UvrD in Deinococcus radiodurans is optimized for processing G-quadruplex DNA

International Nuclear Information System (INIS)

Das, Anubrata; Misra, H.S.

2015-01-01

Deinococcus radiodurans R1 is a radiation resistant Gram-positive bacterium capable of tolerating very high doses of DNA-damaging agents such as gamma radiation (D10 ∼ 12kGy) desiccation (∼ 5% relative humidity), UVC radiation (D10 ∼ 800J/m 2 ) and hydrogen peroxide (40 mM). It achieves this by using a complex regulatory mechanism and novel proteins. Recently bioinformatic analysis showed several stretches of guanine runs in D.radiodurans genome, which could form G-quartets. The role of G-quartets in regulatory processes is well documented in various organisms. The presence of G -quartets in D. radiodurans means that there are regulatory or structural proteins which would bind to these elements. Several proteins are known to bind G-quartets. Finding the proteins which would bind to G4 DNA is difficult as no specific motifs are available for binding these elements. Also most of the known proteins that are shown to bind to G-quadruplex DNA are of eukaryotic nature. To overcome these challenges we defined a set of known G-quadruplex binding proteins and used a smith-waterman algorithm with our own scoring matrix to homologs of G-quadruplex binding proteins in D.radiodurans. Using bioinformatics analysis, we showed that UvrD (DR 1775) of D. radiodurans has ability to bind/translocate along G-quadruplex DNA, a novel feature in prokaryotes. The translocase activity of DR1775 is ATP specific and this ATPase activity is attenuated by ssDNA. Data supporting UvrD of D. radiodurans as a G-quadruplex DNA metabolizing proteins would be presented. (author)

PprA phosphorylation by STPK of Deinococcus radiodurans changes its in vitro functions

International Nuclear Information System (INIS)

Rajpurohit, Yogendra S.; Misra, H.S.

2011-01-01

Deinococcus radiodurans shows amazing resistance to both ionizing and non-ionizing radiations. This phenotype is attributed also to its efficient DNA double strand breaks (DSB) repair capability of this bacterium. PprA (pleiotropic protein promoting DNA repair) is unique to D. radiodurans and its role in gamma radiation resistance and DSB repair has been shown in this bacterium. Recombinant PrA protects dsDNA from exonuclease degradation and stimulates the DNA ends joining activity of both T4 DNA ligase and E.coli NAD ligase in vitro. Phosphomotif search showed that PprA has putative phosphorylation site similar to that is characterized for Ser/Thr protein kinases in eukaryotic system. A eukaryotic type Ser/Thr protein kinase (DR2518) of D. radiodurans, could phosphorylate recombinant PprA at Thr amino acid in vitro and the phosphorylation of PprA was also observed in vivo. DR2518 kinase mediated protein phosphorylation of PprA, improves its DNA binding affinity by nearly four fold and stimulated T4 DNA ligase activity more towards intermolecular ligation, as compared to unphosphorylated PprA. Interestingly, the phospho-PprA showed lesser protection of dsDNA than unphospho-PprA when incubated with exonuclease III in solution. The putative Thr of PprA was replaced with Ala (T48A) by site directed mutagenesis, which resulted in significant reduction of PprA phosphorylation by DR2518 kinase. Detailed studies on PprA phosphorylation and its functional significance would be presented. (author)

Final Report for Grant No. DE-FG02-98ER62583 ''Functional Analysis of the Genome Sequence of Deinococcus radiodurans''

International Nuclear Information System (INIS)

Daly, Michael J.

2003-01-01

Extremophiles are nearly always defined with singular characteristics that allow existence within a singular extreme environment. The bacterium Deinococcus radiodurans qualifies as a polyextremeophile, showing remarkable resistance to a range of damage caused by ionizing radiation, dessication, ultraviolet radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is most famous for its extreme resistance to ionizing radiation; it not only can grow continuously in the presence of chronic radiation (6,000 rad per hour), but it can survive acute exposures to gamma radiation that exceed 1,500,000 rads without lethality or induced mutation. These characteristics were the impetus for sequencing its genome. We completed an extensive comparative sequence analysis of the Deinococcus radiodurans (strain R1) genome. Deinococcus is the first representative with a completely sequenced genome from a bacterial branch of extremophiles - the Thermus/Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, support that it is a very ancient branch localized in the vicinity of the bacterial tree root. Distinctive features of the Deinoccoccus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to a collection of Clusters of Orthologous Groups of proteins (COGs). Analysis of paralogs in Deinococcus has revealed some unique protein families. In addition, specific expansions of several protein families including phosphatases, proteases, acyl transferases and MutT pyrophosphohydrolases, were detected. Genes that potentially affect DNA repair and recombination were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes, and are not present in other bacteria. For example, three proteins homologous to plant desiccation-resistance proteins were identified and these are particularly interesting

Repair of DNA damage in Deinococcus radiodurans

International Nuclear Information System (INIS)

Evans, D.M.

1984-01-01

The repair of DNA lesions in Deinococcus radiodurans was examined with particular reference to DNA excision repair of ultraviolet light (UV) induced pyrimidine dimers. The characteristics of excision repair via UV endonucleases α and β in vivo varied with respect to (a) the substrate range of the enzymes, (b) the rate of repair of DNA damage (c) the requirement for a protein synthesised in response to DNA damage to attenuate exonuclease action at repairing regions. UV endonuclease α is postulated to incise DNA in a different manner from UV endonuclease β thus defining the method of subsequent repair. Several DNA damage specific endonuclease activities independent of α and β are described. Mutations of the uvsA, uvsF and uvsG genes resulted in an increase in single-strand breaks in response to DNA damage producing uncontrolled DNA degradation. Evidence is presented that these genes have a role in limiting the access of UV endonuclease β to DNA lesions. uvsF and uvsG are also shown to be linked to the mtoA gene. Mutation of uvsH and reo-1 produces further distinct phenotypes which are discussed. An overall model of excision repair of DNA damage in Deinococcus radiodurans is presented. (author)

The three catalases in Deinococcus radiodurans: Only two show catalase activity.

Science.gov (United States)

Jeong, Sun-Wook; Jung, Jong-Hyun; Kim, Min-Kyu; Seo, Ho Seong; Lim, Heon-Man; Lim, Sangyong

2016-01-15

Deinococcus radiodurans, which is extremely resistant to ionizing radiation and oxidative stress, is known to have three catalases (DR1998, DRA0146, and DRA0259). In this study, to investigate the role of each catalase, we constructed catalase mutants (Δdr1998, ΔdrA0146, and ΔdrA0259) of D. radiodurans. Of the three mutants, Δdr1998 exhibited the greatest decrease in hydrogen peroxide (H2O2) resistance and the highest increase in intracellular reactive oxygen species (ROS) levels following H2O2 treatments, whereas ΔdrA0146 showed no change in its H2O2 resistance or ROS level. Catalase activity was not attenuated in ΔdrA0146, and none of the three bands detected in an in-gel catalase activity assay disappeared in ΔdrA0146. The purified His-tagged recombinant DRA0146 did not show catalase activity. In addition, the phylogenetic analysis of the deinococcal catalases revealed that the DR1998-type catalase is common in the genus Deinococcus, but the DRA0146-type catalase was found in only 4 of 23 Deinococcus species. Taken together, these results indicate that DR1998 plays a critical role in the anti-oxidative system of D. radiodurans by detoxifying H2O2, but DRA0146 does not have catalase activity and is not involved in the resistance to H2O2 stress. Copyright © 2015 Elsevier Inc. All rights reserved.

A PerR-like protein involved in response to oxidative stress in the extreme bacterium Deinococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Liu, Chengzhi; Wang, Liangyan; Li, Tao; Lin, Lin; Dai, Shang; Tian, Bing, E-mail: tianbing@zju.edu.cn; Hua, Yuejin, E-mail: yjhua@zju.edu.cn

2014-07-18

Highlights: • We report a novel PerR-like protein of Fur family in D. radiodurans that is not annotated in the current database. • drperR responses to H{sub 2}O{sub 2} and functions as a negative regulator of katE and dps. • We provided implications on how to utilize sequenced genome data and the importance of genome data mining. • This study adds knowledge to complicated regulatory network that responds to ROS stress in D. radiodurans. - Abstract: Response and defense systems against reactive oxygen species (ROS) contribute to the remarkable resistance of Deinococcus radiodurans to oxidative stress induced by oxidants or radiation. However, mechanisms involved in ROS response and defense systems of D. radiodurans are not well understood. Fur family proteins are important in ROS response. Only a single Fur homolog is predicted by sequence similarity in the current D. radiodurans genome database. Our bioinformatics analysis demonstrated an additional guanine nucleotide in the genome of D. radiodurans that is not in the database, leading to the discovery of another Fur homolog DrPerR. Gene disruption mutant of DrPerR showed enhanced resistance to hydrogen peroxide (H{sub 2}O{sub 2}) and increased catalase activity in cell extracts. Real-time PCR results indicated that DrPerR functions as a repressor of the catalase gene katE. Meanwhile, derepression of dps (DNA-binding proteins from starved cells) gene under H{sub 2}O{sub 2} stress by DrPerR point to its regulatory role in metal ions hemostasis. Thus, DrPerR might function as a Fur homolog protein which is involved in ROS response and defense. These results help clarify the complicated regulatory network that responds to ROS stress in D. radiodurans.

A PerR-like protein involved in response to oxidative stress in the extreme bacterium Deinococcus radiodurans

International Nuclear Information System (INIS)

Liu, Chengzhi; Wang, Liangyan; Li, Tao; Lin, Lin; Dai, Shang; Tian, Bing; Hua, Yuejin

2014-01-01

Highlights: • We report a novel PerR-like protein of Fur family in D. radiodurans that is not annotated in the current database. • drperR responses to H 2 O 2 and functions as a negative regulator of katE and dps. • We provided implications on how to utilize sequenced genome data and the importance of genome data mining. • This study adds knowledge to complicated regulatory network that responds to ROS stress in D. radiodurans. - Abstract: Response and defense systems against reactive oxygen species (ROS) contribute to the remarkable resistance of Deinococcus radiodurans to oxidative stress induced by oxidants or radiation. However, mechanisms involved in ROS response and defense systems of D. radiodurans are not well understood. Fur family proteins are important in ROS response. Only a single Fur homolog is predicted by sequence similarity in the current D. radiodurans genome database. Our bioinformatics analysis demonstrated an additional guanine nucleotide in the genome of D. radiodurans that is not in the database, leading to the discovery of another Fur homolog DrPerR. Gene disruption mutant of DrPerR showed enhanced resistance to hydrogen peroxide (H 2 O 2 ) and increased catalase activity in cell extracts. Real-time PCR results indicated that DrPerR functions as a repressor of the catalase gene katE. Meanwhile, derepression of dps (DNA-binding proteins from starved cells) gene under H 2 O 2 stress by DrPerR point to its regulatory role in metal ions hemostasis. Thus, DrPerR might function as a Fur homolog protein which is involved in ROS response and defense. These results help clarify the complicated regulatory network that responds to ROS stress in D. radiodurans

ParA encoded on chromosome II of Deinococcus radiodurans binds ...

Indian Academy of Sciences (India)

2013-07-22

Jul 22, 2013 ... Introduction. Cell division ..... Subsequently, the level of total FtsZ (FtsZ + FtsZ-. YFP) in cells ... could affect the productive pattern of FtsZ localization and .... maintenance and disassembly of the Z ring. Nat. ... cation tolerance of plants sensitizes Deinococcus radiodurans ... metal shadowing and decoration.

Deinococcus radiodurans strain R1 contains N6-methyladenine in its genome

International Nuclear Information System (INIS)

Prasad, Bhaskar Jyoti; Sabnis, Ketaki; Deobagkar, Deepti D.; Deobagkar, Dileep N.

2005-01-01

Methylation of DNA is known to be involved in DNA repair mechanisms in bacteria. Deinococcus radiodurans strain R1 on exposure to high radiation undergoes significant DNA damage, which is repaired without mutations. However, the presence of modified nucleotides has not been reported in its genome. We report here the detection of N6-methyladenine in the genome of D. radiodurans strain R1 using immunochemical techniques. This N6-methyladenine is not a part of GATC restriction-modification system. D. radiodurans cell extract also exhibited a DNA adenine methyltransferase activity which was reduced in the early post-irradiation recovery phase

Bioprecipitation of uranium from alkaline waste solutions using recombinant Deinococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Kulkarni, Sayali; Ballal, Anand; Apte, Shree Kumar, E-mail: aptesk@barc.gov.in

2013-11-15

Highlights: • Deinococcus radiodurans was genetically engineered to overexpress alkaline phosphatase (PhoK). • Deino-PhoK bioprecipitated U efficiently over a wide range of input U concentration. • A maximal loading of 10.7 g U/g of biomass at 10 mM input U was observed. • Radioresistance and U precipitation by Deino-PhoK remained unaffected by γ radiation. • Immobilization of Deino-PhoK facilitated easy separation of precipitated U. -- Abstract: Bioremediation of uranium (U) from alkaline waste solutions remains inadequately explored. We engineered the phoK gene (encoding a novel alkaline phosphatase, PhoK) from Sphingomonas sp. for overexpression in the radioresistant bacterium Deinococcus radiodurans. The recombinant strain thus obtained (Deino-PhoK) exhibited remarkably high alkaline phosphatase activity as evidenced by zymographic and enzyme activity assays. Deino-PhoK cells could efficiently precipitate uranium over a wide range of input U concentrations. At low uranyl concentrations (1 mM), the strain precipitated >90% of uranium within 2 h while a high loading capacity of around 10.7 g U/g of dry weight of cells was achieved at 10 mM U concentration. Uranium bioprecipitation by Deino-PhoK cells was not affected in the presence of Cs and Sr, commonly present in intermediate and low level liquid radioactive waste, or after exposure to very high doses of ionizing radiation. Transmission electron micrographs revealed the extracellular nature of bioprecipitated U, while X-ray diffraction and fluorescence analysis identified the precipitated uranyl phosphate species as chernikovite. When immobilized into calcium alginate beads, Deino-PhoK cells efficiently removed uranium, which remained trapped in beads, thus accomplishing physical separation of precipitated uranyl phosphate from solutions. The data demonstrate superior ability of Deino-PhoK, over earlier reported strains, in removal of uranium from alkaline solutions and its potential use in

Effect of Deinococcus radiodurans on uptake of 134Cs by Brassica oleracea

International Nuclear Information System (INIS)

Zhu Cong; Guo Jiangfeng

2008-01-01

Deinococcus radiodurans was inoculated into the soil which was spiked with 134 Cs to investigate its effect on chemical speciation of 134 Cs. The relationship between chemical speciation of 134 Cs and its absorbtion capacity by cabbage (Brassica oleracea) in the presence of D. radiodurans was also investigated. The results showed that an increase of 28.64%-38.17 % in content of 134 Cs in residual phase was observed with presence of D. radiodurans in comparison with the aseptic control. The amounts of radiocesium uptaken by cabbage were about 12100Bq/g under aseptic conditions, however, which were about 8500Bq/g with the presence of D. radiodurans. The proportion of 134 Cs taken up by cabbage decreased about 29% in comparison with the aseptic control. The chemical speciation could be influenced by D. radiodurans so that its uptake by plants could be reduced. (authors)

Conservation of the LexA repressor binding site in Deinococcus radiodurans

Directory of Open Access Journals (Sweden)

Khan Feroz

2008-03-01

Full Text Available The LexA protein is a transcriptional repressor of the bacterial SOS DNA repair system, which comprises a set of DNA repair and cellular survival genes that are induced in response to DNA damage. Its varied DNA binding motifs have been characterized and reported in the Escherichia coli, Bacillus subtilis, rhizobia family members, marine magnetotactic bacterium, Salmonella typhimurium and recently in Mycobacterium tuberculosis and this motifs information has been used in our theoretical analysis to detect its novel regulated genes in radio-resistant Deinococcus radiodurans genome. This bacterium showed presence of SOS-box like consensus sequence in the upstream sequences of 3166 genes with >60% motif score similarity percentage (MSSP on both strands. Attempts to identify LexA-binding sites and the composition of the putative SOS regulon in D. radiodurans have been unsuccessful so far. To resolve the problem we performed theoretical analysis with modifications on reported data set of genes related to DNA repair (61 genes, stress response (145 genes and some unusual predicted operons (21 clusters. Expression of some of the predicted SOS-box regulated operon members then was examined through the previously reported microarray data which confirm the expression of only single predicted operon i.e. DRB0143 (AAA superfamily NTPase related to 5-methylcytosine specific restriction enzyme subunit McrB and DRB0144 (homolog of the McrC subunit of the McrBC restriction modification system. The methodology involved weight matrix construction through CONSENSUS algorithm using information of conserved upstream sequences of eight known genes including dinB, tagC, lexA, recA, uvrB, yneA of B. subtilis while lexA and recA of D. radiodurans through phylogenetic footprinting method and later detection of similar conserved SOS-box like LexA binding motifs through both RSAT & PoSSuMsearch programs. The resultant DNA consensus sequence had highly conserved 14 bp SOS

The three catalases in Deinococcus radiodurans: Only two show catalase activity

Energy Technology Data Exchange (ETDEWEB)

Jeong, Sun-Wook [Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185 (Korea, Republic of); Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 305-764 (Korea, Republic of); Jung, Jong-Hyun; Kim, Min-Kyu; Seo, Ho Seong [Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185 (Korea, Republic of); Lim, Heon-Man [Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 305-764 (Korea, Republic of); Lim, Sangyong, E-mail: saylim@kaeri.re.kr [Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185 (Korea, Republic of)

2016-01-15

Deinococcus radiodurans, which is extremely resistant to ionizing radiation and oxidative stress, is known to have three catalases (DR1998, DRA0146, and DRA0259). In this study, to investigate the role of each catalase, we constructed catalase mutants (Δdr1998, ΔdrA0146, and ΔdrA0259) of D. radiodurans. Of the three mutants, Δdr1998 exhibited the greatest decrease in hydrogen peroxide (H{sub 2}O{sub 2}) resistance and the highest increase in intracellular reactive oxygen species (ROS) levels following H{sub 2}O{sub 2} treatments, whereas ΔdrA0146 showed no change in its H{sub 2}O{sub 2} resistance or ROS level. Catalase activity was not attenuated in ΔdrA0146, and none of the three bands detected in an in-gel catalase activity assay disappeared in ΔdrA0146. The purified His-tagged recombinant DRA0146 did not show catalase activity. In addition, the phylogenetic analysis of the deinococcal catalases revealed that the DR1998-type catalase is common in the genus Deinococcus, but the DRA0146-type catalase was found in only 4 of 23 Deinococcus species. Taken together, these results indicate that DR1998 plays a critical role in the anti-oxidative system of D. radiodurans by detoxifying H{sub 2}O{sub 2}, but DRA0146 does not have catalase activity and is not involved in the resistance to H{sub 2}O{sub 2} stress. - Highlights: • The dr1998 mutant strain lost 90% of its total catalase activity. • Increased ROS levels and decreased H{sub 2}O{sub 2} resistance were observed in dr1998 mutants. • Lack of drA0146 did not affect any oxidative stress-related phenotypes. • The purified DRA0146 did not show catalase activity.

The three catalases in Deinococcus radiodurans: Only two show catalase activity

International Nuclear Information System (INIS)

Jeong, Sun-Wook; Jung, Jong-Hyun; Kim, Min-Kyu; Seo, Ho Seong; Lim, Heon-Man; Lim, Sangyong

2016-01-01

Deinococcus radiodurans, which is extremely resistant to ionizing radiation and oxidative stress, is known to have three catalases (DR1998, DRA0146, and DRA0259). In this study, to investigate the role of each catalase, we constructed catalase mutants (Δdr1998, ΔdrA0146, and ΔdrA0259) of D. radiodurans. Of the three mutants, Δdr1998 exhibited the greatest decrease in hydrogen peroxide (H_2O_2) resistance and the highest increase in intracellular reactive oxygen species (ROS) levels following H_2O_2 treatments, whereas ΔdrA0146 showed no change in its H_2O_2 resistance or ROS level. Catalase activity was not attenuated in ΔdrA0146, and none of the three bands detected in an in-gel catalase activity assay disappeared in ΔdrA0146. The purified His-tagged recombinant DRA0146 did not show catalase activity. In addition, the phylogenetic analysis of the deinococcal catalases revealed that the DR1998-type catalase is common in the genus Deinococcus, but the DRA0146-type catalase was found in only 4 of 23 Deinococcus species. Taken together, these results indicate that DR1998 plays a critical role in the anti-oxidative system of D. radiodurans by detoxifying H_2O_2, but DRA0146 does not have catalase activity and is not involved in the resistance to H_2O_2 stress. - Highlights: • The dr1998 mutant strain lost 90% of its total catalase activity. • Increased ROS levels and decreased H_2O_2 resistance were observed in dr1998 mutants. • Lack of drA0146 did not affect any oxidative stress-related phenotypes. • The purified DRA0146 did not show catalase activity.

Laboratory simulation of interplanetary ultraviolet radiation (broad spectrum) and its effects on Deinococcus radiodurans

Science.gov (United States)

Paulino-Lima, Ivan Gláucio; Pilling, Sérgio; Janot-Pacheco, Eduardo; de Brito, Arnaldo Naves; Barbosa, João Alexandre Ribeiro Gonçalves; Leitão, Alvaro Costa; Lage, Claudia de Alencar Santos

2010-08-01

The radiation-resistant bacterium Deinococcus radiodurans was exposed to a simulated interplanetary UV radiation at the Brazilian Synchrotron Light Laboratory (LNLS). Bacterial samples were irradiated on different substrates to investigate the influence of surface relief on cell survival. The effects of cell multi-layers were also investigated. The ratio of viable microorganisms remained virtually the same (average 2%) for integrated doses from 1.2 to 12 kJ m -2, corresponding to 16 h of irradiation at most. The asymptotic profiles of the curves, clearly connected to a shielding effect provided by multi-layering cells on a cavitary substrate (carbon tape), means that the inactivation rate may not change significantly along extended periods of exposure to radiation. Such high survival rates reinforce the possibility of an interplanetary transfer of viable microbes.

Involvement of recQ in the ultraviolet damage repair pathway in Deinococcus radiodurans

International Nuclear Information System (INIS)

Hua Xiaoting; Huang Lifen; Tian Bing; Hua Yuejin

2008-01-01

Deinococcus radiodurans is a bacterium which can survive extremely DNA damage. To investigate the relationship between recQ and the ultraviolet radiation (UV) damage repair pathway, we created a four mutant strain by constructing recQ knockout mutants in uvrA1, uvrA2, and uvsE backgrounds. Using the rpoB/Rif r system, we measured the mutation frequencies and rates in wild type, recQ (MQ), uvsE uvrA1 uvrA2 (TNK006), and uvsE uvrA1 uvrA2 recQ (TQ). We then isolated Rif r mutants of these strains and sequenced the rpoB gene. The mutation frequency of TQ was 6.4, 10.1, and 2.43 times that of wild type, MQ, and TNK006, respectively, and resulted in rates of 4.7, 6.71, and 2.15 folds higher than that of wild type, MQ, and TNK006, respectively. All the strains demonstrated specific mutational hotspots. Furthermore, the TQ strain showed a transversion bias that was different from the other three strains. The results indicate that recQ is involved in the ultraviolet damage repair pathway via the interaction between recQ and uvrA1, uvrA2, and uvsE in D. radiodurans

Identifying the Proteins that Mediate the Ionizing Radiation Resistance of Deinococcus Radiodurans R1

Energy Technology Data Exchange (ETDEWEB)

Battista, John R

2010-02-22

The primary objectives of this proposal was to define the subset of proteins required for the ionizing radiation (IR) resistance of Deinococcus radiodurans R1, characterize the activities of those proteins, and apply what was learned to problems of interest to the Department of Energy.

