF01 oxidized elemental sulfur to thiosulfate and then sulfate. Germination of the spores of strain THIF01 was observed in a liqui...

2010-01-01

Extraribosomal functions associated with the C terminus of the 37/67?kDa laminin receptor are required for maintaining cell viability

Discrimination of Listeria monocytogenes from other Listeria species by ligase chain reaction.

The 37/67 kDa laminin receptor (LAMR) is a multifunctional protein, acting as an extracellular receptor, localizing to the nucleus, and playing roles in rRNA processing and ribosome assembly....Full Text Available

2010-05-01

Detection of Atopobium vaginae in postmenopausal women by cultivation-independent methods warrants further investigation.

A ligase chain reaction assay based on a single-base-pair difference in the V9 region of the 16S rRNA gene (16S rDNA) was developed to distinguish between Listeria monocytogenes and other Listeria species....Full Text Available

1992-11-01

Application of a Newly Developed ARB Software-Integrated Tool for In Silico Terminal Restriction Fragment Length Polymorphism Analysis Reveals the Dominance of a Novel pmoA Cluster in a Forest Soil

We sequenced 16S rRNA genes from the vaginal swab contents of a postmenopausal woman with asymptomatic bacterial vaginosis (BV). Sequences from Atopobium vaginae were the most commonly detected. In a survey of 35 other postmenopausal women, this organism was detected in 44% with BV but not in any subjects deemed healthy. PMID:15071062

2004-04-01

Source tracking of Escherichia coli by 16S-23S intergenic spacer region denaturing gradient gel electrophoresis (DGGE) of the rrnB ribosomal operon.

TRF-CUT, an ARB-implemented tool, was developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. Application of this new tool...Full Text Available

2005-03-01

Direct observation of polymerization in the oleic acid-ozone heterogeneous reaction system by photoelectron resonance capture ionization aerosol mass spectrometry

This research validates a novel approach for source tracking based on denaturing gradient gel electrophoresis (DGGE) analysis of DNA extracted from Escherichia coli isolates. Escherichia coli from different animal sources and from river samples upstream from, at, and downstream of a combined sewer overflow were subjected to DGGE to determine sequence variations within the 16S-23S intergenic spacer region (ISR) of the rrnB ribosomal operon. The ISR was analyzed to determine if E. coli isolates from various animal sources could be differentiated from each other. DNA isolated from the E. coli animal sources was PCR amplified to isolate the rrnB operon. To prevent amplification of all 7 E. coli ribosomal operons by PCR amplification using universal primers, sequence-specific primers were utilized for the rrnB operon. Another primer set was then used to prepare samples of the 16S-23S ISR for DGGE. Comparison ...

2007-10-01

British Library Electronic Table of Contents (United Kingdom)

High molecular weight products of the ozonolysis reaction of particle-phase 9-octadecenoic acid (oleic acid) have been studied by photoelectron resonance capture ionization (PERCI) mass spectrometry (MS). Oleic acid particles ( Formula Not Shown , Formula Not Shown ) were reacted with ozone (1.8x10-4atm) in a flow reactor at reaction times of 8 and 23s. Particles were sampled on-line with a differentially pumped particle inlet and chemically analyzed by PERCI-MS. PERCI is a soft ionization method that permits the direct measurement of relatively high molecular weight compounds, facilitating molecular identification. In addition to cyclic oxygenates, such as secondary ozonides and geminal diperoxides that were reported previously, we demonstrate the formation of polymers at the particle sur...

2006-01-01

mtDNA mutation C1494T, haplogroup A, and hearing loss in Chinese

British Library Electronic Table of Contents (United Kingdom)

Mutation C1494T in mitochondrial 12S rRNA gene was recently reported in two large Chinese families with aminoglycoside-induced and nonsyndromic hearing loss (AINHL) and was claimed to be pathogenic. This mutation, however, was first reported in a sample from central China in our previous study that was aimed to reconstruct East Asian mtDNA phylogeny. All these three mtDNAs formed a subclade defined by mutation C1494T in mtDNA haplogroup A. It thus seems that mutation C1494T is a haplogroup A-associated mutation and this matrilineal background may contribute a high risk for the penetrance of mutation C1494T in Chinese with AINHL. To test this hypothesis, we first genotyped mutation C1494T in 553 unrelated individuals from three regional Chinese populations and performed an extensive search ...

2006-01-01

Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

British Library Electronic Table of Contents (United Kingdom)

Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also va...