The essential role of the Deinococcus radiodurans ssb gene in cell survival and radiation tolerance.

Directory of Open Access Journals (Sweden)

J Scott Lockhart

Full Text Available Recent evidence has implicated single-stranded DNA-binding protein (SSB expression level as an important factor in microbial radiation resistance. The genome of the extremely radiation resistant bacterium Deinococcus radiodurans contains genes for two SSB homologs: the homodimeric, canonical Ssb, encoded by the gene ssb, and a novel pentameric protein encoded by the gene ddrB. ddrB is highly induced upon exposure to radiation, and deletions result in decreased radiation-resistance, suggesting an integral role of the protein in the extreme resistance exhibited by this organism. Although expression of ssb is also induced after irradiation, Ssb is thought to be involved primarily in replication. In this study, we demonstrate that Ssb in D. radiodurans is essential for cell survival. The lethality of an ssb deletion cannot be complemented by providing ddrB in trans. In addition, the radiation-sensitive phenotype conferred by a ddrB deletion is not alleviated by providing ssb in trans. By altering expression of the ssb gene, we also show that lower levels of transcription are required for optimal growth than are necessary for high radiation resistance. When expression is reduced to that of E. coli, ionizing radiation resistance is similarly reduced. UV resistance is also decreased under low ssb transcript levels where growth is unimpaired. These results indicate that the expression of ssb is a key component of both normal cellular metabolism as well as pathways responsible for the high radiation tolerance of D. radiodurans.

Whole cell Deinococcus radiodurans ameliorates salt stress in Indian mustard through pyrroloquinoline quinone

International Nuclear Information System (INIS)

Srivastava, A.K.; Jadhav, P.; Suprasanna, P.; Rajpurohit, Y.S.; Misra, H.S.

2015-01-01

Salinity stress is considered as one of the major abiotic stresses limiting crop productivity. A variety of symbiotic and non-symbiotic bacteria are currently being used worldwide with the aim to boost built-in defense system in plants. Deinococcus radiodurans is a highly desiccation and radiation tolerant bacterium which synthesizes PQQ (pyrroloquinoline quinone) that has been shown to have a versatile role in crop productivity and as a general stress response regulator in bacteria and mammals. PQQ also acts as scavenger of reactive oxygen species and hence, can module redox signaling, one of the major regulator of stress tolerance in plants. In view of this, present research was conducted to evaluate the potential of whole cell D. radiodurans for ameliorating salt stress in plants. The soil colonization with wild-type cells led to partial amelioration of salt stress. The PQQ mutant showed an intermediate phenotype between wild-type seedlings and those grown on non-colonized soils which confirmed that the effects are largely associated with PQQ. The differential phenotype was also correlated with ROS level and ABA accumulation. The flame photometry data showed that there was no significant reduction in water soluble Na + level in control plant and those treated with either wild-type or PQQ mutant. Further, the elevated levels of antioxidant enzymes and reduced ascorbate in the plants treated with bacterial cells indicated its positive role in oxidative stress management. Although, the exact molecular basis to these effects is yet to be understood, present findings support the use of whole cell D. radiodurans for managing the growth and productivity of Indian mustard in salt affected fields. (author)

Characterization of radiation-induced proteins in Deinococcus radiodurans

International Nuclear Information System (INIS)

Tanaka, A.; Watanabe, H.; Nozawa, R.; Hu, Q.; Kitayama, S.

1992-01-01

Induction of proteins after gamma-irradiation in Deinococcus radiodurans were investigated. 10 proteins were induced and about 15 proteins were reduced after irradiation with 6kGy. These proteins were classified to four groups by responses to gamma-rays, UV light, mitomycin C(MMC) treatment and heating. Additional studies were carried out for the characterization of two induced proteins. One protein was induced by gamma-rays, UV light as well as heating. This protein appeared to be a glycoprotein from its reaction with lectin. From the amino acid sequences of N-terminal and internal region, it was found that this protein is homologous to EF-Tu protein of E. coli. Meanwhile the other protein was induced not only by gamma-rays but also by UV light and MMC treatment. This protein seems to be a new enzyme as it has no homology to the known proteins which have ever been analyzed. No accumulations of these two proteins were observed in radiation sensitive strain of D. radiodurans and in both of E. coli and Bacillus pumilus, suggesting that induction of these two proteins would be specific for high resistant strain. (author)

Final Report for Grant No. DE-FG02-97ER62492 ''Engineering Deinococcus radiodurans for Metal Remediation in Radioactive Mixed Waste Sites''

International Nuclear Information System (INIS)

Michael J.; Daly, Ph.D.

2005-01-01

The groundwater and sediments of numerous U. S. Department of Energy (DOE) field sites are contaminated with mixtures of heavy metals (e.g., Hg, Cr, Pd) and radionuclides (e.g., U, Tc), as well as the fuel hydrocarbons benzene, toluene, ethylbenzene and xylenes (BTEX); chlorinated hydrocarbons, such as trichloroethylene (TCE); and polychlorinated biphenyls (PCBs). The remediation of such mixed wastes constitutes an immediate and complex waste management challenge for DOE, particularly in light of the costliness and limited efficacy of current physical and chemical strategies for treating mixed wastes. In situ bioremediation via natural microbial processes (e.g., metal reduction) remains a potent, potentially cost-effective approach to the reductive immobilization or detoxification of environmental contaminants. Seventy million cubic meters of soil and three trillion liters of groundwater have been contaminated by leaking radioactive waste generated in the United States during the Cold War. A cleanup technology is being developed based on the extremely radiation resistant bacterium Deinococcus radiodurans. Our recent isolation and characterization of D. radiodurans from a variety of DOE environments, including highly radioactive sediments beneath one of the leaking tanks (SX-108) at the Hanford Site in south-central Washington state, underscores the potential for this species to survive in such extreme environments. Research aimed at developing D. radiodurans for metal remediation in radioactive waste sites was started by this group in September 1997 with support from DOE NABIR grant DE-FG02-97ER62492. Our grant was renewed for the period 2000-2003, which includes work on the thermophilic radiation resistant bacterium Deinococcus geothermalis. Work funded by the existing grant contributed to 18 papers in the period 1997-2004 on the fundamental biology of D. radiodurans and its design for bioremediation of radioactive waste environments. Our progress since September

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

Directory of Open Access Journals (Sweden)

Daly Michael J

2005-10-01

Full Text Available Abstract Background Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria. Results By reconstructing the evolution of Thermus and Deinococcus after the divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria; many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27 and Deinococcus megaplasmid (DR177. Conclusion After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of

Investigation of DNA damage and repair mechanism using deinococcus radiodurans

International Nuclear Information System (INIS)

Lau How Mooi; Kikuchi, M.; Kobayashi, Y.; Narumi, I.; Watanabe, H.

1997-01-01

Deninococcus Radiodurans, formerly known as Micrococcus Radiodurans, is a popular bacterium because of its high resistance to damage by carcinogens such as ionizing radiation (Dean et. al. 1966; Kitayama and Matsuyama 1968) and UV radiation (Gasvon et. al., 1995; Arrange et. al. 1993). In this report, we investigated the high resistance to ionizing radiation by this bacterium. The bacteria had been exposed from I to 5 kGy of gamma radiation and then incubated in TGY medium to study their ability to repair the broken DNA. The repair time was measured by Pulse Field Gel Electrophoresis (PFGE) method. The repair time for each dose was determined. Also in order to ensure that the repair was perfect, the bacterium was subjected to a second exposure of ionizing radiation after it has fully repaired. It was found that the 'second' repair characteristic was similar to the first repair. This confirmed that the repair after the exposure to the ionizing radiation was perfect

Effect of N+ beam exposure on the activities of Mn-SOD and catalase in deinococcus radiodurans

International Nuclear Information System (INIS)

Song Daojun; Chen Ruolei; Wu Lifang; Li Hong; Yao JIanming; Shao Chunlin; Wu Lijun; Yu Zengliang

2000-01-01

Though the radiation-resistant bacteria Deinococcus radiodurans (D. radiodurans) have a high resistance to the lethal and mutagenic effects of many DNA-damaging agents, the mechanisms involved in the response of these bacteria to oxidative stress are poorly understood. The superoxide dismutase (SOD) and catalase (CAT) activities produced in bacteria (D. radiodurans AS1.633) and their change caused by 20 keV N'+ beam exposure were examined. Results showed that the activities of the enzymes were increased in the case of N + beam exposure from 8 x 10 14 ions/cm 2 to 6 x 10 15 ions/cm 2 . In addition, the treatment of H 2 O 2 and [CHCl 3 + CH 3 CH 2 OH] and the measurement of absorption spectrum showed that the increase of whole SOD activity resulted from inducible activities of Mn-SOD in (a sub-type) D. radiodurans AS1.633. These results suggested that these bacteria possess inducible defense mechanisms against the deleterious effects of oxidization

Synthesis and extracellular accumulation of silver nanoparticles by employing radiation-resistant Deinococcus radiodurans, their characterization, and determination of bioactivity

Directory of Open Access Journals (Sweden)

Kulkarni RR

2015-01-01

Full Text Available Rasika R Kulkarni, Nayana S Shaiwale, Dileep N Deobagkar, Deepti D Deobagkar Molecular Biology Research Laboratory, Center of Advanced Studies, Department of Zoology, University of Pune, Pune, India Abstract: There has been rapid progress in exploring microorganisms for green synthesis of nanoparticles since microbes show extraordinary diversity in terms of species richness and niche localization. Microorganisms are easy to culture using relatively inexpensive and simple nutrients under varied conditions of temperature, pressure, pH, etc. In this work, Deinococcus radiodurans that possesses the ability to withstand extremely high radiation and desiccation stress has been employed for the synthesis of silver nanoparticles (AgNPs. D. radiodurans was able to accumulate AgNPs in medium under various conditions, and process optimization was carried out with respect to time, temperature, pH, and concentration of silver salt. AgNPs were characterized using UV/vis spectroscopy, scanning electron microscopy, transmission electron microscopy, X-ray diffraction, energy-dispersive X-ray spectroscopy, and Fourier transform infrared spectroscopy. The microbially synthesized AgNPs exhibited good antimicrobial activity against both Gram-negative and Gram-positive organisms and anti-biofouling activity. Their ability to inhibit growth and proliferation of cancer cell line was also examined, and it could be seen that AgNPs synthesized using D. radiodurans exhibited excellent anticancer activity. Keywords: Deinococcus radiodurans, silver nanoparticles, anticancer, radiation resistance, antibacterial, anti-biofouling 

Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans

Directory of Open Access Journals (Sweden)

Barkallah Insaf

2009-04-01

Full Text Available Abstract Interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (IRRB might be a part of the answer to the question as to how IRRB, particularly Deinococcus radiodurans R1 (Deira, resist ionizing radiation. Here, using the Database of Interacting Proteins (DIP and the Protein Structural Interactome (PSI-base server for PSI map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in Deira and other IRRB, but which are absent in IRSB. Among these, 18 domains and their interactomes have been identified in DNA checkpoint and repair; kinases pathways; energy and nucleotide metabolisms were the important biological processes that were found to be involved. This finding provides new clues to the cellular pathways that can to be important for ionizing-radiation resistance in Deira.

Metabolic engineering of deinococcus radiodurans based on computational analysis and functional genomics

Energy Technology Data Exchange (ETDEWEB)

Edwards, Jeremy, S.

2005-02-02

The objective of our work is to develop novel computational tools to analyze the Deinococcus radiodurans DNA repair pathways and the influence of the metabolic flux distribution on DNA repair. These tools will be applied to provide insights for metabolic engineering of strains capable of growing under nutrient poor conditions similar to those found in mixed contaminant sites of interest to the DOE. Over the entire grant period we accomplished all our specific aims and were also able to pursue new directions of research. Below, I will list the major accomplishments over the previous 3 years. (1) Performed Monte Carlo Simulations of RecA Mediated Pairing of Homologous DNA Molecules. (2) Developed a statistical approach to study the gene expression data from D. radiodurans. We have been studying the data from John Batista's. (3) Developed an expression profiling technology to generate very accurate and precise expression data. We followed up on results from John Batista's group using this approach. (4) Developed and put online a database for metabolic reconstructions. (5) We have developed and applied new Monte Carlo algorithms that are optimized for studying biological systems. (6) We developed a flux balance model for the D. radiodurans metabolic network

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Energy Technology Data Exchange (ETDEWEB)

Makarova, Kira S.; Omelchenko, Marina V.; Gaidamakova, Elena K.; Matrosova, Vera Y.; Vasilenko, Alexander; Zhai, Min; Lapidus, Alla; Copeland, Alex; Kim, Edwin; Land, Miriam; Mavrommatis, Konstantinos; Pitluck, Samuel; Richardson, Paul M.; Detter, Chris; Brettin, Thomas; Saunders, Elizabeth; Lai, Barry; Ravel, Bruce; Kemner, Kenneth M.; Wolf, Yuri I.; Sorokin, Alexander; Gerasimova, Anna V.; Gelfand, Mikhail S.; Fredrickson, James K.; Koonin, Eugene V.; Daly, Michael J.

2007-07-24

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at itsoptimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to

High-resolution structure of the antibiotic resistance protein NimA from Deinococcus radiodurans

International Nuclear Information System (INIS)

Leiros, Hanna-Kirsti S.; Tedesco, Consiglia; McSweeney, Seán M.

2008-01-01

In this paper, the 1.2 Å atomic resolution crystal structure of the 5-nitroimidazole antibiotic resistance protein NimA from Deinococcus radiodurans (DrNimA) is presented. Many anaerobic human pathogenic bacteria are treated using 5-nitroimidazole-based (5-Ni) antibiotics, a class of inactive prodrugs that contain a nitro group. The nitro group must be activated in an anaerobic one-electron reduction and is therefore dependent on the redox system in the target cells. Antibiotic resistance towards 5-Ni drugs is found to be related to the nim genes (nimA, nimB, nimC, nimD, nimE and nimF), which are proposed to encode a reductase that is responsible for converting the nitro group of the antibiotic into a nonbactericidal amine. A mechanism for the Nim enzyme has been proposed in which two-electron reduction of the nitro group leads to the generation of nontoxic derivatives and confers resistance against these antibiotics. The cofactor was found to be important in the mechanism and was found to be covalently linked to the reactive His71. In this paper, the 1.2 Å atomic resolution crystal structure of the 5-nitroimidazole antibiotic resistance protein NimA from Deinococcus radiodurans (DrNimA) is presented. A planar cofactor is clearly visible and well defined in the electron-density map adjacent to His71, the identification of the cofactor and its properties are discussed

Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1

International Nuclear Information System (INIS)

Fredrickson, J.K.; Kostandarithes, H.M.; Li, S.W.; Plymake, A.E.; Daly, M.J.

2000-01-01

Deinococcus radiodurans is an exceptionally radiation-resistant microorganism capable of surviving acute exposures to ionizing radiation doses of 15,000 Gy and previously described as having a strictly aerobic respiratory metabolism. Under strict anaerobic conditions, D. radiodurans R1 reduced Fe(III)-nitrilotriacetic acid coupled to the oxidation of lactate to CO 2 and acetate but was unable to link this process to growth. D. radiodurans reduced the humic acid analog anthraquinone-2,6-disulfonate (AQDS) to its dihydroquinone form, AH 2 DS, which subsequently transferred electrons to the Fe(III) oxides hydrous ferric oxide and goethite via a previously described electron shuttle mechanism. D. radiodurans reduced the solid-phase Fe(III) oxides in the presence of either 0.1 mM AQDS or leonardite humic acids (2 mg ml -1 ) but not in their absence. D. radiodurans also reduced U(VI) and Tc(VII) in the presence of AQDS. In contrast, Cr(VI) was directly reduced in anaerobic cultures with lactate although the rate of reduction was higher in the presence of AQDS. The results are the first evidence that D. radiodurans can reduce Fe(III) coupled to the oxidation of lactate or other organic compounds. Also, D. radiodurans, in combination with humic acids or synthetic electron shuttle agents, can reduce U and Tc and thus has potential applications for remediation of metal- and radionuclide-contaminated sites where ionizing radiation or other DNA-damaging agents may restrict the activity of more sensitive organisms

Design of Deinococcus radiodurans thioredoxin reductase with altered thioredoxin specificity using computational alanine mutagenesis

OpenAIRE

Obiero, Josiah; Sanders, David AR

2011-01-01

In this study, the X-ray crystal structure of the complex between Escherichia coli thioredoxin reductase (EC TrxR) and its substrate thioredoxin (Trx) was used as a guide to design a Deinococcus radiodurans TrxR (DR TrxR) mutant with altered Trx specificity. Previous studies have shown that TrxRs have higher affinity for cognate Trxs (same species) than that for Trxs from different species. Computational alanine scanning mutagenesis and visual inspection of the EC TrxR–Trx interface suggested...

THE ROLE OF IRON IN Deinococcus radiodurans ENGINEERED FOR GROWTH ON TOLUENE AND THE ROLE OF MANGANESE IN THE EXTREME RADIATION RESISTANCE PHENOTYPE

International Nuclear Information System (INIS)

Hassan Brim; Elena K. Gaidamakova; Vera Y. Matrosova; Min Zhai; Amudhan Venkateswaran; Marina Omelchenko; Kira S. Makarova; Lawrence P. Wackett; James K. Fredrickson; Michael J. Daly

2004-01-01

Toluene and other fuel hydrocarbons are commonly found in association with radionuclides at numerous Department of Energy (DOE) sites, frequently occurring together with Cr(VI) and other heavy metals. In this study, the extremely radiation resistant bacterium Deinococcus radiodurans was engineered for complete toluene mineralization by cloned expression of tod and xyl genes of Pseudomonas putida. The recombinant Tod/Xyl strain showed significant incorporation of carbon from the toluene aromatic ring into cellular macromolecules and carbon dioxide, in the absence or presence of chronic radiation. We have shown that intracellular iron concentrations in wild-type D. radiodurans in minimal medium are exceptionally low and not sufficient to support growth on toluene using Fe-dependent oxygenases cloned from P. putida. Introducing the fur mutation into D. radiodurans increased intracellular Fe levels, and imparted on the engineered strain the ability to grow on meta-toluate as the sole carbon and energy source. The organism's native Cr(VI) reduction capabilities were facilitated by toluene when present as the sole carbon and energy source in natural sediment analogues of DOE contaminated environments. The engineered bacteria were able to oxidize toluene under both minimal and complex nutrient conditions, which is important since both conditions have environmental equivalents in the context of bioremediation processes. As such, the Tod/Xyl strain is providing a model for understanding the role of Fe and reduction of metals coupled to organic contaminant oxidation in aerobic radionuclide contaminated sediments. We have shown that D. radiodurans contains high intracellular manganese levels, and that Mn restriction sensitizes cells to irradiation. We propose that the unusually high Mn/Fe ratio of D. radiodurans facilitates survival by quenching oxidative stress during recovery.

THE ROLE OF IRON IN Deinococcus radiodurans ENGINEERED FOR GROWTH ON TOLUENE AND THE ROLE OF MANGANESE IN THE EXTREME RADIATION RESISTANCE PHENOTYPE

Energy Technology Data Exchange (ETDEWEB)

Hassan Brim; Elena K. Gaidamakova; Vera Y. Matrosova; Min Zhai; Amudhan Venkateswaran; Marina Omelchenko; Kira S. Makarova; Lawrence P. Wackett; James K. Fredrickson; Michael J. Daly

2004-03-17

Toluene and other fuel hydrocarbons are commonly found in association with radionuclides at numerous Department of Energy (DOE) sites, frequently occurring together with Cr(VI) and other heavy metals. In this study, the extremely radiation resistant bacterium Deinococcus radiodurans was engineered for complete toluene mineralization by cloned expression of tod and xyl genes of Pseudomonas putida. The recombinant Tod/Xyl strain showed significant incorporation of carbon from the toluene aromatic ring into cellular macromolecules and carbon dioxide, in the absence or presence of chronic radiation. We have shown that intracellular iron concentrations in wild-type D. radiodurans in minimal medium are exceptionally low and not sufficient to support growth on toluene using Fe-dependent oxygenases cloned from P. putida. Introducing the fur mutation into D. radiodurans increased intracellular Fe levels, and imparted on the engineered strain the ability to grow on meta-toluate as the sole carbon and energy source. The organism's native Cr(VI) reduction capabilities were facilitated by toluene when present as the sole carbon and energy source in natural sediment analogues of DOE contaminated environments. The engineered bacteria were able to oxidize toluene under both minimal and complex nutrient conditions, which is important since both conditions have environmental equivalents in the context of bioremediation processes. As such, the Tod/Xyl strain is providing a model for understanding the role of Fe and reduction of metals coupled to organic contaminant oxidation in aerobic radionuclide contaminated sediments. We have shown that D. radiodurans contains high intracellular manganese levels, and that Mn restriction sensitizes cells to irradiation. We propose that the unusually high Mn/Fe ratio of D. radiodurans facilitates survival by quenching oxidative stress during recovery.

in Deinococcus radiodurans

African Journals Online (AJOL)

STORAGESEVER

2010-05-10

May 10, 2010 ... from oxidation during irradiation (Daly et al., 2007; 2009). According to the first .... radiodurans R1 for bioprecipitation of Uranium from dilute nuclear waste. ... Eide DJ (1998). The molecular biology of metal ion transport in.

Expression of PprI from Deinococcus radiodurans Improves Lactic Acid Production and Stress Tolerance in Lactococcus lactis.

Directory of Open Access Journals (Sweden)

Xiangrong Dong

Full Text Available PprI is a general switch protein that regulates the expression of certain proteins involved in pathways of cellular resistance in the extremophilic bacterium Deinococcus radiodurans. In this study, we transformed pprI into Lactococcus lactis strain MG1363 using the lactococcal shuttle vector pMG36e and investigated its effects on the tolerance and lactic acid production of L. lactis while under stress. PprI was stably expressed in L. lactis as confirmed by western blot assays. L. lactis expressing PprI exhibited significantly improved resistance to oxidative stress and high osmotic pressure. This enhanced cellular tolerance to stressors might be due to the regulation of resistance-related genes (e.g., recA, recO, sodA, and nah by pprI. Moreover, transformed L. lactis demonstrated increased lactic acid production, attributed to enhanced lactate dehydrogenase activity. These results suggest that pprI can improve the tolerance of L. lactis to environmental stresses, and this transformed bacterial strain is a promising candidate for industrial applications of lactic acid production.

Expression of PprI from Deinococcus radiodurans Improves Lactic Acid Production and Stress Tolerance in Lactococcus lactis.

Science.gov (United States)

Dong, Xiangrong; Tian, Bing; Dai, Shang; Li, Tao; Guo, Linna; Tan, Zhongfang; Jiao, Zhen; Jin, Qingsheng; Wang, Yanping; Hua, Yuejin

2015-01-01

PprI is a general switch protein that regulates the expression of certain proteins involved in pathways of cellular resistance in the extremophilic bacterium Deinococcus radiodurans. In this study, we transformed pprI into Lactococcus lactis strain MG1363 using the lactococcal shuttle vector pMG36e and investigated its effects on the tolerance and lactic acid production of L. lactis while under stress. PprI was stably expressed in L. lactis as confirmed by western blot assays. L. lactis expressing PprI exhibited significantly improved resistance to oxidative stress and high osmotic pressure. This enhanced cellular tolerance to stressors might be due to the regulation of resistance-related genes (e.g., recA, recO, sodA, and nah) by pprI. Moreover, transformed L. lactis demonstrated increased lactic acid production, attributed to enhanced lactate dehydrogenase activity. These results suggest that pprI can improve the tolerance of L. lactis to environmental stresses, and this transformed bacterial strain is a promising candidate for industrial applications of lactic acid production.

Imposed Environmental Stresses Facilitate Cell-Free Nanoparticle Formation by Deinococcus radiodurans.

Science.gov (United States)

Chen, Angela; Contreras, Lydia M; Keitz, Benjamin K

2017-09-15

The biological synthesis of metal nanoparticles has been examined in a wide range of organisms, due to increased interest in green synthesis and environmental remediation applications involving heavy metal ion contamination. Deinococcus radiodurans is particularly attractive for environmental remediation involving metal reduction, due to its high levels of resistance to radiation and other environmental stresses. However, few studies have thoroughly examined the relationships between environmental stresses and the resulting effects on nanoparticle biosynthesis. In this work, we demonstrate cell-free nanoparticle production and study the effects of metal stressor concentrations and identity, temperature, pH, and oxygenation on the production of extracellular silver nanoparticles by D. radiodurans R1. We also report the synthesis of bimetallic silver and gold nanoparticles following the addition of a metal stressor (silver or gold), highlighting how production of these particles is enabled through the application of environmental stresses. Additionally, we found that both the morphology and size of monometallic and bimetallic nanoparticles were dependent on the environmental stresses imposed on the cells. The nanoparticles produced by D. radiodurans exhibited antimicrobial activity comparable to that of pure silver nanoparticles and displayed catalytic activity comparable to that of pure gold nanoparticles. Overall, we demonstrate that biosynthesized nanoparticle properties can be partially controlled through the tuning of applied environmental stresses, and we provide insight into how their application may affect nanoparticle production in D. radiodurans during bioremediation. IMPORTANCE Biosynthetic production of nanoparticles has recently gained prominence as a solution to rising concerns regarding increased bacterial resistance to antibiotics and a desire for environmentally friendly methods of bioremediation and chemical synthesis. To date, a range of organisms

Gel-based proteomic approach to unravel the extreme radiation resistance of deinococcus radiodurans

International Nuclear Information System (INIS)

Basu, Bhakti; Apte, Shree Kumar

2013-01-01

The extremophile, Deinococcus radiodurans, is endowed with an extraordinary DNA repair ability and oxidative stress alleviation mechanisms that render it virtually resistant to all types of DNA damaging stressors such as ionizing radiations, UV or years of desiccation. Following DNA damage, the microbe reassembles its complete genome from multiple DNA fragments with impeccable fidelity. The deinococcal genome encodes functional homologues of both prokaryotic and eukaryotic DNA repair pathways, such as RecFOR mediated homologous recombination (HR), nucleotide/base excision repair (NER/BER), strand annealing (SA) and non-homologous end joining (NHEJ), but lacks homologues for universal prokaryotic DNA repair pathways such as RecBCD mediated HR, photo-reactivation and SOS response. It also harbors multiple enzymatic and non-enzymatic oxidative stress defense mechanisms. Proteomic approaches were employed to study the response of D. radiodurans to LD50 dose of gamma irradiation during the post-irradiation growth arrest phase by two dimensional protein electrophoresis coupled with mass spectrometry to reveal kinetics and dynamics of DNA repair, oxidative stress alleviation and resynthesis of damaged proteins, preceding growth recovery

PprA contributes to Deinococcus radiodurans resistance to nalidixic acid, genome maintenance after DNA damage and interacts with deinococcal topoisomerases.

Directory of Open Access Journals (Sweden)

Swathi Kota

Full Text Available PprA is known to contribute to Deinococcus radiodurans' remarkable capacity to survive a variety of genotoxic assaults. The molecular bases for PprA's role(s in the maintenance of the damaged D. radiodurans genome are incompletely understood, but PprA is thought to promote D. radiodurans's capacity for DSB repair. PprA is found in a multiprotein DNA processing complex along with an ATP type DNA ligase, and the D. radiodurans toposiomerase IB (DraTopoIB as well as other proteins. Here, we show that PprA is a key contributor to D. radiodurans resistance to nalidixic acid (Nal, an inhibitor of topoisomerase II. Growth of wild type D. radiodurans and a pprA mutant were similar in the absence of exogenous genotoxic insults; however, the pprA mutant exhibited marked growth delay and a higher frequency of anucleate cells following treatment with DNA-damaging agents. We show that PprA interacts with both DraTopoIB and the Gyrase A subunit (DraGyrA in vivo and that purified PprA enhances DraTopoIB catalysed relaxation of supercoiled DNA. Thus, besides promoting DNA repair, our findings suggest that PprA also contributes to preserving the integrity of the D. radiodurans genome following DNA damage by interacting with DNA topoisomerases and by facilitating the actions of DraTopoIB.

The study of the extreme radiation tolerance mechanisms of the bacterium Deinococcus deserti by a functional genomics approach

International Nuclear Information System (INIS)

Dulermo, R.

2009-12-01

The genome of Deinococcus deserti, a highly radiation-tolerant bacterium, was analyzed and compared to those of D. radiodurans and D. geothermalis. About 230 proteins are specifically conserved in these 3 species, including IrrE, a regulator protein essential for radio tolerance. D.deserti has several supplementary DNA repair genes, like imuY and dnaE2 (trans-lesion DNA polymerases). Moreover, D. deserti has 3 recA that code for 2 different RecA proteins (RecAC et RecAP). To study these genes, genetic tools were developed for D. deserti. Different results suggest that IrrE, required for the induction of several genes after irradiation, has peptidase activity. The 2 RecA proteins are functional for DNA repair. D. deserti is mutable by UV, which requires ImuY, DnaE2 and RecAC, but not RecAP. (author)

Cyclic AMP Receptor Protein Acts as a Transcription Regulator in Response to Stresses in Deinococcus radiodurans.

Directory of Open Access Journals (Sweden)

Su Yang

Full Text Available The cyclic AMP receptor protein family of transcription factors regulates various metabolic pathways in bacteria, and also play roles in response to environmental changes. Here, we identify four homologs of the CRP family in Deinococcus radiodurans, one of which tolerates extremely high levels of oxidative stress and DNA-damaging reagents. Transcriptional levels of CRP were increased under hydrogen peroxide (H2O2 treatment during the stationary growth phase, indicating that CRPs function in response to oxidative stress. By constructing all CRP single knockout mutants, we found that the dr0997 mutant showed the lowest tolerance toward H2O2, ultraviolet radiation, ionizing radiation, and mitomycin C, while the phenotypes of the dr2362, dr0834, and dr1646 mutants showed slight or no significant differences from those of the wild-type strain. Taking advantage of the conservation of the CRP-binding site in many bacteria, we found that transcription of 18 genes, including genes encoding chromosome-partitioning protein (dr0998, Lon proteases (dr0349 and dr1974, NADH-quinone oxidoreductase (dr1506, thiosulfate sulfurtransferase (dr2531, the DNA repair protein UvsE (dr1819, PprA (dra0346, and RecN (dr1447, are directly regulated by DR0997. Quantitative real-time polymerase chain reaction (qRT-PCR analyses showed that certain genes involved in anti-oxidative responses, DNA repair, and various cellular pathways are transcriptionally attenuated in the dr0997 mutant. Interestingly, DR0997 also regulate the transcriptional levels of all CRP genes in this bacterium. These data suggest that DR0997 contributes to the extreme stress resistance of D. radiodurans via its regulatory role in multiple cellular pathways, such as anti-oxidation and DNA repair pathways.

Regulation of MntH by a dual Mn(II- and Fe(II-dependent transcriptional repressor (DR2539 in Deinococcus radiodurans.

Directory of Open Access Journals (Sweden)

Hongxing Sun

Full Text Available The high intracellular Mn/Fe ratio observed within the bacteria Deinococcus radiodurans may contribute to its remarkable resistance to environmental stresses. We isolated DR2539, a novel regulator of intracellular Mn/Fe homeostasis in D. radiodurans. Electrophoretic gel mobility shift assays (EMSAs revealed that DR2539 binds specifically to the promoter of the manganese acquisition transporter (MntH gene, and that DR0865, the only Fur homologue in D. radiodurans, cannot bind to the promoter of mntH, but it can bind to the promoter of another manganese acquisition transporter, MntABC. β-galactosidase expression analysis indicated that DR2539 acts as a manganese- and iron-dependent transcriptional repressor. Further sequence alignment analysis revealed that DR2539 has evolved some special characteristics. Site-directed mutagenesis suggested that His98 plays an important role in the activities of DR2539, and further protein-DNA binding activity assays showed that the activity of H98Y mutants decreased dramatically relative to wild type DR2539. Our study suggests that D. radiodurans has evolved a very efficient manganese regulation mechanism that involves its high intracellular Mn/Fe ratio and permits resistance to extreme conditions.

DR2539 is a novel DtxR-like regulator of Mn/Fe ion homeostasis and antioxidant enzyme in Deinococcus radiodurans

International Nuclear Information System (INIS)

Chen, Huan; Wu, Rongrong; Xu, Guangzhi; Fang, Xu; Qiu, Xiaoli; Guo, Hongyin; Tian, Bing; Hua, Yuejin

2010-01-01

Transcriptional regulators of the diphtheria toxin repressor (DtxR) family control the expression of genes involved in the uptake of iron and manganese, which is not only necessitous nutrients but also was suggested to be essential for intracellular redox cycling of microorganisms. We identified a unique DtxR homologue (DR2539) with special characteristics from Deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. The dr2539 mutant showed higher resistance to hydrogen peroxide than the wild-type strain R1. Intracellular catalase activity assay and semiquantitative PCR analysis demonstrated that this DtxR is a negative regulator of catalase (katE). Furthermore, quantitative real-time PCR, global transcription profile and inductively coupled plasma-mass spectrometry analysis showed that the DtxR is involved in the regulation of antioxidant system by maintaining the intracellular Mn/Fe ion homeostasis of D. radiodurans. However, unlike the other DtxR homologues, the DtxR of D. radiodurans acts as a negative regulator of a Mn transporter gene (dr2283) and as a positive regulator of Fe-dependent transporter genes (dr1219, drb0125) in D. radiodurans.

DR2539 is a novel DtxR-like regulator of Mn/Fe ion homeostasis and antioxidant enzyme in Deinococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Chen, Huan [Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029 (China); Zhejiang Institute of Microbiology, Zhejiang Province, Hangzhou 310012 (China); Wu, Rongrong [Department of Cardiology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009 (China); Xu, Guangzhi [Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029 (China); Fang, Xu; Qiu, Xiaoli; Guo, Hongyin [Zhejiang Institute of Microbiology, Zhejiang Province, Hangzhou 310012 (China); Tian, Bing, E-mail: tianbing@zju.edu.cn [Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029 (China); Hua, Yuejin, E-mail: yjhua@zju.edu.cn [Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029 (China)

2010-05-28

Transcriptional regulators of the diphtheria toxin repressor (DtxR) family control the expression of genes involved in the uptake of iron and manganese, which is not only necessitous nutrients but also was suggested to be essential for intracellular redox cycling of microorganisms. We identified a unique DtxR homologue (DR2539) with special characteristics from Deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. The dr2539 mutant showed higher resistance to hydrogen peroxide than the wild-type strain R1. Intracellular catalase activity assay and semiquantitative PCR analysis demonstrated that this DtxR is a negative regulator of catalase (katE). Furthermore, quantitative real-time PCR, global transcription profile and inductively coupled plasma-mass spectrometry analysis showed that the DtxR is involved in the regulation of antioxidant system by maintaining the intracellular Mn/Fe ion homeostasis of D. radiodurans. However, unlike the other DtxR homologues, the DtxR of D. radiodurans acts as a negative regulator of a Mn transporter gene (dr2283) and as a positive regulator of Fe-dependent transporter genes (dr1219, drb0125) in D. radiodurans.

Deinococcus antarcticus sp. nov., isolated from soil.

Science.gov (United States)

Dong, Ning; Li, Hui-Rong; Yuan, Meng; Zhang, Xiao-Hua; Yu, Yong

2015-02-01

A pink-pigmented, non-motile, coccoid bacterial strain, designated G3-6-20(T), was isolated from a soil sample collected in the Grove Mountains, East Antarctica. This strain was resistant to UV irradiation (810 J m(-2)) and slightly more sensitive to desiccation as compared with Deinococcus radiodurans. Phylogenetic analyses based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus. Highest sequence similarities were with Deinococcus ficus CC-FR2-10(T) (93.5 %), Deinococcus xinjiangensis X-82(T) (92.8 %), Deinococcus indicus Wt/1a(T) (92.5 %), Deinococcus daejeonensis MJ27(T) (92.3 %), Deinococcus wulumuqiensis R-12(T) (92.3 %), Deinococcus aquaticus PB314(T) (92.2 %) and Deinococcus radiodurans DSM 20539(T) (92.2 %). Major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), anteiso-C15 : 0 and C16 : 0. The G+C content of the genomic DNA of strain G3-6-20(T) was 63.1 mol%. Menaquinone 8 (MK-8) was the predominant respiratory quinone. Based on its phylogenetic position, and chemotaxonomic and phenotypic characteristics, strain G3-6-20(T) represents a novel species of the genus Deinococcus, for which the name Deinococcus antarcticus sp. nov. is proposed. The type strain is G3-6-20(T) ( = DSM 27864(T) = CCTCC AB 2013263(T)). © 2015 IUMS.

Molecular cloning and analysis of DNA repair gene from the radioresistant bacterium deinococcus radiodurans

International Nuclear Information System (INIS)

Du Zeji; Wang Mingsuo

1998-12-01

Deinococcus radiodurans (Dr) possesses a prominent ability to repair DNA injury induced by various DNA-damaging agents including mitomycin C (MC), ultraviolet light (UV) and ionizing radiation. A DNA repair mutant Dr KH3111 is a streptomycin resistant (Sm R ) derivative of KH311 which is generated by treatment with nitrosoguanidine and is sensitive to MC, 8-trimethyl-psoralen, UV and γ-ray irradiation. Gene affected by a mutation in the mutant is identified and its nucleotide sequence is determined. A complete open reading frame (ORF) which encompassed the KH3111 mutation region is found and tentatively designated as orf144b. The deduced amino acid (aa) sequence of orf144b consists of 284 aa and has no significant homology to other known proteins. The exact KH3111 mutation site is one nucleotide altered (G to A) in the sequence of orf144b in the mutant. The KH3111 mutation causes the substitution of Gly for Glu at aa position 149 of Orf144b. Survival measurements of a revertant KH3112 which was produced by transforming with DNA containing a part of the orf144b gene of KD8301 showed that the resistances to MC, UV and γ-ray in the revertant were fully restored at a level equal to the wild type. Thus, the orf144b gene required for the multiple-DNA-damaging agent resistance of Dr was designated with the name of pprA (Pleiotropic gene promoting DNA repair). This new gene can express in E. coli at very high level, and make the host E. coli resistant to MC, UV and γ-ray. The pprA gene does not express in normal Dr, but it can be induced to express by treatment with MC, UV and γ-ray. It was thought that the PprA polypeptide is a cytoplasmic protein because of the absence of characteristics found in the aa sequence of membrane proteins

Single Strand Annealing Plays a Major Role in RecA-Independent Recombination between Repeated Sequences in the Radioresistant Deinococcus radiodurans Bacterium.

Directory of Open Access Journals (Sweden)

Solenne Ithurbide

2015-10-01

Full Text Available The bacterium Deinococcus radiodurans is one of the most radioresistant organisms known. It is able to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Our work aims to highlight the genes involved in recombination between 438 bp direct repeats separated by intervening sequences of various lengths ranging from 1,479 bp to 10,500 bp to restore a functional tetA gene in the presence or absence of radiation-induced DNA double strand breaks. The frequency of spontaneous deletion events between the chromosomal direct repeats were the same in recA+ and in ΔrecA, ΔrecF, and ΔrecO bacteria, whereas recombination between chromosomal and plasmid DNA was shown to be strictly dependent on the RecA and RecF proteins. The presence of mutations in one of the repeated sequence reduced, in a MutS-dependent manner, the frequency of the deletion events. The distance between the repeats did not influence the frequencies of deletion events in recA+ as well in ΔrecA bacteria. The absence of the UvrD protein stimulated the recombination between the direct repeats whereas the absence of the DdrB protein, previously shown to be involved in DNA double strand break repair through a single strand annealing (SSA pathway, strongly reduces the frequency of RecA- (and RecO- independent deletions events. The absence of the DdrB protein also increased the lethal sectoring of cells devoid of RecA or RecO protein. γ-irradiation of recA+ cells increased about 10-fold the frequencies of the deletion events, but at a lesser extend in cells devoid of the DdrB protein. Altogether, our results suggest a major role of single strand annealing in DNA repeat deletion events in bacteria devoid of the RecA protein, and also in recA+ bacteria exposed to ionizing radiation.

Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.

Directory of Open Access Journals (Sweden)

Omar Awile

Full Text Available The proteome of the radiation- and desiccation-resistant bacterium D. radiodurans features a group of proteins that contain significant intrinsically disordered regions that are not present in non-extremophile homologues. Interestingly, this group includes a number of housekeeping and repair proteins such as DNA polymerase III, nudix hydrolase and rotamase. Here, we focus on a member of the nudix hydrolase family from D. radiodurans possessing low-complexity N- and C-terminal tails, which exhibit sequence signatures of intrinsic disorder and have unknown function. The enzyme catalyzes the hydrolysis of oxidatively damaged and mutagenic nucleotides, and it is thought to play an important role in D. radiodurans during the recovery phase after exposure to ionizing radiation or desiccation. We use molecular dynamics simulations to study the dynamics of the protein, and study its hydration free energy using the GB/SA formalism. We show that the presence of disordered tails significantly decreases the hydration free energy of the whole protein. We hypothesize that the tails increase the chances of the protein to be located in the remaining water patches in the desiccated cell, where it is protected from the desiccation effects and can function normally. We extrapolate this to other intrinsically disordered regions in proteins, and propose a novel function for them: intrinsically disordered regions increase the "surface-properties" of the folded domains they are attached to, making them on the whole more hydrophilic and potentially influencing, in this way, their localization and cellular activity.

Extremely radioresistant microbe Deinococcus radiodurans does not survive tellurite-mediated oxidative stress: revelation of molecular basis

International Nuclear Information System (INIS)

Apte, Shree Kumar; Narasimha, Anaganti; Basu, Bhakti

2014-01-01

Deinococcus radiodurans exhibits extraordinary resistance to gamma radiation as well as oxidative stress. Comparison of tellurite stress with gamma irradiation, both of which impart severe oxidative stress, revealed that tellurite induced less ROS and caused less oxidative damage to proteins, but was much more lethal to D. radiodurans than gamma irradiation. The proteomic changes induced by tellurite exposure were mapped by two dimensional protein electrophoresis followed by mass spectrometry. Seventy proteins belonging to major functional categories of oxidative stress alleviation, protein translation/folding and metabolism were identified. Tellurite responsive proteome dynamics displayed (i) up-regulation of proteins involved in tellurite stress resistance and oxidative stress alleviation, dehydrogenases involved in generation of reducing potential, and chaperones (such DnaK), and (ii) down regulation of key glycolysis and TCA cycle enzymes, proteins involved in protein translation/folding and energy production. Tellurite stress also resulted in nearly 50% loss in the cellular reducing potential within 1h of exposure while gamma irradiation had no such effect. The findings provide a better insight into the mechanism of tellurite toxicity, beyond metal mediated oxidative stress, in this extremophile. (author)

Understanding the role of RecN in DSB repair pathway in Deinococcus radiodurans

International Nuclear Information System (INIS)

Pellegrino, S.

2012-01-01

Deinococcus radiodurans is a Gram-positive bacterium known for its extreme resistance to a broad variety of DNA damaging agents. Among these, Ionizing Radiations and desiccation are the most harmful for the cell, since they introduce breaks in the genome. Double Strand Breaks (DSB) are particularly hazardous for the cell and they need to be repaired very efficiently, in order to avoid mutations leading to altered, if not lethal, phenotypes. Homologous Recombination (HR) is the most efficient mechanism by which DSBs are repaired. D. radiodurans is able to completely restore its genome in only 3 hours, and it accomplishes the entire process through the RecFOR pathway. In order to be repaired, DSBs first need to be recognized. The protein believed to be responsible for this important step that takes place soon after the damage occurs in the cell, is RecN. RecN is recruited at the early stages of DNA repair and in vivo studies have demonstrated its propensity to localize to discrete foci. In vitro studies also suggest that RecN possesses a DNA end-joining activity previously observed for SMC proteins (such as cohesin), which are structurally related to RecN. Several structural studies have been carried out on the SMC-like protein, Rad50, but so far no structural information is available for RecN. The work presented here focused on the structural characterization of RecN and its constitutive domains. We obtained crystal structures of three partially overlapping constructs of RecN and Small Angle X-ray Scattering was performed on the individual domains and the full-length protein. The study of RecN in solution complemented our crystallographic study and enabled us to build a reliable, atomic model of the full-length protein. Mutations were designed and the mutant RecN proteins were produced in order to characterize the ATP hydrolysis activity of RecN, which is a conserved feature of this family of proteins. Extensive biochemical studies were carried out on wild-type and

Effect of N+ beam exposure on superoxide dismutase and catalase activities and induction of Mn-SOD in Deinococcus radiodurans

International Nuclear Information System (INIS)

Song Daojun; Chen Ruolei; Shao Chunlin; Wu Lijun; Yu Zengliang

2000-01-01

Though bacteria of the radiation-resistant Deinococcus radiodurans have a high resistance to the lethal and mutagenic effects of many DNA-damaging agents, the mechanisms involved in the response of these bacteria to oxidative stress are poorly understood. The superoxide dismutase (SOD) and catalase (CAT) activities produced by these bacteria were measured, and the change of SOD and CAT activities by 20 keV N + beam exposure was examined. Their activities were increased by N + beam exposure from 8 x 10 14 ions/cm 2 to 6 x 10 15 ions/cm 2 . The treatment of H 2 O 2 and [CHCl 3 + CH 3 CH 2 OH] and the measurement of absorption spectrum showed that the increase in SOD activity was resulted from inducible activities of Mn-SOD in D. radiodurans AS1.633 by N + beam exposure. These results suggested that this bacteria possess inducible defense mechanisms against the deleterious effects of oxidisation

Effects of Low-Temperature Plasma-Sterilization on Mars Analog Soil Samples Mixed with Deinococcus radiodurans

Directory of Open Access Journals (Sweden)

Janosch Schirmack

2016-05-01

Full Text Available We used Ar plasma-sterilization at a temperature below 80 °C to examine its effects on the viability of microorganisms when intermixed with tested soil. Due to a relatively low temperature, this method is not thought to affect the properties of a soil, particularly its organic component, to a significant degree. The method has previously been shown to work well on spacecraft parts. The selected microorganism for this test was Deinococcus radiodurans R1, which is known for its remarkable resistance to radiation effects. Our results showed a reduction in microbial counts after applying a low temperature plasma, but not to a degree suitable for a sterilization of the soil. Even an increase of the treatment duration from 1.5 to 45 min did not achieve satisfying results, but only resulted in in a mean cell reduction rate of 75% compared to the untreated control samples.