2011-01-01

Molecular environment of the IIId subdomain of the IRES element of hepatitits C virus RNA on the human 40S ribosomal subunit

British Library Electronic Table of Contents (United Kingdom)

The molecular environment of the key subdomain IIId of the internal ribosome entry site (IRES) element of hepatitis C virus (HCV) RNA in the binary complex with the human 40S ribosomal subunit was studied. To this end, HCV IRES derivatives bearing perfluorophenylazido groups activatable by mild UV at nucleotides G263 or A275 in the subdomain IIId stem were used. They were prepared by the complementary addressed modification of the corresponding RNA transcript with alkylating oligodeoxyribonucleotide derivatives. None of the RNA derivatives were shown to be crosslinked to the 18S rRNA. It was found that the photoreactive groups of the IRES G263 and A275 nucleotides are crosslinked to ribosomal proteins S3a, S14, and S16. For the IRES derivative with the photoreactive group in nucleotide G26...

2009-01-01

Methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets

British Library Electronic Table of Contents (United Kingdom)

Abstract Development of inhibitors and vaccines that mitigate rumen-derived methane by targeting methanogens relies on knowledge of the methanogens present. We investigated the composition of archaeal communities in the rumens of farmed sheep (Ovis aries), cattle (Bos taurus) and red deer (Cervus elaphus) using denaturing gradient gel electrophoresis (DGGE) to generate fingerprints of archaeal 16S rRNA genes. The total archaeal communities were relatively constant across species and diets, and were less variable and less diverse than bacterial communities. There were diet- and ruminant-species-based differences in archaeal community structure, but the same dominant archaea were present in all rumens. These were members of three coherent clades: species related to Methanobrevibacter ruminan...

2011-01-01

Functional adaptation of microbial communities from jet fuel-contaminated soil under bioremediation treatment: simulation of pollutant rebound

British Library Electronic Table of Contents (United Kingdom)

Abstract To investigate the link between the functionality and the diversity of microbial communities under strong selective pressure from pollutants, two types of mesocosms that simulate natural attenuation and phytoremediation were generated using soil from a site highly contaminated with jet fuel and under air-sparging treatment. An increase in the petroleum hydrocarbon concentration from 4900 to 18-500-mg-kg-1-dw soil simulated a pollutant rebound (postremediation pollutant reversal due to residual contamination). Analysis of soil bacterial communities by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments showed stronger changes and selection for a phylogenetically diverse microbial population in the mesocosms with pollutant-tolerant willow trees. Enumerat...

2011-01-01

Distinctive Responses of Metabolically Active Microbiota to Acidification in a Thermophilic Anaerobic Digester

British Library Electronic Table of Contents (United Kingdom)

Acidification is one of the most common and serious problems inducing process failure in anaerobic digesters. The production of volatile fatty acids (VFAs) mainly triggers acidic shock. However, little is known about the bacteria involved in the processes of acidogenic metabolism, such as fermentation and reductive acetogenesis. Here, the metabolic responses of a methanogenic community to the acidification and resulting process deterioration were investigated using transcriptional profiling of both the 16S rRNA and formyltetrahydrofolate synthetase (FTHFS) genes. The 16S rRNA-based analyses demonstrated that the dynamic shift of bacterial populations was closely correlated with reactor performance, especially with VFA accumulation levels. The pH drop accompanied by an increase in VFAs stim...

2011-01-01

The mitochondrial genome of the entomophagous endoparasite Xenosvesparum (Insecta: Strepsiptera)

Report on a survey in fiscal 1999. Survey on industrial utilization of microorganism reaction mechanisms under anaerobic condition; 1999 nendo kenki jokenka ni okeru biseibutsu hanno kiko no kogyoteki riyo ni kansuru chosa hokokusho

In this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward As and Ts, as is typical for insect mtDNAs. There is also significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and the N-strand showing an opposite skew for complementary pairs of ...

2005-12-01

Identification of culturable and originally non-culturable endophytic bacteria isolated from shoot tip cultures of banana cv. Grand Naine

Industrial utilization of reaction mechanisms of microorganisms under anaerobic condition permits structuring energy saving type production processes. The present survey has investigated features of new microorganisms under anaerobic condition and the status of researches thereon inside and outside the country, and discussed their future applications. Chapter 1 compares anaerobic microorganisms and functions of microorganism under anaerobic condition with those aerobic to describe their general features, and describes the purpose of this survey and the summary of the investigations. Chapter 2 surveys the current status of technologies to utilize microorganisms under anaerobic condition. Chapter 3 outlines metabolic characteristics of the anaerobic microorganisms, and extracts functions effective for material production by different anaerobic microorganisms to describe their applicability. Chapter 4 evaluates the system classification for the anaerobic microorganisms utilizing the basic ...