PprM is necessary for up-regulation of katE1, encoding the major catalase of Deinococcus radiodurans, under unstressed culture conditions.

Science.gov (United States)

Jeong, Sun-Wook; Seo, Ho Seong; Kim, Min-Kyu; Choi, Jong-Il; Lim, Heon-Man; Lim, Sangyong

2016-06-01

Deinococcus radiodurans is a poly-extremophilic organism, capable of tolerating a wide variety of different stresses, such as gamma/ultraviolet radiation, desiccation, and oxidative stress. PprM, a cold shock protein homolog, is involved in the radiation resistance of D. radiodurans, but its role in the oxidative stress response has not been investigated. In this study, we investigated the effect of pprM mutation on catalase gene expression. pprM disruption decreased the mRNA and protein levels of KatE1, which is the major catalase in D. radiodurans, under normal culture conditions. A pprM mutant strain (pprM MT) exhibited decreased catalase activity, and its resistance to hydrogen peroxide (H2O2) decreased accordingly compared with that of the wild-type strain. We confirmed that RecG helicase negatively regulates katE1 under normal culture conditions. Among katE1 transcriptional regulators, the positive regulator drRRA was not altered in pprM (-), while the negative regulators perR, dtxR, and recG were activated more than 2.5-fold in pprM MT. These findings suggest that PprM is necessary for KatE1 production under normal culture conditions by down-regulation of katE1 negative regulators.

Regulation of potassium dependent ATPase (kdp) operon of Deinococcus radiodurans.

Science.gov (United States)

Dani, Pratiksha; Ujaoney, Aman Kumar; Apte, Shree Kumar; Basu, Bhakti

2017-01-01

The genome of D. radiodurans harbors genes for structural and regulatory proteins of Kdp ATPase, in an operon pattern, on Mega plasmid 1. Organization of its two-component regulatory genes is unique. Here we demonstrate that both, the structural as well as regulatory components of the kdp operon of D. radiodurans are expressed quickly as the cells experience potassium limitation but are not expressed upon increase in osmolarity. The cognate DNA binding response regulator (RR) effects the expression of kdp operon during potassium deficiency through specific interaction with the kdp promoter. Deletion of the gene encoding RR protein renders the mutant D. radiodurans (ΔRR) unable to express kdp operon under potassium limitation. The ΔRR D. radiodurans displays no growth defect when grown on rich media or when exposed to oxidative or heat stress but shows reduced growth following gamma irradiation. The study elucidates the functional and regulatory aspects of the novel kdp operon of this extremophile, for the first time.

Method for detecting DNA strand breaks in mammalian cells using the Deinococcus radiodurans PprA protein

International Nuclear Information System (INIS)

Satoh, Katsuya; Wada, Seiichi; Kikuchi, Masahiro; Funayama, Tomoo; Narumi, Issay; Kobayashi, Yasuhiko

2006-01-01

In a previous study, we identified the novel protein PprA that plays a critical role in the radiation resistance of Deinococcus radiodurans. In this study, we focussed on the ability of PprA protein to recognize and bind to double-stranded DNA carrying strand breaks, and attempted to visualize radiation-induced DNA strand breaks in mammalian cultured cells by employing PprA protein using an immunofluorescence technique. Increased PprA protein binding to CHO-K1 nuclei immediately following irradiation suggests the protein is binding to DNA strand breaks. By altering the cell permeabilization conditions, PprA protein binding to CHO-K1 mitochondria, which is probably resulted from DNA strand break immediately following irradiation, was also detected. The method developed and detailed in this study will be useful in evaluating DNA damage responses in cultured cells, and could also be applicable to genotoxic tests in the environmental and pharmaceutical fields

Comparative proteomics reveals key proteins recruited at the nucleoid of Deinococcus after irradiation-induced DNA damage

International Nuclear Information System (INIS)

Bouthier de la Tour, Claire; Passot, Fanny Marie; Toueille, Magali; Servant, Pascale; Sommer, Suzanne; Mirabella, Boris; Blanchard, Laurence; Groot, Arjan de; Guerin, Philippe; Armengaud, Jean

2013-01-01

The nucleoids of radiation-resistant Deinococcus species show a high degree of compaction maintained after ionizing irradiation. We identified proteins recruited after irradiation in nucleoids of Deinococcus radiodurans and Deinococcus deserti by means of comparative proteomics. Proteins in nucleoid-enriched fractions from unirradiated and irradiated Deinococcus were identified and semi quantified by shotgun proteomics. The ssDNA-binding protein SSB, DNA gyrase subunits GyrA and GyrB, DNA topoisomerase I, RecA recombinase, UvrA excinuclease, RecQ helicase, DdrA, DdrB, and DdrD proteins were found in significantly higher amounts in irradiated nucleoids of both Deinococcus species. We observed, by immunofluorescence microscopy, the subcellular localization of these proteins in D. radiodurans, showing for the first time the recruitment of the DdrD protein into the D. radiodurans nucleoid. We specifically followed the kinetics of recruitment of RecA, DdrA, and DdrD to the nucleoid after irradiation. Remarkably, RecA proteins formed irregular filament-like structures 1 h after irradiation, before being redistributed throughout the cells by 3 h post-irradiation. Comparable dynamics of DdrD localization were observed, suggesting a possible functional interaction between RecA and DdrD. Several proteins involved in nucleotide synthesis were also seen in higher quantities in the nucleoids of irradiated cells, indicative of the existence of a mechanism for orchestrating the presence of proteins involved in DNA metabolism in nucleoids in response to massive DNA damage. All MS data have been deposited in the ProteomeXchange with identifier PXD00196. (authors)

Stress induction in the bacteria Shewanella oneidensis and Deinococcus radiodurans in response to below-background ionizing radiation.

Science.gov (United States)

Castillo, Hugo; Schoderbek, Donald; Dulal, Santosh; Escobar, Gabriela; Wood, Jeffrey; Nelson, Roger; Smith, Geoffrey

2015-01-01

The 'Linear no-threshold' (LNT) model predicts that any amount of radiation increases the risk of organisms to accumulate negative effects. Several studies at below background radiation levels (4.5-11.4 nGy h(-1)) show decreased growth rates and an increased susceptibility to oxidative stress. The purpose of our study is to obtain molecular evidence of a stress response in Shewanella oneidensis and Deinococcus radiodurans grown at a gamma dose rate of 0.16 nGy h(-1), about 400 times less than normal background radiation. Bacteria cultures were grown at a dose rate of 0.16 or 71.3 nGy h(-1) gamma irradiation. Total RNA was extracted from samples at early-exponential and stationary phases for the rt-PCR relative quantification (radiation-deprived treatment/background radiation control) of the stress-related genes katB (catalase), recA (recombinase), oxyR (oxidative stress transcriptional regulator), lexA (SOS regulon transcriptional repressor), dnaK (heat shock protein 70) and SOA0154 (putative heavy metal efflux pump). Deprivation of normal levels of radiation caused a reduction in growth of both bacterial species, accompanied by the upregulation of katB, recA, SOA0154 genes in S. oneidensis and the upregulation of dnaK in D. radiodurans. When cells were returned to background radiation levels, growth rates recovered and the stress response dissipated. Our results indicate that below-background levels of radiation inhibited growth and elicited a stress response in two species of bacteria, contrary to the LNT model prediction.

DNA damage response in a radiation resistant bacterium Deinococcus radiodurans: a paradigm shift

International Nuclear Information System (INIS)

Misra, H.S.

2015-01-01

Deinococcusradiodurans is best known for its extraordinary resistance to gamma radiation with its D 10 12kGy, and several other DNA damaging agents including desiccation to less than 5% humidity and chemical xenotoxicants. An efficient DNA double strand break (DSB) repair and its ability to protect biomolecules from oxidative damage are a few mechanisms attributed to these phenotypes in this bacterium. Although it regulates its proteome and transcriptome in response to DNA damage for its growth and survival, it lacks LexA mediated classical SOS response mechanism. Since LexA mediated damages response mechanism is highly and perhaps only, characterized DNA damage response processes in prokaryotes, this bacterium keeps us guessing how it responds to extreme doses of DNA damage. Interestingly, this bacterium encodes a large number of eukaryotic type serine threonine/tyrosine protein kinases (eST/YPK), phosphatases and response regulators and roles of eST/YPKs in cellular response to DNA damage and cell cycle regulations are well established in eukaryotes. Here, we characterized an antioxidant and DNA damage inducible eST/YPK (RqkA) and established its role in extraordinary radioresistance and DSB repair in this bacterium. We identified native phosphoprotein substrates for this kinase and demonstrated the involvement of some of these proteins phosphorylation in the regulation of DSB repair and growth under radiation stress. Findings suggesting the possible existence of eST/YPK mediated DNA damage response mechanism as an alternate to classical SOS response in this prokaryote would be discussed. (author)

Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica.

Science.gov (United States)

Hirsch, Peter; Gallikowski, Claudia A; Siebert, Jörg; Peissl, Klaus; Kroppenstedt, Reiner; Schumann, Peter; Stackebrandt, Erko; Anderson, Robert

2004-11-01

Six Gram-positive, non-motile, UV- and draught-tolerant bacteria were isolated from antarctic soil and rock samples. The pink to orange cocci grew well on oligotrophic medium PYGV (pH 7.5) at 9-18 degrees C. They tolerated 0-10% NaCl, were aerobic to facultatively anaerobic and contained ornithine in their cell wall (type A3beta, Orn-Gly2). The lipid profiles of four strains were found to be typical for those of D. radiodurans. Major fatty acids were 16:1cis9, 15:1cis9, 17:1cis9 and i17:1cis9, the respiratory quinone of three strains was MK-8. Comparative 16S rDNA gene sequencing revealed phylogenetic relationships to the Deinococcus clade, especially to D. radiopugnans. The levels of 16S rRNA gene sequence similarity and DNA-DNA hybridisation data showed the six isolates represented new taxa. Phenotypic properties supported the description of three new species which were different from the eight known Deinococcus species and particularly from D. radiopugnans. Soil isolate AA-692T (DSM 12807T) is the type strain of Deinococcus frigens sp. nov., with AA-752 (DSM 15993) and AA-829 (DSM 15994) as additional strains from soil. The endolithic isolate AA-1444T, Deinococcus saxicola sp. nov., (DSM 15974T) came from antarctic sandstone, and Deinococcus marmoris sp. nov. (isolate AA-63T [DSM 12784T]) as well as AA-69 (DSM 15951) were isolated from antarctic marble.

Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

Science.gov (United States)

Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

2015-10-01

Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues

Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes. Final Report

International Nuclear Information System (INIS)

Lidstrom, Mary E.

2003-01-01

Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

Energy Technology Data Exchange (ETDEWEB)

Daly, Michael J.

2007-07-23

Progress is briefly summarized in these areas: ionizing radiation resistance in bacteria; a hypothesis regarding ionizing radiation resistance emerging for bacterial cells; transcriptome analysis of irradiated D. radiodurans and Shewanella oneidensis; the role of metal reduction in Mn-dependnet Deinococcal species; and engineered Deinococcus strains as models for bioremediation. Key findings are also reported regarding protein oxidation as a possible key to bacterial desiccation resistance, and the whole-genome sequence of the thermophile Deinococcus geothermalis.

Study of resistance of D. radiodurans to the combined action of ionizing radiation with an electric or magnetic fields exogenous

International Nuclear Information System (INIS)

Prado, Georgia Reis

2011-01-01

The key goal in radiotherapy is to maximize damages in a tumor while minimizing them in nearby health tissues. Several strategies have been worked out toward the enhancement of cellular radiosensitivity, as the use of exogenous fields. It is studied in this work the resistance of Deinococcus radiodurans to the combined action of conventional and non conventional radiations, with external agents (electric and magnetic fields). D. radiodurans is a bacterium having an extraordinary ability to cope with lethal and mutagenic agents harmful to the DNA, particularly ionizing radiations as gammas and UV. Given its high radioresistance and fast growing, D. radiodurans has been used as solid tumors simulators. Peculiarities associated with radioresistance at the exponential and stationary phases were delineated from growing curves. By measuring survival curves information on radiosensitivity was obtained. In gamma irradiation D. radiodurans exhibited repairing shoulders of 2 and 8 kGy at the exponential and stationary phases, respectively. When gamma irradiations were combined with expositions to the electric field the repairing shoulders were reduced to 1 and 4 kGy at the exponential and stationary phases, respectively. Radioresistance was similar in both growing phases when the number of cells were approximately equalized in these two processes. On the other hand, when gamma irradiations were combined with expositions to the magnetic field the repairing shoulders were reduced to 4 and 6 kGy at the exponential and stationary phases, respectively. In irradiations with electron beams the repairing shoulder at the exponential phase was totally depleted, while at the stationary phase it was only 1 kGy. The findings of this work revealed new and important information on the radioresistance of D. radiodurans, while providing hints to the improvement of radiotherapy protocols in association with exogenous physical agents. (author)

Extreme Ionizing-Radiation-Resistant Bacterium

Science.gov (United States)

Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

2013-01-01

potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin.

Science.gov (United States)

Schlünzen, Frank; Pyetan, Erez; Fucini, Paola; Yonath, Ada; Harms, Jörg M

2004-12-01

Tiamulin, a prominent member of the pleuromutilin class of antibiotics, is a potent inhibitor of protein synthesis in bacteria. Up to now the effect of pleuromutilins on the ribosome has not been determined on a molecular level. The 3.5 A structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin provides for the first time a detailed picture of its interactions with the 23S rRNA, thus explaining the molecular mechanism of the antimicrobial activity of the pleuromutilin class of antibiotics. Our results show that tiamulin is located within the peptidyl transferase center (PTC) of the 50S ribosomal subunit with its tricyclic mutilin core positioned in a tight pocket at the A-tRNA binding site. Also, the extension, which protrudes from its mutilin core, partially overlaps with the P-tRNA binding site. Thereby, tiamulin directly inhibits peptide bond formation. Comparison of the tiamulin binding site with other PTC targeting drugs, like chloramphenicol, clindamycin and streptogramins, may facilitate the design of modified or hybridized drugs that extend the applicability of this class of antibiotics.

Identification of uvrA gene mutation sites in two mitomycin-sensitive deinococcus radiodurans strains

International Nuclear Information System (INIS)

Du Zeji; Kong Xianrong

1999-01-01

Deinococcus radiodurans (Dr) possesses a prominent ability to repair the DNA injury induced by various DNA- damaging agents including mitomycin C(MC), ultraviolet light (UV) and ionizing radiation. DNA damage resistance was restored in MC sensitive (MC s ) mutants 2621 and 3021 by transforming with DNAs of four cosmids clones derived from the gene library of strain KD8301 which showed the property of wild type phenotype to DNA-damaging agents. Gene affected by mutation (mtcA or mtcB) in both mutants was cloned and its nucleotide sequence was determined. The deduced amino acid (aa) sequence of Dr uvrA gene product consists of 1016 aa and shares homology with many bacterial UvrA proteins. The mutation sites in both mutants were identified by analyzing the polymerase chain reaction (PCR) fragments derived from the genomic DNA of the mutants. A 144-base pairs (bp) deletion including the start codon for the uvr A gene was observed in DNA of the mutant 3021, causing a defect in the gene. On the other hand, an insertion sequence (IS) element intervened in the uvrA gene of the mutant 2621, suggesting the insertional inactivation of the gene. The IS element comprise 1322-bp long, flanked by 19-bp inverted terminal repeats (ITR), and generated a 6-bp target duplication (TD). Two open reading frames (ORF) were found in the IS element. The deduced aa sequences of large and small ORF show homology to a putative transposes found in IS4 of Escherichia coli (E. coli) and to a resolvent found in IS Xc5 of Xanthomonas campestris (Xc), respectively. This is the first discovery of IS element in deino-bacteria, and the IS element was designated IS2621

Genetic engineering of a radiation-resistant bacterium for biodegradation of mixed wastes. 1998 annual progress report

International Nuclear Information System (INIS)

Lidstrom, M.E.

1998-01-01

'Because of their tolerance to very high levels of ionizing radiation, members of the genus Deinococcus have received considerable attention over the past years. The type species of the genus, Deinococcus radiodurans, has been studied extensively in several labs. Although researchers are only beginning to understand the mechanisms by which this Gram-positive bacterium is able to repair massive DNA damage after radiation dosages as high as 5 Mrad, it has become evident that its recombination machinery has several unique characteristics (1--4). The aim of the present studies is to engineer D. radiodurans into a detoxifier for bioremediation of complex waste mixtures, containing heavy metals, halo-organics and radionuclides, making use of its ability to be biologically active in environments where they will be exposed to high levels of radiation. For that purpose, the authors aim to clone and express several broad spectrum oxygenases and heavy metal resistance determinants, and test survival and activities of these strains in artificial mixtures of contaminants, designed to simulate DOE mixed waste streams. This report summarizes work after 0.5 year of a 3-year project. The initial studies have focused on the development of an insertional expression system for D. radiodurans R1. This effort has involved two parts, namely: (1) promoter analysis, and (2) development of insertion systems. Several studies have shown that the expression signals used by D. radiodurans differ considerably from those found in other bacteria. Although D. radiodurans contains a typical eubacterial RNA polymerase core enzyme (based on TBLASTN searches on the genome sequence), Escherichia coli promoters are not recognized in D. radiodurans and vice versa (5). To expand the basic understanding of the requirements for transcription, and to optimize expression of (heterologous) genes, they will follow two strategies. First, a promoter-probe vector is being developed for the selection of promoter

Protease activity of PprI facilitates DNA damage response: Mn2+-dependence and substrate sequence-specificity of the proteolytic reaction.

Directory of Open Access Journals (Sweden)

Yunguang Wang

Full Text Available The extremophilic bacterium Deinococcus radiodurans exhibits an extraordinary resistance to ionizing radiation. Previous studies established that a protein named PprI, which exists only in the Deinococcus-Thermus family, acts as a general switch to orchestrate the expression of a number of DNA damage response (DDR proteins involved in cellular radio-resistance. Here we show that the regulatory mechanism of PprI depends on its Mn(2+-dependent protease activity toward DdrO, a transcription factor that suppresses DDR genes' expression. Recognition sequence-specificity around the PprI cleavage site is essential for DNA damage repair in vivo. PprI and DdrO mediate a novel DNA damage response pathway differing from the classic LexA-mediated SOS response system found in radiation-sensitive bacterium Escherichia coli. This PprI-mediated pathway in D. radiodurans is indispensable for its extreme radio-resistance and therefore its elucidation significantly advances our understanding of the DNA damage repair mechanism in this amazing organism.

Proteomics of post-irradiation recovery in D. radiodurans

International Nuclear Information System (INIS)

Basu, Bhakti; Apte, Shree Kumar

2012-01-01

An extremophile Deinococcus radiodurans is bestowed with an extraordinary DNA repair ability that renders it virtually resistant to all known forms of DNA damage caused by ionizing radiations (10 kGy of gamma rays), UV (1 kJ/m 2 ) or weeks of desiccation etc. The genome of D. radiodurans encodes a unique combination of DNA repair pathways such as prokaryotic type RecFOR mediated homologous recombination (HR) and nucleotide/base excision repair along with eukaryotic type strand annealing (SA) and non-homologous end joining (NHEJ), but is devoid of universal prokaryotic DNA repair pathways such as RecBCD mediated HR, photo-reactivation and SOS response. Collective evidence obtained so far from multiple approaches, have indicated (i) that all genes essential for DNA repair are not necessarily induced following radiation stress (ii) early RecA independent DNA assembly occurs, and (iii) absolute necessity of RecA dependent HR for final genome restitution. The 6 kGy gamma irradiation inducible proteome dynamics were mapped during the post-irradiation growth arrest phase by 2D protein electrophoresis coupled with mass spectrometry. Radiation inducible expression of at least 33 proteins was evident in the first 1h of post irradiation recovery

Inactivation of the Radiation-Resistant Spoilage Bacterium Micrococcus radiodurans

Science.gov (United States)

Duggan, D. E.; Anderson, A. W.; Elliker, P. R.

1963-01-01

A simplified technique permitting the pipetting of raw puréed meats for quantitative bacteriological study is described for use in determining survival of these non-sporing bacteria, which are exceptionally resistant to radiation. Survival curves, using gamma radiation as the sterilizing agent, were determined in raw beef with four strains of Micrococcus radiodurans. Survival curves of the R1 strain in other meat substrates showed that survival was significantly greater in raw beef and raw chicken than in raw fish or in cooked beef. Resistance was lowest in the buffer. Cells grown in broth (an artificial growth medium) and resuspended in beef did not differ in resistance from cells that had been grown and irradiated in beef. Survival rate was statistically independent of the initial cell concentration, even though there appeared to be a correlation between lower death rate and lower initial cell concentrations. The initial viable count of this culture of the domesticated R1 strain in beef was reduced by a factor of about 10-5 by 3.0 megarad, and 4.0 megarad reduced the initial count by a factor of more than 10-9. Data suggest that M. radiodurans R1 is more resistant to radiation than spore-forming spoilage bacteria for which inactivation rates have been published. PMID:14063780

Design and construction of deinococcus radiodurans for biodegradation of organic toxins at radioactive DOE waste sites. 1998 annual progress report

International Nuclear Information System (INIS)

Daly, M.J.; Minton, K.W.; Wackett, L.P.

1998-01-01

'A 1992 survey of DOE waste sites indicates that about 32% of soils and 45% of groundwaters at these sites contain radionuclides and metals plus an organic toxin class. The most commonly reported combinations of these hazardous compounds being radionuclides and metals (e.g., U, Pu, Cs, Pb, Cr, As) plus chlorinated hydrocarbons (e.g., trichloroethylene), fuel hydrocarbons (e.g., toluene), or polychlorinated biphenyls (e.g., Arochlor 1248). These wastes are some of the most hazardous pollutants and pose an increasing risk to human health as they leach into the environment. The objective of this research is to develop novel organisms, that are highly resistant to radiation and the toxic effects of metals and radionuclides, for in-situ bioremediation of organic toxins. Few organisms exist that are able to remediate such environmental organic pollutants, and among those that can, the bacteria belonging to the genus Pseudomonas are the most characterized. Unfortunately, these bacteria are very radiation sensitive. For example, Pseudomonas spp. is even more sensitive than Escherichia coli and, thus, is not suitable as a bioremediation host in environments subjected to radiation. By contrast, D. radiodurans, a natural soil bacterium, is the most radiation resistant organism yet discovered; it is several thousand times more resistant to ionizing radiation than Pseudomonas. The sophisticated gene transfer and expression systems the authors have developed for D. radiodurans over the last eight years make this organism an ideal candidate for high-level expression of genes that degrade organic toxins, in radioactive environments. The authors ultimate aim is to develop organisms and approaches that will be useful for remediating the large variety of toxic organic compounds found in DOE waste sites that are too radioactive to support other bioremediation organisms. This report summarizes work after the first 6 months of a 3-year project.'

Multiplicity of genome equivalents in the radiation-resistant bacterium Micrococcus radiodurans.

Science.gov (United States)

Hansen, M T

1978-01-01

The complexity of the genome of Micrococcus radiodurans was determined to be (2.0 +/- 0.3) X 10(9) daltons by DNA renaturation kinetics. The number of genome equivalents of DNA per cell was calculated from the complexity and the content of DNA. A lower limit of four genome equivalents per cell was approached with decreasing growth rate. Thus, no haploid stage appeared to be realized in this organism. The replication time was estimated from the kinetics and amount of residual DNA synthesis after inhibiting initiation of new rounds of replication. From this, the redundancy of terminal genetic markers was calculated to vary with growth rate from four to approximately eight copies per cell. All genetic material, including the least abundant, is thus multiply represented in each cell. The potential significance of the maintenance in each cell of multiple gene copies is discussed in relation to the extreme radiation resistance of M. radiodurans. PMID:649572

Isolation and properties of strains of Micrococcus (Deinococcus) radiodurans unable to excise ultraviolet light-induced pyrimidine dimers from DNA: evidence for two excision pathways

International Nuclear Information System (INIS)

Moseley, B.E.B.; Evans, D.M.

1983-01-01

A mutant of Deinococcus (formerly Micrococcus) radiodurans sensitive to both the lethal effect of mitomycin C and the mutagenic effect of simple alkylating agents, but having wild-type resistance to UV light, was treated with the mutagen N-methyl-N'-nitro-N-nitrosoguanidine. Three strains were isolated that were UV-sensitive, but had wild-type resistance to the lethal effect of methyl methanesulphonate and all were shown to be unable to excise pyrimidine dimers. The three strains UVS9, UVS25 and UVS78 had, in addition to the mutation in mtcA, mutations in loci designated uvsC, uvsD and uvsE, respectively. When the mutant mtcA gene was replaced by its wild-type allele in all three strains they became UV- and mitomycin C-resistant. On incubating the double mutants UVS9, UVS25 and UVS78 with wild-type DNA about 50% of the transformants selected for UV resistance were mitomycin C-sensitive and about 50% resistant depending on whether the mutant mtcA or the uvsC, D or E genes had been replaced by their wild-type alleles. Although strains mutant singly in uvsC, D or E were UV-resistant the rates of excision of pyrimidine dimers differed between them and was slower in all of them than in the wild-type and strain 302. (author)

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

International Nuclear Information System (INIS)

Daly, Michael J.

2006-01-01

Ionizing Radiation (IR) Resistance in Bacteria. Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR) and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus and Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella and Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

Energy Technology Data Exchange (ETDEWEB)

Daly, Michael J.

2006-05-01

Ionizing Radiation (IR) Resistance in Bacteria. Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR) and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus & Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella & Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR.

RNA-Seq analysis of D. radiodurans find non coding RNAs expressed in response to radiation stress

International Nuclear Information System (INIS)

Gadewal, Nikhil; Mukhopadhyaya, Rita

2015-01-01

In bacteria discovery of functional RNA molecules that are not translated into protein, noncoding RNAs, became possible with advent of Next Generation Sequencing technology. Bacterial non coding RNAs are typically 50-300 nucleotides long and work as internal signals controlling various levels of gene expression. Deep sequencing of total cellular RNA captures all coding and noncoding transcripts with their differential levels of expression in the transcriptome. It provides a powerful approach to study bacterial gene expression and mechanisms of gene regulation. We subjected the 3 h transcriptome of Deinococcus radiodurans R1 cells post exposure to 6 KGy gamma radiation to 100 x 2 cycles of deep sequencing on the Illumina HiSeq 2000 to look for ncRNA transcripts. Bioinformatics pipeline for analysis and interpretation of RNA Seq data was done in house using Softwares available in public domains. Our sequence data aligned with 21 putative ncRNAs expressed in the intergenic regions of annotated genome of D radiodurans. Verification of 2 ncRNA candidates and 3 transcription factor genes by Real Time PCR confirmed presence of these transcripts in the 3 h transcriptome sequenced by us. Any relationship between ncRNAs and control of radiation induced gene expression in D radiodurans can be proved only after specific gene knock outs in future. (author)

Repair of gamma radiation damage in wild type and a radiation sensitive mutant of Deinococcus radiodurans

International Nuclear Information System (INIS)

Mizuma, Nagayo

1989-01-01

In an effort to examine production and repair of radiation-induced single and double strand breaks in the DNA, a repair-deficient wild type and a repair-deficient mutant, UV17, of Deinococcus radiodurans were subjected to Co-60 gamma irradiation at a dose rate of 6.3 kGy/hr for wild type and 3.9 kGy/hr for UV17 mutant. The shoulder of the curve of UV17 mutant was narrow but existed with the intercept of 0.7 kGy and the corresponding value of the wild type was 4.2 kGy. Mutant cells exhibited about 6 fold increases in sensitivity for the shoulder relative to the wild type. The D 37 doses in the wild type and the mutant were 0.57 kGy and 0.25 kGy, respectively. From the survival curves, difference in the sensitivity between two strains was mainly due to difference of repair capacity than the number of radiation sensitive target. Sedimentation rate of the main component in the irradiated cells of UV17 mutant increased almost to the level of unirradiated control by the postincubation at 30deg C for 3 hrs. The results indicated that this sensitive mutant also exhibited an ability to restore single strand breaks after exposure to a sublethal dose of 0.6 kGy. When restitution of double strand breaks was analyzed by sedimentation in a neutral sucrose gradient, the wild type showed restitution to DNA-membrane complex from large part of the breaks. For UV17 mutant, the apparent increase in DNA-membrane complex formation was seen after 3 hours incubation. Large part of the decrease in the activities of peak 2 was recovered in the peak 1 for the wild type. For the mutant, there was little restitution to peak 1. Almost free DNA component in UV17 mutant, therefore, was merely degraded into shorter pieces. Restoration of DNA-membrane complex from free DNA derived from gamma-ray induced double strand scission involved closely in the repair of gamma-induced damage and survival. (N.K.)

The in vivo association of manganese with the chromosome of Micrococcus radiodurans

International Nuclear Information System (INIS)

Leibowitz, P.J.; Schwartzberg, L.S.; Bruce, A.K.

1976-01-01

Extremely high levels of paramagnetic manganese (Mn 2+ ) which quench phosphorescent reactions have been found to inhibit the formation of thymine-containing dimers in M. radiodurans. Lowering the concentration of Mn 2+ in the culture medium resulted in a lower intracellular concentration of Mn 2+ , an increase in the UV-sensitivity of this bacterium, and a larger photochemical yield of thymine-containing dimers. High levels of paramagnetic Mn 2+ were not found in other test organisms which are more sensitive to UV-irradiation. One interpretation of this data is that in Micrococcus radiodurans Mn2 + + may bind to the chromosome and thereby reduce the photochemical yield of thymine-containing dimers. (author)

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

International Nuclear Information System (INIS)

Fredrickson, Jim K.; Daly, Michael J.

2006-01-01

Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR), desiccation, and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus and Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella and Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR (http://cfyn.ifas.ufl.edu/radiation.pdf)

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

Energy Technology Data Exchange (ETDEWEB)

Fredrickson, Jim K.; Daly, Michael J.

2006-06-01

Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR), desiccation, and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus & Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella & Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR (http://cfyn.ifas.ufl.edu/radiation.pdf).

The in vivo association of manganese with the chromosome of Micrococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Leibowitz, P J; Schwartzberg, L S; Bruce, A K [State Univ. of New York, Buffalo (USA). Dept. of Biology

1976-01-01

Extremely high levels of paramagnetic manganese (Mn/sup 2 +/) which quench phosphorescent reactions have been found to inhibit the formation of thymine-containing dimers in M. radiodurans. Lowering the concentration of Mn/sup 2 +/ in the culture medium resulted in a lower intracellular concentration of Mn/sup 2 +/, an increase in the uv-sensitivity of this bacterium, and a larger photochemical yield of thymine-containing dimers. High levels of paramagnetic Mn/sup 2 +/ were not found in other test organisms which are more sensitive to uv-irradiation. One interpretation of this data is that in Micrococcus radiodurans Mn2/sup +/+ may bind to the chromosome and thereby reduce the photochemical yield of thymine-containing dimers.

Radioprotection in E. coli by an agent from M. radiodurans

Energy Technology Data Exchange (ETDEWEB)

Goldstein, L S; Gersten, D M; Bruce, A K [State Univ. of New York, Buffalo (USA). Dept. of Biology

1978-10-01

An agent extracted from the radioresistant bacterium M. radiodurans was found to protect several strains of E. coli from X-radiation. Optimal radioprotection was observed when the repair-proficient B/r strain was irradiated in the presence of the agent under hypoxic conditions. It is proposed that this agent acts to modify damage incurred in the presence of reduced oxygen concentrations so that this damage might be subsequently repaired.

ORF Alignment: NC_001263 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available NC_001263 gi|15805432 >1bplA 2 169 309 525 3e-10 ... gb|AAF09983.1| alpha-dextran end...o-1,6-alpha-glucosidase [Deinococcus radiodurans] ... pir||D75524 alpha-dextran endo-1,6-alpha-glucos...idase - ... Deinococcus radiodurans (strain R1) ref|NP_294128.1| ... alpha-dextran endo-1,6-al

Comparison of radiation-induced proteins in two revertants with those in a radiation sensitive mutant of Deinococcus radiodurans

International Nuclear Information System (INIS)

Hu Qian; Tanaka, Atsushi; Kobayashi, Yasuhiko; Nozawa, Ranko; Watanabe, Hiroshi.

1992-01-01

In order to search proteins responsible for DNA repair, the intracellular proteins in gamma-irradiated cells of D.radiodurans R1 and its three mutants were analyzed by means of two-dimensional gel electrophoresis. Two new proteins, P35 (M.W. 35 kDa) and P92 (M.W. 92 kDa), were found in the cells of the radioresistant revertant (KH8401-1-5) and D.radiodurans R1. However, only P92 was detected in the moderately radioresistant revertant (KH8401-10-7). Both proteins were not detected in the cells of the radiosensitive mutant (KH8401). On the other hand, one protein, P25 (M.W. 25 kDa), which was detected either before or after gamma-irradiation, was only found in KH8401-10-7. These results suggest that these special induced proteins, P35 and P92, might be directly responsible for radiation resistance. The analyses of similar proteins in the cells of E.coli B/r and Deinobactor grandis KS0460 were also carried out. (author)

Studies on the Mechanism of Radiation Resistance in Micrococcus Radiodurans and its Sensitization

Energy Technology Data Exchange (ETDEWEB)

Kitayama, S.; Matsuyama, A. [Radiobiology Laboratory, Institute of Physical and Chemical Research, Wako-shi, Saitama-ken (Japan)

1978-06-15

Efficient and accurate repair of radiation-induced lesions in M. radiodurans was investigated as to the cause of its extreme radioresistance. The cells were made permeable to deoxyribonucleoside triphosphate by treatment with non-ionic detergent, Triton X-100. After irradiation with 2 krad gamma rays more than 80% of the single-strand scissions were rejoined in the permeable cells within 10 min at 37 Degree-Sign C. This fast repair process requires the presence of deoxyribonucleoside triphosphates and NAD. However, rejoining of DNA strand scission was incomplete after prolonged incubation in the permeable cells. This suggests that alternate repair reaction(s) is necessary for complete recovery. The other type of radiation lesion was found by postirradiation incubation at non-permissive temperature, which markedly sensitizes this bacterium to radiation. Postincubation at this temperature also sensitizes the cells to chemicals that damage DNA. The extreme radioresistance of this bacterium was also lost by mutation and an isolated radiosensitive mutant showed almost the same radiosensitivity as E. coli K12 or B/r. These results are discussed in connection with the extreme radioresistance of M. radiodurans. (author)

Studies on the mechanism of radiation resistance in Micrococcus radiodurans and its sensitization

International Nuclear Information System (INIS)

Kitayama, S.; Matsuyama, A.

1978-01-01

Efficient and accurate repair of radiation-induced lesions in M. radiodurans was investigated as to the cause of its extreme radioresistance. The cells were made permeable to deoxyribonucleoside triphosphate by treatment with non-ionic detergent, Triton X-100. After irradiation with 2 krad gamma rays more than 80% of the single-strand scissions were rejoined in the permeable cells within 10 min at 37 0 C. This fast repair process requires the presence of deoxyribonucleoside triphosphates and NAD. However, rejoining of DNA strand scission was incomplete after prolonged incubation in the permeable cells. This suggests that alternate repair reaction(s) is necessary for complete recovery. The other type of radiation lesion was found by post-irradiation incubation at non-permissive temperature, which markedly sensitizes this bacterium to radiation. Postincubation at this temperature also sensitizes the cells to chemicals that damage DNA. The extreme radioresistance of this bacterium was also lost by mutation and an isolated radiosensitive mutant showed almost the same radiosensitivity as E. coli K12 or B/r. These results are discussed in connection with the extreme radioresistance of M. radiodurans. (author)

Radiation and desiccation response motif mediates radiation induced gene expression in D. radiodurans

International Nuclear Information System (INIS)

Anaganti, Narasimha; Basu, Bhakti; Apte, Shree Kumar

2015-01-01

Deinococcus radiodurans is an extremophile that withstands lethal doses of several DNA damaging agents such as gamma irradiation, UV rays, desiccation and chemical mutagens. The organism responds to DNA damage by inducing expression of several DNA repair genes. At least 25 radiation inducible gene promoters harbour a 17 bp palindromic sequence known as radiation and desiccation response motif (RDRM) implicated in gamma radiation inducible gene expression. However, mechanistic details of gamma radiation-responsive up-regulation in gene expression remain enigmatic. The promoters of highly radiation induced genes ddrB (DR0070), gyrB (DR0906), gyrA (DR1913), a hypothetical gene (DR1143) and recA (DR2338) from D. radiodurans were cloned in a green fluorescence protein (GFP)-based promoter probe shuttle vector pKG and their promoter activity was assessed in both E. coli as well as in D. radiodurans. The gyrA, gyrB and DR1143 gene promoters were active in E. coli although ddrB and recA promoters showed very weak activity. In D. radiodurans, all the five promoters were induced several fold following 6 kGy gamma irradiation. Highest induction was observed for ddrB promoter (25 fold), followed by DR1143 promoter (15 fold). The induction in the activity of gyrB, gyrA and recA promoters was 5, 3 and 2 fold, respectively. To assess the role of RDRM, the 17 bp palindromic sequence was deleted from these promoters. The promoters devoid of RDRM sequence displayed increase in the basal expression activity, but the radiation-responsive induction in promoter activity was completely lost. The substitution of two conserved bases of RDRM sequence yielded decreased radiation induction of PDR0070 promoter. Deletion of 5 bases from 5'-end of PDR0070 RDRM increased basal promoter activity, but radiation induction was completely abolished. Replacement of RDRM with non specific sequence of PDR0070 resulted in loss of basal expression and radiation induction. The results demonstrate that

Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation

International Nuclear Information System (INIS)

Dedieu, Alain; Sahinovic, Elodie; Guerin, Philippe; Armengaud, Jean; Blanchard, Laurence; Fochesato, Sylvain; Groot, Arjan de; Meunier, Bruno

2013-01-01

Deinococcus deserti VCD115 has been isolated from Sahara surface sand. This radio-tolerant bacterium represents an experimental model of choice to understand adaptation to harsh conditions encountered in hot arid deserts. We analysed the soluble proteome dynamics in this environmentally relevant model after exposure to 3 kGy gamma radiation, a non-lethal dose that generates massive DNA damages. For this, cells were harvested at different time lapses after irradiation and their soluble proteome contents have been analysed by 2-DE and mass spectrometry. In the first stage of the time course we observed accumulation of DNA damage response protein DdrB (that shows the highest fold change ∼11), SSB, and two different RecA proteins (RecAP and RecAC). Induction of DNA repair protein PprA, DNA damage response protein DdrD and the two gyrase subunits (GyrA and GyrB) was also detected. A response regulator of the SarP family, a type II site-specific deoxyribonuclease and a putative N-acetyltransferase are three new proteins found to be induced. In a more delayed stage, we observed accumulation of several proteins related to central metabolism and protein turn-over, as well as helicase UvrD and novel forms of both gyrase subunits differing in terms of isoelectric point and molecular weight. Conclusions: Post-translational modifications of GyrA (N-terminal methionine removal and acetylation) have been evidenced and their significance discussed. We found that the Deide-02842 restriction enzyme, which is specifically found in D. deserti, is a new potential member of the radiation/desiccation response regulon, highlighting the specificities of D. deserti compared to the D. radiodurans model. (authors)

DE-FG02-04ER63746 FinalTechnicalReport

Energy Technology Data Exchange (ETDEWEB)

Lidstrom, M.E.

2009-09-05

This is the final technical report for a project involving the study of stress response systems in the radiation-resistant bacterium, Deinococcus radiodurans. Three stresses of importance for a mixed waste treatment strain were studied, heat shock, solvent shock, and phosphate starvation. In each case, specific genes involved in the ability to survive the stress were identified using a systems biology approach, and analysis of mutants was used to understand mechanisms. This study has led to increased understanding of the ways in which a potential treatment strain could be manipulated to survive multiple stresses for treatment of mixed wastes.

Comparative analyses reveal different consequences of two oxidative stress inducers, gamma irradiation and potassium tellurite, in the extremophile Deinococcus radiodurans

International Nuclear Information System (INIS)

Narasimha, Anaganti; Basu, Bhakti; Apte, Shree Kumar

2014-01-01

Proteomic and mass spectrometric analyses revealed differential responses of D. radiodurans to two oxidative stressors. While both elicited oxidative stress alleviation response, major divergence was observed at the level of DNA repair, metabolic pathways and protein homeostasis. Response to gamma irradiation was focused on DNA repair and ROS scavenging but supported metabolism as well as protein homeostasis. Tellurite, induced oxidative stress alleviation but decreased reducing affected and adversely affected metabolism and protein homeostasis

Detection of DNA strand breaks in mammalian cells using the radioresistant bacterium PprA protein

International Nuclear Information System (INIS)

Satoh, Katsuya; Wada, Seiichi; Narumi, Issay; Kikuchi, Masahiro; Funayama, Tomoo; Kobayashi, Yasuhiko

2003-01-01

We have previously found that the PprA protein from Deinococcus radiodurans possesses ability to recognize DNA carrying strand breaks. In the present study, we attempted to visualize radiation-induced DNA strand breaks with PprA protein using immunofluorescence technique to elucidate the DNA damage response mechanism in mammalian cultured cells. As a result, colocalization of Cy2 and DAPI fluorescent signals was observed. This observation suggests that DNA strand breaks in the nucleus of CHO-K1 cells were effectively detected using the PprA protein. The amount of DNA strand breaks (integrated density of Cy2 fluorescent signals) was increased with the increase in the radiation dose. (author)

Deinococcus Mn2+-peptide complex: A novel approach to alphavirus vaccine development.

Science.gov (United States)

Gayen, Manoshi; Gupta, Paridhi; Morazzani, Elaine M; Gaidamakova, Elena K; Knollmann-Ritschel, Barbara; Daly, Michael J; Glass, Pamela J; Maheshwari, Radha K

2017-06-22

Over the last ten years, Chikungunya virus (CHIKV), an Old World alphavirus has caused numerous outbreaks in Asian and European countries and the Americas, making it an emerging pathogen of great global health importance. Venezuelan equine encephalitis virus (VEEV), a New World alphavirus, on the other hand, has been developed as a bioweapon in the past due to its ease of preparation, aerosol dispersion and high lethality in aerosolized form. Currently, there are no FDA approved vaccines against these viruses. In this study, we used a novel approach to develop inactivated vaccines for VEEV and CHIKV by applying gamma-radiation together with a synthetic Mn-decapeptide-phosphate complex (MnDpPi), based on manganous-peptide-orthophosphate antioxidants accumulated in the extremely radiation-resistant bacterium Deinococcus radiodurans. Classical gamma-irradiated vaccine development approaches are limited by immunogenicity-loss due to oxidative damage to the surface proteins at the high doses of radiation required for complete virus-inactivation. However, addition of MnDpPi during irradiation process selectively protects proteins, but not the nucleic acids, from the radiation-induced oxidative damage, as required for safe and efficacious vaccine development. Previously, this approach was used to develop a bacterial vaccine. In the present study, we show that this approach can successfully be applied to protecting mice against viral infections. Irradiation of VEEV and CHIKV in the presence of MnDpPi resulted in substantial epitope preservation even at supra-lethal doses of gamma-rays (50,000Gy). Irradiated viruses were found to be completely inactivated and safe in vivo (neonatal mice). Upon immunization, VEEV inactivated in the presence of MnDpPi resulted in drastically improved protective efficacy. Thus, the MnDpPi-based gamma-inactivation approach described here can readily be applied to developing vaccines against any pathogen of interest in a fast and cost

ORF Alignment: NC_001263 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available | ... protease I [Deinococcus radiodurans R1] ... Length = 173 ... Query: 10 ... KKIAILAADGVEEIELTSP...RAAIEAAGGTTELISLEPGEIQSMKGDIEPQEKYRVDHVVS 69 ... KKIAILAADGVEEIELTSPRAAIEA...AGGTTELISLEPGEIQSMKGDIEPQEKYRVDHVVS Sbjct: 1 ... KKIAILAADGVEEIELTSPRAAIEAAGGTTELISLEPGEIQSMKGDIEPQEKYRVDHVVS

Deinococcus hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (mugunghwa flower).

Science.gov (United States)

Moya, Gabriela; Yan, Zheng-Fei; Chu, Dong-Hun; Won, KyungHwa; Yang, Jung-Eun; Wang, Qi-Jun; Kook, Moo-Chang; Yi, Tae-Hoo

2018-01-01

A Gram-stain-positive, pink-pigmented, coccus-shaped, strictly aerobic, non-motile bacterium, strain THG-AG1.5 T , was isolated from rhizosphere of Hibiscus syriacus L. (Mugunghwa flower) located in Kyung Hee University, Yongin, Gyeonggi, Republic of Korea. The isolated strain grew optimally at 25-30 °C, at pH 6.0-7.5 and in the presence of additional 0-1.5 % (w/v) NaCl. Strain THG-AG1.5 T exhibited tolerance to UV radiation (>1500 J m -2 ) and to gamma radiation (>12 kGy). Based on 16S rRNA gene sequence comparisons, strain THG-AG1.5 T was closely related to Deinococcus daejeonensis MJ27 T (98.03 %), Deinococcus radiotolerans C1 T (97.61 %) and Deinococcus grandis DSM 3963 T (97.32 %). The genomic DNA G+C content of strain THG-AG1.5 T was 74.8 mol%. The DNA-DNA hybridization values between strain THG-AG1.5 T and its closest phylogenetically neighbours were below 63.0 %. The peptidoglycan amino acids were alanine, valine, glutamic acid, glycine, ornithine, lysine and aspartic acid. Strain THG-AG1.5 T contained ribose, mannose and glucose as whole-cell-wall sugars and menaquinone-8 (MK-8) as the only isoprenoid quinone. The major component in the polyamine pattern was spermidine. The major polar lipids of strain THG-AG1.5 T were a phosphoglycolipid, six unidentified glycolipids and an unidentified aminophospholipid. The major fatty acids were identified as iso-C15 : 0, C15 : 1ω6c, C16 : 0, iso-C17 : 0, C17 : 0, C18 : 0 and summed feature 3. On the basis of our polyphasic taxonomy study, strain THG-AG1.5 T represents a novel species within the genus Deinococcus, for which the name Deinococcushibisci sp. nov. is proposed. The type strain is THG-AG1.5 T (=KACC 18850 T =CCTCC AB 2016078 T ).