2000-03-01

British Library Electronic Table of Contents (United Kingdom)

In this article we describe the identification of endophytic bacteria belonging to three groups isolated from shoot tip cultures of banana cv. Grand Naine in a recent study (Thomas et?al. 2008) based on partial 16S rRNA gene sequence homology analysis. The first group included banana stocks that displayed obvious colony growth on MS based tissue culture medium during the first in?vitro passage. The second group constituted stocks that were tissue index-negative for cultivable bacteria initially but turned index-positive after a few to several (4?8) in?vitro passages while the third group formed one sub-stock that turned index-positive after about 18 passages. The organisms belonged to about 20 different genera comprising of ?, ?, ?-proteobacteria, Gram-positive firmicutes and actinobacteri...

2008-01-01

Two and 8-azido photoaffinity probes. 1. Enzymatic synthesis, characterization, and biological properties of 2- and 8-azido photoprobes of 2-5A and photolabeling of 2-5A binding proteins

Single protein omission reconstitution studies of tetracycline binding to the 30S subunit of Escherichia coli ribosomes

The 2- and 8-azido trimer 5'-triphosphate photoprobes of 2-5A have been enzymatically synthesized from [#gamma#-"3"2P]2-azidoATP and [#alpha#-"3"2P]8-azidoAPT by 2-5A synthetase from rabbit reticulocyte lysates. Identification and structural determination of the 2- and 8-azido adenylate trimer 5'-triphosphates were accomplished by enzymatic hydrolyses with T2 RNase, snake venom phosphodiesterase, and bacterial alkaline phosphatase. Hydrolysis products were identified by HPLC and PEI-cellulose TLC analyses. The 8-azido photoprobe of 2-5A displaces p_3A_4["3"2P]pCp from RNase L with affinity equivalent to p_3A_3. The 8-azido photoprobe also activates RNase L to hydrolyze poly(U)["3"2P]pCp 50% at 7 /times/ 10/sup /minus/9/ M in core-cellulose assays. The 2- and 8-azido photoprobes and authentic p_3A_3 activate RNase L to cleave 28S and 18S rRNA to specific cleavage products at 10/sup /minus/9/ M in rRNA cleavage assays. The nucleotide binding ...

Microbial community analysis of ambient temperature anaerobic digesters

In previous work the authors showed that on photolysis of Escherichia coli ribosomes in the presence of ({sup 3}H)tetracycline (TC) the major protein labeled is S7, and they presented strong evidence that such labeling takes place from a high-affinity site related to the inhibitory action of TC. In this work they use single protein omission reconstitution (SPORE) experiments to identify those proteins that are important for high-affinity TC binding to the 30S subunit, as measured by both cosedimentation and filter binding assays. With respect to both sedimentation coefficients and relative Phe-tRNA{sup Phe} binding, the properties of the SPORE particles they obtain parallel very closely those measured earlier, with the exception of the SPORE particle lacking S13. A total of five proteins, S3, S7, S8, S14, and S19, are shown to be important for TC binding, with the largest effects seen on omission of proteins S7 and S14. Determination of the protein compositions of the corresponding ...

1990-06-05

Mapping a nucleolar targeting sequence of an RNA binding nucleolar protein, Nop25

This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. ...

2010-07-01

Biogeochemistry of the compost bioreactor components of a composite acid mine drainage passive remediation system

Nop25 is a putative RNA binding nucleolar protein associated with rRNA transcription. The present study was undertaken to determine the mechanism of Nop25 localization in the nucleolus. Deletion experiments of Nop25 amino acid sequence showed Nop25 to contain a nuclear targeting sequence in the N-terminal and a nucleolar targeting sequence in the C-terminal. By expressing derivative peptides from the C-terminal as GFP-fusion proteins in the cells, a lysine and arginine residue-enriched peptide (KRKHPRRAQDSTKKPPSATRTSKTQRRRR) allowed a GFP-fusion protein to be transported and fully retained in the nucleolus. When the peptide was fused with cMyc epitope and expressed in the cells, a cMyc epitope was then detected in the nucleolus. Nop25 did not localize in the nucleolus by deletion of the peptide from Nop25. Furthermore, deletion of a subdomain (KRKHPRRAQ) in the peptide or amino acid substitution of lysine and arginine residues in the subdomain resulted in the loss ...

2006-06-10

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