Effects of Deinococcus spp. supplement on egg quality traits in laying hens.

Science.gov (United States)

Li, I-Chen; Wu, Szu-Yin; Liou, Jenn-Fa; Liu, Hsiao-Hui; Chen, Jiau-Hua; Chen, Chin-Chu

2018-01-01

To counter the ill effects of synthetic dyes, bacterial pigment production as an alternative is now one of the promising and emerging fields of research. This study was conducted to evaluate the applicability of Deinococcus genus on the egg quality traits in laying hens. In study I, 24 single comb White Leghorn layers were fed with various 1 wt % Deinococcus bacterial strains for 10 d. In study II, 84 brown Hendrix layers were fed with one of 4 diets containing 0, 0.2, 1, or 5 wt % Deinococcus sp. GKB-Aid 1995 powder for 12 wk. In study III, 60 White Leghorn laying hens were fed either with or without 1 wt % Deinococcus sp. GKB-Aid 1995 powder, 1 wt % Deinococcus sp. GKB-Aid 1995 granules, or 1 wt % Deinococcus sp. GKB-Aid 1995 oily granules for 10 successive d. In all of the experiments, feeding Deinococcus powder did not affect egg quality traits except for the yolk color. In particular, supplementation with all Deinococcus powder treatments changed the yolk color (P 1995. Moreover, longer supplementation of Deinococcus sp. GKB-Aid 1995 in study II had a significant effect on feed conversion ratio. With these findings under consideration, the present study suggests that the Deinococcus species, especially Deinococcus sp. GKB-Aid 1995, can be an excellent candidate for improving egg yolk color in laying hens. © 2017 Poultry Science Association Inc.

Deinococcus metallilatus sp. nov. and Deinococcus carri sp. nov., isolated from a car air-conditioning system.

Science.gov (United States)

Kim, Dong-Uk; Lee, Hyosun; Lee, Ji-Hyeong; Ahn, Jae-Hyung; Lim, Sangyong; Jeong, Sunwook; Park, So Yoon; Seong, Chi Nam; Ka, Jong-Ok

2015-09-01

Two bacterial strains, designated MA1002(T) and MA1003(T), were isolated from the air-conditioning system of a car. Cells of both strains were Gram-reaction-positive, non-motile, non-spore-forming coccoids, catalase- and oxidase-positive and UV-radiation resistant. The major fatty acids of strain MA1002(T) were iso-C17 : 0 and iso-C15 : 0 and those of strain MA1003(T) were iso-C16 : 0 and iso-C16 : 1 H. The polar lipid profile of MA1002(T) contained phosphatidylethanolamine, two unidentified phosphoglycolipids, an unidentified phospholipid, an unidentified aminophospholipid, an unidentified aminolipid and an unidentified lipid. MA1003(T) had three unidentified phosphoglycolipids, six unidentified phospholipids, two unidentified glycolipids and two unidentified polar lipids as the polar lipids. The G+C contents of the genomic DNA of MA1002(T) and MA1003(T) were 70.5 and 76.0 mol%, respectively. MK-8 was the predominant respiratory quinone for both strains. 16S rRNA gene sequence analysis showed that strain MA1002(T) was phylogenetically related to Deinococcus apachensis DSM 19763(T), D. geothermalis DSM 11300(T), D. aerius TR0125(T) and D. aetherius ST0316(T) (92.9, 92.6, 92.0 and 91.9% sequence similarity, respectively), and MA1003(T) showed the highest sequence similarity to Deinococcus hopiensis KR-140(T) (92.9%) and D. xinjiangensis X-82(T) (91.4%). The results of genotypic and phenotypic characterizations showed that both strains could be distinguished from phylogenetically related species, and that the strains represented novel species within the genus Deinococcus, for which we propose the names Deinococcus metallilatus sp. nov. (type strain MA1002(T) = KACC 17964(T) = NBRC 110141(T)) and Deinococcus carri sp. nov. (type strain is MA1003(T) = KACC 17965(T) = NBRC 110142(T)).

Antibiotic Sensitivity of Micrococcus radiodurans

Science.gov (United States)

Hawiger, J.; Jeljaszewicz, J.

1967-01-01

A wild-type strain of Micrococcus radiodurans and its nonpigmented mutant W1 were tested for sensitivity to 10 antibiotics selected from the standpoint of their mechanism of action. Representatives of groups of antibiotics inhibiting deoxyribonucleic acid (DNA) synthesis, DNA-dependent ribonucleic acid synthesis, protein synthesis, and cell wall synthesis were selected. M. radiodurans and its mutant exhibited full susceptibility to all antibiotics tested (mitomycin C, actinomycin D, chloramphenicol, dihydrostreptomycin, erythromycin, neomycin, kanamycin, benzylpenicillin, bacitracin, and vancomycin), the degree of susceptibility being of the same order as that of a standard strain of Staphylococcus aureus 209 P, with the exception of dihydrostreptomycin. PMID:4166078

Review of anticancer and antioxidant activities of radioresistant ...

African Journals Online (AJOL)

Prof. Ogunji

mechanism underlying the tolerance of these organisms to ionizing radiation. ... radiation dose environment, drastic temperature variations and high salinity ... extremophile like Deinococcus radiodurans for instance, is highly dependent on.

Microbial survival of space vacuum and extreme ultraviolet irradiation: strain isolation and analysis during a rocket flight.

Science.gov (United States)

Saffary, Roya; Nandakumar, Renu; Spencer, Dennis; Robb, Frank T; Davila, Joseph M; Swartz, Marvin; Ofman, Leon; Thomas, Roger J; DiRuggiero, Jocelyne

2002-09-24

We have recovered new isolates from hot springs, in Yellowstone National Park and the Kamchatka Peninsula, after gamma-irradiation and exposure to high vacuum (10(-6) Pa) of the water and sediment samples. The resistance to desiccation and ionizing radiation of one of the isolates, Bacillus sp. strain PS3D, was compared to that of the mesophilic bacterium, Deinococcus radiodurans, a species well known for its extraordinary resistance to desiccation and high doses of ionizing radiation. Survival of these two microorganisms was determined in real and simulated space conditions, including exposure to extreme UV radiation (10-100 nm) during a rocket flight. We found that up to 15 days of desiccation alone had little effect on the viability of either bacterium. In contrast, exposure to space vacuum ( approximately 10(-6) Pa) decreased cell survival by two and four orders of magnitude for Bacillus sp. strain PS3D and D. radiodurans, respectively. Simultaneous exposure to space vacuum and extreme UV radiation further decreased the survival of both organisms, compared to unirradiated controls. This is the first report on the isolated effect of extreme UV at 30 nm on cell survival. Extreme UV can only be transmitted through high vacuum, therefore its penetration into the cells may only be superficial, suggesting that in contrast to near UV, membrane proteins rather than DNA were damaged by the radiation.

γ-irradiated ribosomes from Micrococcus radiodurans in a cell-free protein synthesizing system

International Nuclear Information System (INIS)

Suessmuth, R.; Widmann, A.

1979-01-01

γ-irradiation inactivation of isolated ribosomes of Micrococcus radiodurans was studied by examining poly U directed synthesis of polyphenylalanine. Ribosomes of M. radiodurans did not show significant γ-radiation sensitivity up to a dose of approx. 11.6 k Gy. Cells of M. radiodurans take up more magnesium than E. coli cells under the same conditions. The magnesium content of ribosomes of M. radiodurans was 18% higher than that of E.coli ribosomes. A possible relation between Mg 2+ -content and γ-resistance is discussed. (orig.) [de

Gene Expression Analysis of Four Radiation-resistant Bacteria

OpenAIRE

Gao, Na; Ma, Bin-Guang; Zhang, Yu-Sheng; Song, Qin; Chen, Ling-Ling; Zhang, Hong-Yu

2009-01-01

To investigate the general radiation-resistant mechanisms of bacteria, bioinformatic method was employed to predict highly expressed genes for four radiation-resistant bacteria, i.e. Deinococcus geothermalis (D. geo), Deinococcus radiodurans (D. rad), Kineococcus radiotolerans (K. rad) and Rubrobacter xylanophilus (R. xyl). It is revealed that most of the three reference gene sets, i.e. ribosomal proteins, transcription factors and major chaperones, are generally highly expressed in the four ...

Deinococcus multiflagellatus sp. nov., isolated from a car air-conditioning system.

Science.gov (United States)

Kim, Dong-Uk; Lee, Hyosun; Lee, Suyeon; Park, Sooyeon; Yoon, Jung-Hoon; Zhao, Lei; Kim, Min-Kyu; Ahn, Jae-Hyung; Ka, Jong-Ok

2018-04-01

A gamma radiation-resistant and pink-to-red pigmented bacterial strain, designated ID1504 T , was isolated from a car air-conditioning system sampled in Korea. The cells were observed to be Gram-stain negative, aerobic, motile with peritrichous flagella and short rod-shaped. Phylogenetically, the strain groups with the members of the genus Deinococcus and exhibits high 16S rRNA gene sequence similarities with Deinococcus arenae SA1 T (94.0%), Deinococcus actinosclerus BM2 T (93.9%) and Deinococcus soli N5 T (93.5%). The predominant fatty acids were identified as C 17:0 , C 16:0 , summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c) and iso-C 17:0 . The major respiratory quinone was identified as MK-8. The polar lipids were found to be comprised of unidentified phospholipids, unidentified glycolipids, an unidentified aminophospholipid and an unidentified lipid. The DNA G+C content of the strain was determined to be 68.3 mol%. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, strain ID1504 T should be classified in a novel species in the genus Deinococcus, for which the name Deinococcus multiflagellatus sp. nov. (= KACC 19287 T  = NBRC 112888 T ) is proposed.

Resistance of Micrococcus radiodurans to killing and mutation by agents which damage DNA

Energy Technology Data Exchange (ETDEWEB)

Sweet, D M; Moseley, B E.B. [Edinburgh Univ. (UK). School of Agriculture

1976-02-01

The resistance of Micrococcus radiodurans to the lethal and mutagenic action of ultraviolet (UV) light, ionising (..gamma..) radiation, mitomycin C (MTC), nitrous acid (NA), hydroxylamine (HA), N-methyl-N'-nitro-N-nitrosoguanidine (NG), ethylmethanesulphonate (EMS) and ..beta..-propiolactone (..beta..PL) has been compared with that of Escherichia coli B/r. M. radiodurans was much more resistant than E. coli B/r to the lethal effects of UV light (by a factor of 33), ..gamma..-radiation (55), NG (15) and NA (62), showed intermediate resistance to MTC (4) and HA (7), but was sensitive to EMS (1) and ..beta..PL (2). M. radiodurans was very resistant to mutagens producing damage which can be repaired by a recombination system, indicating that it possesses an extremely efficient recombination repair mechanism. Both species were equally sensitive to mutation to trimethoprim resistance by NG, but M. radiodurans was more resistant than E. coli B/r to the other mutagens tested, being non-mutable by UV light, ..gamma..-radiation, MTC and HA, and only slightly sensitive to mutation by NA, EMS, and ..beta..PL. The resistance of M. radiodurans to mutation by UV light, ..gamma.. radiation and MTC is consistent with an hypothesis that recombination repair in M. radiodurans is accurate since these mutagens may depend on an 'error-prone' recombination system for their mutagenic effect in E. coli B/r. However, because M. radiodurans is also resistant to mutagens such as HA and EMS, which are mutagenic in E. coli in the absence of an 'error-prone' system, we propose that all the mutagens tested may have a common mode of action in E. coli B/r, but that this mutagenic pathway is missing in M. radiodurans.

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Effect of zinc and calcium ions on the rat kidney membrane-bound form of dipeptidyl ... ParA encoded on chromosome II of Deinococcus radiodurans binds to .... Repeated oral administration of capsaicin increases anxiety-like behaviours with ...

Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant.

Science.gov (United States)

Srinivasan, Sathiyaraj; Kim, Myung Kyum; Lim, Sangyong; Joe, Minho; Lee, Myungjin

2012-06-01

A Gram-stain-positive, strictly aerobic, spherical, non-motile red-pigmented bacterial strain, designated MJ27(T), was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was used to study the taxonomic position of strain MJ27(T). Strain MJ27(T) shared highest 16S rRNA gene sequence similarity with Deinococcus grandis DSM 3963(T) (98.8 %), Deinococcus caeni Ho-08(T) (97.5 %) and Deinococcus aquaticus PB314(T) (96.6 %.); levels of sequence similarity with the type strains of other Deinococcus species were less than 96.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ27(T) belonged to the clade formed by members of the genus Deinococcus in the family Deinococcaceae. The G+C content of the genomic DNA of strain MJ27(T) was 67.6 mol%. The chemotaxonomic characteristics of strain MJ27(T) were typical of members of the genus Deinococcus, with MK-8 as the predominant respiratory quinone, C(16:1)ω7c, C(15:1)ω6c, C(16:0) and C(15:0) as major fatty acids (>12 %), ornithine as the diamino acid in the cell-wall peptidoglycan and resistance to gamma radiation [D(10) (dose required to reduce the bacterial population by tenfold) >9 kGy]. The low levels of DNA-DNA relatedness reported here (5.3±1.5-29.2±2.3 %) indicate that strain MJ27(T) represents a species that is separate from its closest relatives in the genus Deinococcus. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ27(T) is considered to represent a novel species of the genus Deinococcus, for which the name Deinococcus daejeonensis sp. nov. is proposed. The type strain is MJ27(T) ( = KCTC 13751(T) = JCM 16918(T)).

The resistance of Micrococcus radiodurans to killing and mutation by agents which damage DNA

International Nuclear Information System (INIS)

Sweet, D.M.; Moseley, B.E.B.

1976-01-01

The resistance of Micrococcus radiodurans to the lethal and mutagenic action of ultraviolet (UV) light, ionising (γ) radiation, mitomycin C (MTC), nitrous acid (NA), hydroxylamine (HA), N-methyl-N'-nitro-N-nitrosoguanidine (NG), ethylmethanesulphonate (EMS) and β-propiolactone (βPL) has been compared with that of Escherichia coli B/r. M. radiodurans was much more resistant than E. coli B/r to the lethal effects of UV light (by a factor of 33), γ-radiation (55), NG (15) and NA (62), showed intermediate resistance to MTC (4) and HA (7), but was sensitive to EMS (1) and βPL (2). M. radiodurans was very resistant to mutagens producing damage which can be repaired by a recombination system, indicating that it possesses an extremely efficient recombination repair mechanism. Both species were equally sensitive to mutation to trimethoprim resistance by NG, but M. radiodurans was more resistant than E. coli B/r to the other mutagens tested, being non-mutable by UV light, γ-radiation, MTC and HA, and only slightly sensitive to mutation by NA, EMS, and βPL. The resistance of M. radiodurans to mutation by UV light, γ-radiation and MTC is consistent with an hypothesis that recombination repair in M. radiodurans is accurate since these mutagens may depend on an 'error-prone' recombination system for their mutagenic effect in E. coli B/r. However, because M. radiodurans is also resistant to mutagens such as HA and EMS, which are mutagenic in E. coli in the absence of an 'error-prone' system, we propose that all the mutagens tested may have a common mode of action in E. coli B/r, but that this mutagenic pathway is missing in M. radiodurans

Spectroelectrochemical insights into structural and redox properties of immobilized endonuclease III and its catalytically inactive mutant

Science.gov (United States)

Moe, Elin; Rollo, Filipe; Silveira, Célia M.; Sezer, Murat; Hildebrandt, Peter; Todorovic, Smilja

2018-01-01

Endonuclease III is a Fe-S containing bifunctional DNA glycosylase which is involved in the repair of oxidation damaged DNA. Here we employ surface enhanced IR spectroelectrochemistry and electrochemistry to study the enzyme from the highly radiation- and desiccation-resistant bacterium Deinococcus radiodurans (DrEndoIII2). The experiments are designed to shed more light onto specific parameters that are currently proposed to govern damage search and recognition by endonucleases III. We demonstrate that electrostatic interactions required for the redox activation of DrEndoIII2 may result in high electric fields that alter its structural and thermodynamic properties. Analysis of inactive DrEndoIII2 (K132A/D150A double mutant) interacting with undamaged DNA, and the active enzyme interacting with damaged DNA also indicate that the electron transfer is modulated by subtle differences in the protein-DNA complex.

Role of manganese in the resistance of Micrococcus radiodurans to ionizing radiation

International Nuclear Information System (INIS)

Wierowski, J.V.

1980-01-01

Micrococcus radiodurans possesses a very high level of intracellular manganese compared to other organisms. This manganese content has previously been shown to participate in the exceptional ulraviolet radiation resistance of M. radiodurans. This study was undertaken to determine the role of manganese in the ionizing radiation resistant of M. radiodurans. The results indicate that manganese is essential for DNA degradation to occur during irradiation. Manganese has also proven essential for the second phase of post-irradiation thymine base damage removal. These factors work together to increase the rate of recovery from radiation damage, which is reflected in a larger Dq, D 37 and exponential portion of the survival curve of high Mn-grown cells

Deinococcus gobiensis cold shock protein improves salt stress tolerance of escherichia coli

International Nuclear Information System (INIS)

Jiang Shijie; Wang Jin; Yang Mingkun; Chen Ming; Zhang Wei; Luo Xuegang

2013-01-01

The Deinococcus gobiensis I-0, an extremely radiation-resistant bacterium, isolated from the Gobi, has superior resistance to abiotic stress (e.g radiation, oxidation, dehydration and so on). The two cold-shock proteins encoded by csp1 (Dgo_CA1136) and csp2 (Dgo_PA0041) were identified in the complete genome sequence of D. gobiensis. In this study, we showed that D. gobiensis Csp1 protected Escherichia coli cells against cold shock and other abiotic stresses such as salt and osmotic shocks. The quantitative real-time PCR assay shows that the expression of trehalose synthase (otsA, otsB) was up-regulated remarkably under salt stress in the csp1-expressing strain, while no difference in the expression of the genes involved in trehalose degradation (treB and treC). The results suggested that Csp1 caused the accumulation of the trehalose was a major feature for improving tolerance to salt stress in E. coli. (authors)

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans · Narasimha Anaganti Bhakti Basu Shree Kumar Apte · More Details Abstract Fulltext PDF. A third generation promoter probe shuttle vector pKG was constructed, using the green fluorescent ...

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

PprA, a pleiotropic protein for radioresistance, works through DNA gyrase and shows cellular dynamics during postirradiation recovery in Deinococcus radiodurans .... Gene interactions and genetics of blast resistance and yield attributes in rice (Oryza ... Molecular mapping of a stripe rust resistance gene in wheat line C51.

High resistance of some oligotrophic bacteria to ionizing radiation

International Nuclear Information System (INIS)

Nikitin, D.I.; Tashtemirova, M.A.; Pitryuk, I.A.; Sorokin, V.V.; Oranskaya, M.S.; Nikitin, L.E.

1994-01-01

The resistance of seven cultures of eutrophic and oligotrophic bacteria to gamma radiation (at doses up to 360 Gy) was investigated. The bacteria under study were divided into three groups according to their survival ability after irradiation. Methylobacterium organophilum and open-quotes Pedodermatophilus halotoleransclose quotes (LD 50 = 270 Gy) were highly tolerant. By their tolerance, these organisms approached Deinococcus radiodurans. Aquatic ring-shaped (toroidal) bacteria Flectobacillus major and open-quotes Arcocella aquaticaclose quotes (LD 5 = 173 and 210 Gy, respectively) were moderately tolerant. Eutrophic Pseudomonas fluorescens and Escherichia coli (LD 50 = 43 and 38 Gy, respectively) were the most sensitive. X-ray microanalysis showed that in tolerant bacteria the intracellular content of potassium increased and the content of calcium decreased after irradiation. No changes in the element composition of the eutrophic bacterium E. coli were detected. Possible mechanisms of the resistance of oligotrophic bacteria to gamma radiation are discussed

Extracellular proteolytic activity of Deinococcus geothermalis ...

African Journals Online (AJOL)

Nonionic detergents like Triton X-100 and Tween 80 did not affect catalytic properties. It suggested that the enzyme produced by D. geothermalis could be used as a component of detergents. Keywords: Deinococcus geothermalis, alkaline protease, detergents, thermostability. African Journal of Biotechnology Vol. 12(25) ...

Four Proteins Synthesized in Response to Deoxyribonucleic Acid Damage in Micrococcus Radiodurans

DEFF Research Database (Denmark)

Hansen, M. T.

1980-01-01

Four proteins, alpha beta, gamma, and delta, preferentially synthesized in ultraviolet light-treated cells of Micrococcus radiodurans, were characterized in terms of their molecular weights and isoelectric points. Within the sublethal-dose range, the differential rate of synthesis for these prote......Four proteins, alpha beta, gamma, and delta, preferentially synthesized in ultraviolet light-treated cells of Micrococcus radiodurans, were characterized in terms of their molecular weights and isoelectric points. Within the sublethal-dose range, the differential rate of synthesis...

DNA repair mechanism in radioresistant bacteria

International Nuclear Information System (INIS)

Kitayama, Shigeru

1992-01-01

Many radiation resistant bacteria have been isolated from various sources which are not in high background field. Since Deinococcus radiodurans had been isolated first in 1956, studies on the mechanism for radioresistance were carried out mostly using this bacterium. DNA in this bacterium isn't protected against injury induced by not only ionizing radiation but also ultraviolet light. Therefore, DNA damages induced by various treatments are efficiently and accurately repaired in this cells. Damages in base and/or sugar in DNA are removed by endonucleases which, if not all, are synthesized during postirradiation incubation. Following the endonucleolytic cleavage the strand scissions in DNA are seemed to be rejoined by a process common for the repair of strand scissions induced by such as ionizing radiations. Induce protein(s) is also involved in this rejoining process of strand scissions. DNA repair genes were classified into three phenotypic groups. (1)Genes which are responsible for the endonucleolytic activities. (2) Genes involved in the rejoining of DNA strand scissions. (3) Genes which participate in genetic recombination and repair. Three genes belong to (1) and (2) were cloned onto approximately 1 kbp DNA fragments which base sequences have been determined. (author)

DNA repair mechanism in radioresistant bacteria

International Nuclear Information System (INIS)

Kitayama, Shigeru

1992-01-01

Many radiation resistant bacteria have been isolated from various sources which are not in high background field. Since Deinococcus radiodurans had been isolated first in 1956, the studies on the mechanism of radioresistance were mostly carried out using this bacterium. DNA in this bacterium isn't protected against injury induced by not only ionizing radiation but also ultraviolet light. Therefore, DNA damages induced by various treatments are efficiently and accurately repaired in this cells. Damages in base and/or sugar in DNA are removed by endonucleases which, if not all, are synthesized during postirradiation incubation. Following the endonucleolytic cleavage the strand scissions in DNA are seemed to be rejoined by a process common for the repair of strand scissions induced by such as ionizing radiations. Induce protein(s) is also involved in this rejoining process of strand scissions. DNA repair genes were classified into three phenotypic groups. (1) Genes which are responsible for the endonucleolytic activities. (2) Genes involved in the rejoining of DNA strand scissions. (3) Genes which participate in genetic recombination and repair. Three genes belong to (1) and (2) were cloned onto approximately 1 kbp DNA fragments which base sequences have been determined. (author)

Separation of DNA-dependent polymerate activities in Micrococcus radiodurans

International Nuclear Information System (INIS)

Kitayama, S.; Matsuyama, A.

1977-01-01

DNA polymerase activities in Micrococcus radiodurans were separated into two fractions after purification more than 2000 fold. They differ in pH optimum and residual activities in the absence of a full deoxyribonucleoside triphosphates complement. NAD partly inhibited one of the activities. Both activities were eluted as a single peak on gel filtration and sedimented at the same rate on glycerol gradient centrifugation. Molecular weight 140000 was calculated from Stokes radius and sedimentation constant. Deoxyribonuclease activity was detected on one of the polymerase activities which preferentially degraded double-stranded DNA. Priming activity of nicked DNA was reduced by γ-radiation. These results have been related to the possible roles in repair synthesis in vivo or DNA synthesis in permeable cells of M. radiodurans

Separation of DNA-dependent polymerase activities in Micrococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Kitayama, S; Matsuyama, A [Institute of Physical and Chemical Research, Wako, Saitama (Japan)

1977-03-02

DNA polymerase activities in Micrococcus radiodurans were separated into two fractions after purification more than 2000 fold. They differ in pH optimum and residual activities in the absence of a full deoxyribonucleoside triphosphates complement. NAD partly inhibited one of the activities. Both activities were eluted as a single peak on gel filtration and sedimented at the same rate on glycerol gradient centrifugation. Molecular weight 140000 was calculated from Stokes radius and sedimentation constant. Deoxyribonuclease activity was detected on one of the polymerase activities which preferentially degraded double-stranded DNA. Priming activity of nicked DNA was reduced by ..gamma.. radiation. These results have been related to the possible roles in repair synthesis in vivo or DNA synthesis in permeable cells of M. radiodurans.

Ionizing radiation damage in Micrococcus radiodurans cell wall: release of polysaccharide

International Nuclear Information System (INIS)

Mitchel, R.E.J.

1976-01-01

Sublethal 60 Co γ-irradiation of the bacterium Micrococcus radiodurans in aqueous suspension results in a loss of up to 6 percent of its cellular dry weight and 30 percent of its wet weight. In the process some specific cell wall polysaccharides, including a polymer of glucose and N-acylated glucosamine, are released into the surrounding medium. These polysaccharides appear to originate from a hydrophobic site in the middle, lipid-rich, cell wall layer. The damage to this layer which results in the release of these and other polymers may be due to a disruption of this hydrophobic site. The polysaccharide containing glucose and N-acylated glucosamine exists as a high molecular weight polymer in unirradiated cells, but irradiation causes some degradation prior to release. In a free state this polysaccharide is considerably less sensitive to radiolytic degradation than in a bound state. Free radicals generated from surrounding water by ionizing radiation initiate the release, hydroxyl radicals being the most important species. Oxygen protects the cell wall against loss of the polysaccharides, apparently by a mechanism which does not depend on the ability of O 2 to scavenge hydrogen atoms and aqueous electrons

Clipboard

Indian Academy of Sciences (India)

Unknown

DNA Repair in Deinococcus radiodurans and in Germinating Bacterial Spores; J. Bacteriol. 186 5973–5977. Frenkiel-Krispin D, Levin-Zaidman S, Shimoni E, Wolf S G, Wachtel E J, Arad T, Finkel S E, Kolter R and. Minsky A 2001 Regulated phase transitions of bacterial chromatin: a non-enzymatic pathway for generic DNA.

Adaptability and variability of the cell functions to the environmental factors

Energy Technology Data Exchange (ETDEWEB)

Kikuchi, Tadatoshi [Kyoto Univ., Kumatori, Osaka (Japan). Research Reactor Inst.

1995-02-01

Adaptive phenomenon of the cells to the environmental factors is one of the most important functions of cells. In the initial research program, yeast, Saccharomyces cerevisiae, as model species of eukaryote was selected to use for the experiments and copper sulfate was adopted as one of the ideal environmental factors, and then adaptation mechanisms of yeast cells in the environment surrounded by copper ions were analyzed metabolically and morphologically. Furthermore, in the relationships between environmental factors and the cells, the researches performed were as follows: (1) Induced mutation in the extranuclear-inheritable system: Mutagenic effect of ethidium bromide on mitochondria and plastids. (2) Induction of gene expression by light exposure in the early development of chloroplast in Chlamydomonas reinhardi. (3) Some features of RNA and protein syntheses in thermophilic alga Cyanidium caldarium. (4) Satellite DNA of Ochromonas danica. (5) Analyses of cell functions using various kinds of radiations. (6) Novel methionine requirement of radiation resistant bacterium, Deinococcus radiodurans. (author).

Quorum sensing circuit and reactive oxygen species resistance in Deinococcus sp.

Science.gov (United States)

Fernandez-Bunster, G; Gonzalez, C; Barros, J; Martinez, M

2012-12-01

Genus Deinococcus is characterized by an increased resistance toward reactive oxygen species (ROS). The chromosome of five strains belonging to this genus has been sequenced and the presence of a luxS-like gene was deduced from their genome sequences. The aim of this study was to assess if a complete QS circuit is present in Deinococcus sp. and if this QS is associated with ROS. Primers for searching luxS-like gene and the putative receptor gene, namely ai2R, were designed. AI-2 signal production was evaluated by luminescence analysis using Vibrio harveyi BB170 as reporter strain. AI-2 signal was also evaluated by competitive assays using cinnamaldehyde, ascorbic acid, and 3-mercaptopropionic acid as interfering molecules. Potassium tellurite and metronidazole were used as oxidative stressors. A luxS-like gene as well as an ai2R gene was detected in strain UDEC-P1 by PCR. Cell-free supernatant of strain UDEC-P1 culture induced luminescence in V. harveyi BB170, and this property was inhibited with the three interfering molecules. The oxidative stressors metronidazole and potassium tellurite decreased Deinococcus sp. viability, but increased luminescence of the reporter strain. The results demonstrate that both a functional luxS-like gene and a putative receptor for AI-2 signal are present in Deinococcus sp. strain UDEC-P1. This finding also suggests that a complete QS circuit is present in this genus, which could be related to oxidative stress.

Repair of double-strand breaks in Micrococcus radiodurans

International Nuclear Information System (INIS)

Burrell, A.D.; Dean, C.J.

1975-01-01

Micrococcus radiodurans has been shown to sustain double-strand breaks in its DNA after exposure to x-radiation. Following sublethal doses of x-rays (200 krad in oxygen or less), the cells were able to repair these breaks, and an intermediate fast-sedimenting DNA component seemed to be involved in the repair process

Topoisomerase IB of Deinococcus radiodurans resolves guanine ...

Indian Academy of Sciences (India)

2015-11-28

Nov 28, 2015 ... All the oligonucleotides men- tioned here were ... further reactions with DraTopoIB were carried out at 37°C ... of G4 DNA moves faster than unfolded and intermolecular .... for its action on intramolecular G4 DNA structure was.

Expression of lycopene biosynthesis genes fused in line with Shine-Dalgarno sequences improves the stress-tolerance of Lactococcus lactis.

Science.gov (United States)

Dong, Xiangrong; Wang, Yanping; Yang, Fengyuan; Zhao, Shanshan; Tian, Bing; Li, Tao

2017-01-01

Lycopene biosynthetic genes from Deinococcus radiodurans were co-expressed in Lactococcus lactis to produce lycopene and improve its tolerance to stress. Lycopene-related genes from D. radiodurans, DR1395 (crtE), DR0862 (crtB), and DR0861 (crtI), were fused in line with S hine-Dalgarno (SD) sequences and co-expressed in L. lactis. The recombinant strain produced 0.36 mg lycopene g -1  dry cell wt after 48 h fermentation. The survival rate to UV irradiation of the recombinant strain was higher than that of the non-transformed strain. The L. lactis with co-expressed genes responsible for lycopene biosynthesis from D. radiodurans produced lycopene and exhibited increased resistance to UV stress, suggesting that the recombinant strain has important application potential in food industry.

The mechanisms of Micrococcus radiodurans radioresistance

International Nuclear Information System (INIS)

Samojlenko, I.I.

1983-01-01

Modern representations on molecular mechanisms of Micrococcus radiodurans viability under the effect of ionizing radiation have been considered. Factors conditioning a high level of micrococcus cell radiostability have been analyzed: peculiarities of structure of a cell wall, DNA, membranes; excess of genetic information; multiplicity of DNA implantation points to a membrane; high level of antioxidation and antiradical systems. It has been shown that on efficiency of accurate, properly balanced system of DNA repair combined with above Micrococcus radiodurant properties provide a high microorganism radioresistance

Deinococcus aluminii sp. nov., isolated from an automobile air conditioning system.

Science.gov (United States)

Kim, Dong-Uk; Lee, Hyosun; Lee, Suyeon; Park, Sooyeon; Yoon, Jung-Hoon; Zhao, Lei; Kim, Min-Kyu; Ahn, Jae-Hyung; Ka, Jong-Ok

2018-01-16

A Gram-stain-positive and pale pink-pigmented bacterial strain, designated ID0501 T , was isolated from an automobile evaporator core collected in the Republic of Korea. The cells were aerobic and coccoidal. The strain grew at 15-40 ˚C (optimum, 37 ˚C), at pH 6.0-7.0 (optimum, pH 6.5), and in the presence of 0-1.5 % (w/v) NaCl. Phylogenetically, the strain was related to members of the genus Deinococcus and showed the highest sequence similarity, of 96.9 %, with Deinococcus metallilatus MA1002 T . The major fatty acids of the strain were iso-C17 : 0, iso-C15 : 0 and iso-C13 : 0. The predominant respiratory quinone was MK-8. The polar lipids profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, unidentified phospholipids, an unidentified aminolipid and unidentified glycolipids. The DNA G+C content of the strain was 68.3 mol%. On the basis of phenotypic, genotypic and chemotaxonomic data, strain ID0501 T represents a novel species of the genus Deinococcus, for which the name Deinococcusaluminii sp. nov. (=KACC 19286 T =NBRC 112889 T ) is proposed.

Genetic control over the processes of postirradiation recovery of a compact chromosome in micrococcus radiodurans

International Nuclear Information System (INIS)

Kudryashova, N.Yu.; Groshev, V.V.; Shestakov, S.V.

1984-01-01

X-irradiation of Micrococcus radiodurans cells with sublethal doses caused disturbances in the structure of a membrane-bound compact chromosome. Recovery of the compact chromosome occurred during the postirradiation incubation of the wild type cells and cells of the UVS-17 mutant deficient in DNA-polymerase. This process was blocked in cells of rec-30 mutant with the impaired system of genetic recombination: this is indicative of an important role played by rec-30 gene product in the postirradiation recovery of the compact chromosome in M. radiodurans cells

Small-Molecule Antioxidant Proteome-Shields in Deinococcus Radiodurans

Science.gov (United States)

2010-09-01

family of proteases [14] which appear to be activated by irradiation (Figure 4B). At least 10 complete open reading frames with considerable sequence...the experiments: MJD EKG VYM JGK RF DYL NBW GAV BSB RLL. Performed the experiments: MJD EKG VYM JGK RF DYL NBW GAV BSB RLL. Analyzed the data: MJD... EKG VYM JGK RF DYL NBW GAV BSB RLL. Wrote the paper: MJD RLL. References 1. Daly MJ, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, et al. (2007

Research of radiation-resistant microbial organisms

Energy Technology Data Exchange (ETDEWEB)

Kim, Dongho; Lim, Sangyong; Joe, Minho; Park, Haejoon; Song, Hyunpa; Im, Seunghun; Kim, Haram; Kim, Whajung; Choi, Jinsu; Park, Jongchun

2012-01-15

Many extremophiles including radiation-resistant bacteria Deinococcus radiodurans have special characteristics such as novel enzymes and physiological active substances different from known biological materials and are being in the spotlight of biotechnology science. In this research, basic technologies for the production of new genetic resources and microbial strains by a series of studies in radiation-resistant microbial organisms were investigated and developed. Mechanisms required for radiation-resistant in Deinococcus radiodurans were partly defined by analyzing the function of dinB, pprI, recG, DRA{sub 0}279, pprM, and two-component signal transduction systems. To apply genetic resource and functional materials from Deinococcus species, omics analysis in response to cadmium, construction of macroscopic biosensor, and characterization of carotenoids and chaperon protein were performed. Additionally, potential use of D. geothermalis in monosaccharide production from non-biodegradable plant materials was evaluated. Novel radiation resistant yeasts and bacteria were isolated and identified from environmental samples to obtain microbial and genomic resources. An optimal radiation mutant breeding method was set up for efficient and rapid isolation of target microbial mutants. Furthermore, an efficient ethanol producing mutant strain with high production yield and productivity was constructed using the breeding method in collaboration with Korea Research Institute of Bioscience and Biotechnology. Three Deinococcal bioindicators for radiation dosage confirmation after radiation sterilization process were developed. These results provide a comprehensive information for novel functional genetic elements, enzymes, and physiological active substances production or application. Eventually, industrial microbial cell factories based on radiation resistant microbial genomes can be developed and the technologies can be diffused to bioindustry continuously by this project.

Research of radiation-resistant microbial organisms

International Nuclear Information System (INIS)

Kim, Dongho; Lim, Sangyong; Joe, Minho; Park, Haejoon; Song, Hyunpa; Im, Seunghun; Kim, Haram; Kim, Whajung; Choi, Jinsu; Park, Jongchun

2012-01-01

Many extremophiles including radiation-resistant bacteria Deinococcus radiodurans have special characteristics such as novel enzymes and physiological active substances different from known biological materials and are being in the spotlight of biotechnology science. In this research, basic technologies for the production of new genetic resources and microbial strains by a series of studies in radiation-resistant microbial organisms were investigated and developed. Mechanisms required for radiation-resistant in Deinococcus radiodurans were partly defined by analyzing the function of dinB, pprI, recG, DRA 0 279, pprM, and two-component signal transduction systems. To apply genetic resource and functional materials from Deinococcus species, omics analysis in response to cadmium, construction of macroscopic biosensor, and characterization of carotenoids and chaperon protein were performed. Additionally, potential use of D. geothermalis in monosaccharide production from non-biodegradable plant materials was evaluated. Novel radiation resistant yeasts and bacteria were isolated and identified from environmental samples to obtain microbial and genomic resources. An optimal radiation mutant breeding method was set up for efficient and rapid isolation of target microbial mutants. Furthermore, an efficient ethanol producing mutant strain with high production yield and productivity was constructed using the breeding method in collaboration with Korea Research Institute of Bioscience and Biotechnology. Three Deinococcal bioindicators for radiation dosage confirmation after radiation sterilization process were developed. These results provide a comprehensive information for novel functional genetic elements, enzymes, and physiological active substances production or application. Eventually, industrial microbial cell factories based on radiation resistant microbial genomes can be developed and the technologies can be diffused to bioindustry continuously by this project

The deoxyribonucleic acid of Micrococcus radiodurans

Science.gov (United States)

Schein, Arnold H.

1966-01-01

The DNA of Micrococcus radiodurans was prepared by three methods. Although the recovery of DNA varied considerably, the percentage molar base ratios of the DNA from the three preparations were essentially the same: guanine, 33±2; adenine, 18±1; cytosine, 33±2; thymine, 17±1. Base compositions calculated from Tm values and from density in caesium chloride gradients also yielded guanine+cytosine contents of 66 and 68% of total bases respectively. No unusual bases were observed. The S20,w values were characteristic of high-molecular-weight DNA. Electron microscopy showed the purified DNA in long strands; occasionally these were coiled. Images(a)(b)(c)(d)(e)Fig. 1. PMID:16742439

Excision repair of 5,6-dihydroxydihydrothymine from the DNA of Micrococcus radiodurans

International Nuclear Information System (INIS)

Targovnik, H.S.; Hariharan, P.V.

1980-01-01

One of the major ionizing radiation products, 5,6-dihydroxydihydrothymine (thymine glycol), was measured in the DNA of Micrococcus radiodurans following exposure of cells to 6.8-MeV electrons or 254-nm ultraviolet light. Removal of 5,6-dihydroxydihydrothymine was measured in both an ionizing radiation-sensitive strain (262) and a highly radioresistant strain (the wild type W + ) of Micrococcus radiodurans. Within 30 min of incubation (33 0 C) following exposure to ultraviolet light (2400 J/m 2 ) approximately 60% of the thymine glycols were excised, whereas in the case of ionizing radiation (250 krad) only 35% were removed from the cellular DNA of the wild-type strain. In contrast less than 50% of the thymine glycols were excised from the sensitive strain. The amount of DNA degradation induced by radiation was less than 10% in both strains. The results suggest a possible correlation between reduced excision repair of base damage and increased radiation sensitivity

Characterization and safety evaluation of a Deinococcus member as feed additive for hens.

Science.gov (United States)

Wu, Szu-Yin; Li, I-Chen; Lin, Yi-Chin; Chen, Chin-Chu

2016-04-01

As previous studies mainly focus on understanding the mechanisms of radioresistance in Deinococcus bacteria, the present study aimed at characterizing and verifying the safety use of the GKB-Aid 1995 strain, a member of the radiation-resistant bacterial genus Deinococcus, as an ingredient in feed supplements. Using Vitek 2 system and 16S rRNA gene sequencing, GKB-Aid 1995 most resembles Deinococcus grandis. The Ames test, in vitro chromosomal test, in vivo micronucleus test and acute toxicity test were performed subsequently for its safety evaluation. As there is a possibility that the pigment of GKB-Aid 1995 can pass from feed to eggs intended for human consumption, an acute toxicity test was also carried out in pigmented egg yolk. The results confirmed that GKB-Aid 1995 was non-genotoxic in three genotoxicity experiments, and the LD50 of GKB-Aid 1995 and the pigmented egg yolk in ICR mice was greater than 10 and 12 g kg(-1) body weight, respectively. Overall, these data indicate that GKB-Aid 1995 is a non-toxic substance with no genotoxicity and is therefore safe to be used as a feed supplement or feed additive. This study suggests there is potential in developing GKB-Aid 1995 as an animal feed additive intended to enhance yolk coloration to meet the demand of consumers. Copyright © 2016 Elsevier Inc. All rights reserved.

Studies on Post-Irradiation DNA Degradation in Micrococcus Radiodurans, Strain RII51

DEFF Research Database (Denmark)

Auda, H.; Emborg, C.

1973-01-01

The influence of irradiation condition on post-irradiation DNA degradation was studied in a radiation resistant mutant of M. radiodurans, strain ${\\rm R}_{{\\rm II}}5$. After irradiation with 1 Mrad or higher more DNA is degraded in cells irradiated in wet condition than in cells irradiated with t...

Catalyst of D. radiodurans LexA protein and its induced catalysis at alkaline pH activated by RecA

International Nuclear Information System (INIS)

Kong Xiangrong; Liu Fenju; Su Liaoyuan

2003-01-01

It is to study the catalytic reaction of LexA at alkaline pH. It has been observed that reaction has taken place under two conditions of D. radiodurans and LexA. Methods: The method of SDS polypropylene amine was adopted to make dyeing with R-250. Results: The result showed that there were no reactions when LexA protein turned to be at pH 7.0 and pH 8.0, the entire LexA protein was decreased a little at pH 9.0, while at pH 10.0, LexA protein started to decompose greatly, the fractions of protein can be seen obviously in the electrophoresis belt. Conclusion: The D. radiodurans and LexA protein will automatically drop at 37 degree C when D radiodurans LexA is at higher pH value, and its dependence on alkaline pH conditions reflects that the catalytic needs to be activated by the reaction of de- pH indicator of LexA protein ionization

Loss of characteristic radiation resistance by mutation of Micrococcus radiodurans

International Nuclear Information System (INIS)

Kitayama, S.; Matusyama, A.

1975-01-01

The exceptional radioresistance of M. radiodurans was lost by a mutation, and the isolated mutant, KH840, had almost the same radiosensitivity as E. coli K12 AB1157 or B/r. DNA-strand scissions in this mutant were rejoined partly during post-irradiation incubation. Reduced DNA polymerizing activity and extensive degradation of the product was observed in vitro in the crude extract from the sensitive strain. The lower repair capability is not accompanied by the reduced transformation frequency

Loss of characteristic radiation resistance by mutation of Micrococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Kitayama, S; Matusyama, A [Institute of Physical and Chemical Research, Wako, Saitama (Japan)

1975-09-01

The exceptional radioresistance of M. radiodurans was lost by a mutation, and the isolated mutant, KH840, had almost the same radiosensitivity as E. coli K12 AB1157 or B/r. DNA-strand scissions in this mutant were rejoined partly during post-irradiation incubation. Reduced DNA polymerizing activity and extensive degradation of the product was observed in vitro in the crude extract from the sensitive strain. The lower repair capability is not accompanied by the reduced transformation frequency.

Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.

Science.gov (United States)

Tkavc, Rok; Matrosova, Vera Y; Grichenko, Olga E; Gostinčar, Cene; Volpe, Robert P; Klimenkova, Polina; Gaidamakova, Elena K; Zhou, Carol E; Stewart, Benjamin J; Lyman, Mathew G; Malfatti, Stephanie A; Rubinfeld, Bonnee; Courtot, Melanie; Singh, Jatinder; Dalgard, Clifton L; Hamilton, Theron; Frey, Kenneth G; Gunde-Cimerman, Nina; Dugan, Lawrence; Daly, Michael J

2017-01-01

Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans . However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

DNA-membrane complex restoration in Micrococcus radiodurans after X-irradiation: relation to repair, DNA synthesis and DNA degradation

Energy Technology Data Exchange (ETDEWEB)

Dardalhon-Samsonoff, M; Averbeck, D [Institut du Radium, 75 - Paris (France). Lab. Curie

1980-07-01

The DNA-membrane complex in Micrococcus radiodurans was shown to be essentially constituted of proteins, lipids and DNA. The complex was dissociated immediately after X-irradiation of cells and restored during post-incubation in complete medium. In X-irradiated protoplasts some DNA remained associated with the complex. Restoration of the complex during post-incubation was only seen in a medium favouring DNA polymerase and ligase activities. Under this condition no DNA synthesis occurred, suggesting that complex restoration may involve ligase activity. The complex restoration in the wild type and the X-ray sensitive mutant UV17 of M. radiodurans was strictly dependent on the X-ray dose. It was correlated with survival and DNA degradation but always preceded the onset of DNA synthesis after X-irradiation. At the same dose the complex restoration was about 2 fold lower in mutant than in wild type cells indicating that the restoration of the complex is related to repair capacity. The results are consistent with the idea that the complex protects X-irradiated DNA of M. radiodurans from further breakdown and, subsequently, permits DNA synthesis and repair to occur.

Development of application technology of radiation-resistant microorganism

International Nuclear Information System (INIS)

Kim, Dong Ho; Lim, Sang Yong; Joe, Min Ho; Jung, Jin Woo; Jung, Sun Wook; Song, Du Sup; Choi, Young Ji

2009-02-01

The scope of the project is divided into of three parts; (i) to define the survival strategy of radiation-resistant microbes, especially Deinococcus (ii) acquisition of gene resources encoding the novel protein and related with the production of functional materials (iii) development of control technology against radiation-resistant microbes. To this aim, first, the whole transcriptional response of the D. radiodurans strain haboring pprI mutation, which plays an important role in radiation resistance, was analyzed by cDNA microarray. The anti-oxidant activity of the major carotenoid of D. radiodurans, deinoxanthin, was analyzed and the strain was constructed, in which the gene necessary for bio- synthesis of deinoxanthin is deleted. The response to cadmium of D. radiodurans was also investigated through cDNA microarray analysis. Radiogenic therapy, one of the cancer treatments, is designed to use radiation-inducible gene for the treatment. To develop the gene-transfer vehicle for radiogenic therapy, we have investigated the virulence mechanism of Salmonella, which is tumor-targeting bacteria and studied the synergistic effect of some anti-cancer agents on radiation treatment for cancer. Finally, we confirmed that irradiation could decompose a fungus toxin, patulin, into various harmless by-products

Development of application technology of radiation-resistant microorganism

Energy Technology Data Exchange (ETDEWEB)

Kim, Dong Ho; Lim, Sang Yong; Joe, Min Ho; Jung, Jin Woo; Jung, Sun Wook; Song, Du Sup; Choi, Young Ji [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2009-02-15

The scope of the project is divided into of three parts; (i) to define the survival strategy of radiation-resistant microbes, especially Deinococcus (ii) acquisition of gene resources encoding the novel protein and related with the production of functional materials (iii) development of control technology against radiation-resistant microbes. To this aim, first, the whole transcriptional response of the D. radiodurans strain haboring pprI mutation, which plays an important role in radiation resistance, was analyzed by cDNA microarray. The anti-oxidant activity of the major carotenoid of D. radiodurans, deinoxanthin, was analyzed and the strain was constructed, in which the gene necessary for bio- synthesis of deinoxanthin is deleted. The response to cadmium of D. radiodurans was also investigated through cDNA microarray analysis. Radiogenic therapy, one of the cancer treatments, is designed to use radiation-inducible gene for the treatment. To develop the gene-transfer vehicle for radiogenic therapy, we have investigated the virulence mechanism of Salmonella, which is tumor-targeting bacteria and studied the synergistic effect of some anti-cancer agents on radiation treatment for cancer. Finally, we confirmed that irradiation could decompose a fungus toxin, patulin, into various harmless by-products.

Validation of a homology model of Mycobacterium tuberculosis DXS: rationalization of observed activities of thiamine derivatives as potent inhibitors of two orthologues of DXS.

Science.gov (United States)

Masini, T; Lacy, B; Monjas, L; Hawksley, D; de Voogd, A R; Illarionov, B; Iqbal, A; Leeper, F J; Fischer, M; Kontoyianni, M; Hirsch, A K H

2015-12-14

The enzyme DXS catalyzes the first, rate-limiting step of the 2-C-methyl-d-erythritol-4-phosphate (MEP, 1) pathway using thiamine diphosphate (ThDP) as cofactor; the DXS-catalyzed reaction constitutes also the first step in vitamin B1 and B6 metabolism in bacteria. DXS is the least studied among the enzymes of this pathway in terms of crystallographic information, with only one complete crystal structure deposited in the Protein Data Bank (Deinococcus radiodurans DXS, PDB: ). We synthesized a series of thiamine and ThDP derivatives and tested them for their biochemical activity against two DXS orthologues, namely D. radiodurans DXS and Mycobacterium tuberculosis DXS. These experimental results, combined with advanced docking studies, led to the development and validation of a homology model of M. tuberculosis DXS, which, in turn, will guide medicinal chemists in rationally designing potential inhibitors for M. tuberculosis DXS.

Epigenetic changes of DNA repair genes in cancer

OpenAIRE

Lahtz, Christoph; Pfeifer, Gerd P.

2011-01-01

‘Every Hour Hurts, The Last One Kills'. That is an old saying about getting old. Every day, thousands of DNA damaging events take place in each cell of our body, but efficient DNA repair systems have evolved to prevent that. However, our DNA repair system and that of most other organisms are not as perfect as that of Deinococcus radiodurans, for example, which is able to repair massive amounts of DNA damage at one time. In many instances, accumulation of DNA damage has been linked to cancer, ...

Effect of cordycepin(3'-deoxyadenosine) on excision repair of 5,6-dihydroxy-dihydrothymine-type products from the DNA of Micrococcus radiodurans

International Nuclear Information System (INIS)

Patil, M.S.; Tundo, V.J.; Locher, S.E.; Hariharan, P.V.

1983-01-01

Cordycepin(3'-deoxyadenosine), a nucleoside analog, has been shown to enhance radiation-induced cell killing. In an effort to elucidate the possible mechanism for enhancement of cell killing, the effect of cordycepin on the excision repair of radiation-induced 5,6-dihydroxy-dihydrothymine-type (t') products from the DNA of wild type Micrococcus radiodurans was investigated. The capacity of M. radiodurans to excise nondimeric (t') products from its DNA was significantly impaired after cordycepin treatment. The results suggest that the increased radiation sensitivity of cordycepin-treated cells could be due to alterations in cellular processes that repair DNA damage

Description of Deinococcus oregonensis sp. nov., from biological soil crusts in the Southwestern arid lands of the United States of America.

Science.gov (United States)

Gundlapally, Sathyanarayana Reddy; Garcia-Pichel, Ferran

2017-01-01

Biological soil crusts are distinct habitats, harbor unique prokaryotic diversity and gave an impetus to isolate novel species. In the present study, a pink-pigmented bacterium, (OR316-6 T ), was isolated from biological soil crusts using oligotrophic BG11-PGY medium. Strain OR316-6 T was Gram-positive, short rods, non-motile and non-spore forming. Cells were positive for catalase, oxidase and β-galactosidase and negative for most of the enzymatic activities. The major fatty acids present were C 16:0 , C 17:0 , and C 16:1 ω7c and contained MK-8 and MK-10 as the predominant menaquinones. The cell wall peptidoglycan was of A3β variant with L-ornithine as the diamino acid. Based on the above characteristics, strain OR316-6 T was assigned to the genus Deinococcus. The phylogenetic analysis indicated that strain OR316-6 T was closely related to D. aquatilis DSM 23025 T with a 16S rRNA gene similarity of 99.3 % and clustered with a bootstrap value of 100 %. DNA-DNA similarity between strain OR316-6 T and D. aquatilis DSM 23025 T was 37.0 % indicating that strain OR316-6 T was a novel species. Further, DNA fingerprinting of stains OR316-6 T and D. aquatilis DSM 23035 T demonstrated that both strains were related to each other with a similarity coefficient of only 0.32 and supported the species status to strain OR316-6 T . In addition, phenotypic characteristics distinguished strain OR316-6 T from D. aquatilis DSM 23025 T . Based on the cumulative differences, strain OR316-16 T exhibited with its closely related species, it was identified as a novel species and proposed the name Deinococcus oregonensis sp. nov. The type strain is D. oregonensis sp. nov. (OR316-6 T  = JCM 13503 T  = DSM 17762 T ).

Dormancy in Deinococcus sp. UDEC-P1 as a survival strategy to escape from deleterious effects of carbon starvation and temperature.

Science.gov (United States)

Guerra, Matías; González, Karina; González, Carlos; Parra, Boris; Martínez, Miguel

2015-09-01

Dormancy is characterized by low metabolism and absence of protein synthesis and cellular division enabling bacterial cells to survive under stress. The aim was to determine if carbon starvation and low temperature are factors that modify the proportion of dormant/active cells in Deinococcus sp. UDEC-P1. By flow cytometry, RedoxSensor Green (RSG) was used to quantify metabolic activity and Propidium Iodide (PI) to evaluate membrane integrity in order to determine the percentage of dormant cells. Cell size and morphology were determined using scanning electronic microscopy. Under carbon starvation at 30°C, Deinococcus sp. UDEC-P1 increased its proportion of dormant cells from 0.1% to 20%, decreased the count of culturable cells and average cell volume decreased 7.1 times. At 4°C, however, the proportion of dormant cells increased only to 6%, without a change in the count of culturable cells and an average cellular volume decrease of 4.1 times and 3% of the dormant cells were able to be awakened. Results indicate a greater proportion of dormant Deinococcus sp. UDEC-P1 cells at 30ºC and it suggests that carbon starvation is more deleterious condition at 30ºC than 4ºC. For this reason Deinococcus sp. UDEC-P1 cells are more likely to enter into dormancy at higher temperature as a strategy to survive. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149

Directory of Open Access Journals (Sweden)

Rok Tkavc

2018-01-01

Full Text Available Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans. However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute, heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

Science.gov (United States)

Holden, Todd; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Gadura, N.; Schneider, P.; Sullivan, R.; Flamholz, A.; Lieberman, D.; Cheung, T. D.

2009-08-01

The Single-Stranded DNA-Binding Protein (RPA) Genes in gamma ray radiation-resistant halophilic archaeon Halobacterium sp. NRC-1 were analyzed in terms of their nucleotide fluctuations. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis in this study. Fractal analysis using the Higuchi method gave fractal dimensions of 2.04 and 2.06 for the gene sequences VNG2160 and VNG2162, respectively. The 16S rRNA sequence has a fractal dimension of 1.99. The di-nucleotide Shannon entropy values were found to be negatively correlated with the observed fractal dimensions (R2~ 0.992, N=3). Inclusion of Deinococcus radiodurans Rad-A in the regression analysis decreases the R2 slightly to 0.98 (N=4). A third VNG2163 RPA gene of unknown function but with upregulation activity under irradiation was found to have a fractal dimension of 2.05 and a Shannon entropy of 3.77 bits. The above results are similar to those found in bacterial Deinococcus radiodurans and suggest that their high radiation resistance property would have favored selection of CG di-nucleotide pairs. The two transcription factors TbpD (VNG7114) and TfbA (VNG 2184) were also studied. Using VNG7114, VNG2184, and VNG2163; the regression analysis of fractal dimension versus Shannon entropy shows that R2 ~ 0.997 for N =3. The VNG2163 unknown function may be related to the pathways with transcriptions closely regulated to sequences VNG7114 and VNG2184.

A New Perspective on Radiation Resistance Based on Deinococcus radiodurans

Science.gov (United States)

2009-03-01

tolerate 3,000–5000 Gy, but are rendered sterile. As a haploid, the basidiomycete fungus Ustilago maydis carries a single set of chromosomes per...salinarum NRC-1. Environ. Microbiol. 5 Jan 2009 (doi:10.1111/j.1462-2920.2008.01828.x). 21. Chan, H. L. et al. Proteomic analysis of UVC irradiation

Isolation and identification of a novel radio-resistant strain

International Nuclear Information System (INIS)

Zhang Zhidong; Mao Jun; Wang Wei; Tang Qiyong; Shi Yuhu

2008-01-01

A novel radio-resistant strain named RL2 was studied polyphasically, which was isolated from the soils in the Gurban-Tunggut Desert, Xinjiang. The strain is Gam-positive, sphere-shaped and pink pigmented; The DNA (G+C) contents of RL2 is 71.62mo1%; The 16S rDNA genes of RL2 and D. radiodurans type strain DSM20539 shows a high level of similarity (97.2%). According to phenotypic characteristics and phylogenetic analysis, it can be suggested that the strain RL2 has been identified as Deinococcus. sp and it may be a novel species. (authors)

Repair of the double-strand breaks produced by /sup 125/I disintegrations in the DNA of micrococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Myers, D K [Atomic Energy of Canada Ltd., Chalk River, Ontario. Chalk River Nuclear Labs.

1978-01-01

Wild-type M. radiodurans and two radiosensitive mutants were used to study the lethal effects of /sup 125/I disintegrations in their DNA. The relative sensitivities of these three strains to inactivation by ..gamma..-radiation were reflected in their relative sensitivities to inactivation by /sup 125/I decay. The number of double-strand (ds) breaks in the DNA appeared to be similar at levels of ..gamma..-radiation and of /sup 125/I decay that reduced survival to 10%. All three strains of M. radiodurans rapidly repaired ds breaks produced in their DNA by either ..gamma..-radiation or /sup 125/I disintegrations. If one ds break per cell is a lethal event (Krisch. et al., 1975), cells of the three strains tested would die when they had left unrepaired one ds break out of an initial 45, 600 or 1800 ds breaks per single cell.

Rescue of Mitomycin C- or Psoralen-Inactivated Micrococcus Radiodurans by Additional Exposure to Radiation or Alkylating Agents

DEFF Research Database (Denmark)

Hansen, M. Trier

1982-01-01

The processing of damaged DNA was altered in a mitomycin C-sensitive mutant (mtcA) of Micrococcus radiodurans. Even though the mutant retained resistance to 254-nm UV radiation, it did not, in contrast to the wild-type strain, show any excessive DNA degradation or cell death when incubated...

Bacteriophytochrome controls carotenoid-independent response to photodynamic stress in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7.

Science.gov (United States)

Kumar, Santosh; Kateriya, Suneel; Singh, Vijay Shankar; Tanwar, Meenakshi; Agarwal, Shweta; Singh, Hina; Khurana, Jitendra Paul; Amla, Devinder Vijay; Tripathi, Anil Kumar

2012-01-01

Ever since the discovery of the role of bacteriophytochrome (BphP) in inducing carotenoid synthesis in Deinococcus radiodurans in response to light the role of BphPs in other non-photosynthetic bacteria is not clear yet. Azospirillum brasilense, a non-photosynthetic rhizobacterium, harbours a pair of BphPs out of which AbBphP1 is a homolog of AtBphP1 of Agrobacterium tumefaciens. By overexpression, purification, biochemical and spectral characterization we have shown that AbBphP1 is a photochromic bacteriophytochrome. Phenotypic study of the ΔAbBphP1 mutant showed that it is required for the survival of A. brasilense on minimal medium under red light. The mutant also showed reduced chemotaxis towards dicarboxylates and increased sensitivity to the photooxidative stress. Unlike D. radiodurans, AbBphP1 was not involved in controlling carotenoid synthesis. Proteome analysis of the ΔAbBphP1 indicated that AbBphP1 is involved in inducing a cellular response that enables A. brasilense in regenerating proteins that might be damaged due to photodynamic stress.

Origin of cell surface proteins released from Micrococcus radiodurans by ionizing radiation

International Nuclear Information System (INIS)

Mitchel, R.E.J.

1975-01-01

The exposure of Micrococcus radiodurans to sublethal doses of ionizing radiation causes the release of certain proteins into the surrounding medium. As estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, these proteins range from approximately 20,000 to 125,000 daltons. At least some of the proteins, including an exonuclease, have a surface location and appear to originate from the lipid-rich midwall layer. The exonuclease has two functionally distinct locations, one with its active site available to external substrate and a second with the active site masked from the exterior. Ionizing radiation releases both the masked and unmasked activity into the surrounding medium

Effects of oxygen during γ-irradiation of Micrococcus radiodurans

International Nuclear Information System (INIS)

Myers, D.K.; Johnson, L.D.

1977-01-01

A study has been made of the effects of oxygen on the yield of double strand breaks in the DNA of Micrococcus radiodurans, and of the relation of these effects to cell death. The o.e.r. values for cell survival were considerably smaller than those for the yield of double strand breaks, although they showed similar trends after irradiation in different media. The o.e.r. values for the inhibition of post-irradiation enzymatic repair were similar to those for cell survival. The o.e.r. for radiation-induced breaks in DNA therefore seems to depend on radiochemical reactions that are occurring during irradiation rather than on a preferential enzymatic repair of those strand breaks that are produced by anoxic irradiation. Cell survival depends less on the number of double strand breaks produced than on the ability of the cell to repair the double strand breaks. The maximum yield of double strand breaks after oxic γ-irradiation was approximately 1.7 breaks/krad/10 10 Daltons, corresponding to 1 break per 610 eV. (U.K.)

Effects of oxygen during. gamma. irradiation of Micrococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Myers, D K; Johnson, L D [Atomic Energy of Canada Ltd., Chalk River, Ontario. Chalk River Nuclear Labs.

1977-09-01

A study has been made of the effects of oxygen on the yield of double strand breaks in the DNA of Micrococcus radiodurans, and of the relation of these effects to cell death. The OER values for cell survival were considerably smaller than those for the yield of double strand breaks, although they showed similar trends after irradiation in different media. The OER values for the inhibition of post-irradiation enzymatic repair were similar to those for cell survival. The OER for radiation-induced breaks in DNA therefore seems to depend on radiochemical reactions that are occurring during irradiation rather than on a preferential enzymatic repair of those strand breaks that are produced by anoxic irradiation. Cell survival depends less on the number of double strand breaks produced than on the ability of the cell to repair the double strand breaks. The maximum yield of double strand breaks after oxic ..gamma.. irradiation was approximately 1.7 breaks/krad/10/sup 10/Daltons, corresponding to 1 break per 610 eV.

Radiation-induced enhancement of enzymatic cell lysis of Micrococcus radiodurans

International Nuclear Information System (INIS)

Watanabe, H.; Takehisa, M.; Iizuka, H.

1981-01-01

The intact cells of M. radiodurans were rendered sensitive to the action of lytic enzyme (P2-2 enzyme) by irradiation. The radiation-induced enhancement of cell lysis with P2-2 enzyme was completely prevented by the addition of t-butanol and irradiation at liquid nitrogen temperature. These results indicate that the enhancement is due to indirect action resulting from OH radicals. Cell lysis by lysozyme was enhanced only when the cells were irradiated under N 2 O. The enhancement of cell lysis with lysozyme was also prevented by adding alcohols. On the other hand, when lipid components in cells were removed by extraction with n-butanol, the radiation-induced enhancement of cell lysis with P2-2 enzyme and lysozyme was not observed. From these results it is concluded that the enhancement of enzymatic cell lysis by irradiation is attributable to alteration in the lipid-rich layer of the cell wall caused by OH radicals

Radiation-induced enhancement of enzymatic cell lysis of Micrococcus radiodurans

Energy Technology Data Exchange (ETDEWEB)

Watanabe, H.; Takehisa, M. [Japan Atomic Energy Research Inst., Takasaki, Gunma, Takasaki Radiation Chemistry Research Establishment (Japan); Iizuka, H.

1981-10-15

The intact cells of M. radiodurans were rendered sensitive to the action of lytic enzyme (P2-2 enzyme) by irradiation. The radiation-induced enhancement of cell lysis with P2-2 enzyme was completely prevented by the addition of t-butanol and irradiation at liquid nitrogen temperature. These results indicate that the enhancement is due to indirect action resulting from OH radicals. Cell lysis by lysozyme was enhanced only when the cells were irradiated under N{sub 2}O. The enhancement of cell lysis with lysozyme was also prevented by adding alcohols. On the other hand, when lipid components in cells were removed by extraction with n-butanol, the radiation-induced enhancement of cell lysis with P2-2 enzyme and lysozyme was not observed. From these results it is concluded that the enhancement of enzymatic cell lysis by irradiation is attributable to alteration in the lipid-rich layer of the cell wall caused by OH radicals.

Cell lysis and superoxide dismutase activities of highly radioresistant bacteria

Energy Technology Data Exchange (ETDEWEB)

Yoshinaka, T; Yano, K; Yamaguchi, H [Tokyo Univ. (Japan). Faculty of Agriculture

1976-01-01

The highly radioresistant bacterium, Arthrobacter radiotolerans, has been isolated from the radioactive hot spring of Misasa, and it does not sporulate, it is Gram-positive, and its color is pink to red. This bacterium shows the highest resistance to gamma-ray among Gram-positive resistants, but the lytic enzyme capable of lysing the cells of strong radioresistants and the surface structure of the cells are little known except those about Micrococcus radiodurans. The cells of the M. radiodurans can be lysed by Achramobacter lyticus enzyme, and electron microscopic observation and chemical analysis revealed the mutilayered surface structure of the cells consisting of an inner membrane, a mucopeptide wall layer and a very outer layer. The superoxide dismutase (SOD) activity of aerobic and anaerobic bacteria was studied, and the relatively high SOD activity of the M. radiodurans was found. The SOD function acts against the threat posed by the reactive superoxide radical being generated biologically, photochemically and radiochemically in the presence of molecular oxygen. In this paper, it is reported that the lytic enzyme No.2 obtained from Cytophaga sp., containing N-acetyl-muramyl-L-alanine amidase, peptidase and endopeptidase, and showing broad lytic spectra, was able to lyse the cells of A. radiotolerans and four radioresistant micrococci, and the radioresistant bacteria showedrelatively high SOD activity except M. sp. 248. It is well known that superoxide anions are generated by aerobic irradiation, and are toxic to microbial cells.

Cell lysis and superoxide dismutase activities of highly radioresistant bacteria

International Nuclear Information System (INIS)

Yoshinaka, Taeko; Yano, Keiji; Yamaguchi, Hikoyuki

1976-01-01

The highly radioresistant bacterium, Arthrobacter radiotolerans, has been isolated from the radioactive hot spring of Misasa, and it does not sporulate, it is Gram-positive, and its color is pink to red. This bacterium shows the highest resistance to gamma-ray among Gram-positive resistants, but the lytic enzyme capable of lysing the cells of strong radioresistants and the surface structure of the cells are little known except those about Micrococcus radiodurans. The cells of the M. radiodurans can be lysed by Achramobacter lyticus enzyme, and electron microscopic observation and chemical analysis revealed the mutilayered surface structure of the cells consisting of an inner membrane, a mucopeptide wall layer and a very outer layer. The superoxide dismutase (SOD) activity of aerobic and anaerobic bacteria was studied, and the relatively high SOD activity of the M. radiodurans was found. The SOD function acts against the threat posed by the reactive superoxide radical being generated biologically, photochemically and radiochemically in the presence of molecular oxygen. In this paper, it is reported that the lytic enzyme No.2 obtained from Cytophaga sp., containing N-acetyl-muramyl-L-alanine amidase, peptidase and endopeptidase, and showing broad lytic spectra, was able to lyse the cells of A. radiotolerans and four radioresistant micrococci, and the radioresistant bacteria showed relatively high SOD activity except M. sp. 248. It is well known that superoxide anions are generated by aerobic irradiation, and are toxic to microbial cells. (Kako, I.)

Methanosarcina acetivorans 16S rRNA and transcription factor nucleotide fluctuation with implications in exobiology and pathology

Science.gov (United States)

Holden, Todd; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Sullivan, R.; Schneider, P.; Flamholz, A.; Marchese, P.; Hiciano, O.; Yao, H.; Lieberman, D.; Cheung, T.

2008-08-01

Cultures of the methane-producing archaea Methanosarcina, have recently been isolated from Alaskan sediments. It has been proposed that methanogens are strong candidates for exobiological life in extreme conditions. The spatial environmental gradients, such as those associated with the polygons on Mars' surface, could have been produced by past methanogenesis activity. The 16S rRNA gene has been used routinely to classify phenotypes. Using the fractal dimension of nucleotide fluctuation, a comparative study of the 16S rRNA nucleotide fluctuation in Methanosarcina acetivorans C2A, Deinococcus radiodurans, and E. coli was conducted. The results suggest that Methanosarcina acetivorans has the lowest fractal dimension, consistent with its ancestral position in evolution. Variation in fluctuation complexity was also detected in the transcription factors. The transcription factor B (TFB) was found to have a higher fractal dimension as compared to transcription factor E (TFE), consistent with the fact that a single TFB in Methanosarcina acetivorans can code three different TATA box proteins. The average nucleotide pair-wise free energy of the DNA repair genes was found to be highest for Methanosarcina acetivorans, suggesting a relatively weak bonding, which is consistent with its low prevalence in pathology. Multitasking capacity comparison of type-I and type-II topoisomerases has been shown to correlate with fractal dimension using the methicillin-resistant strain MRSA 252. The analysis suggests that gene adaptation in a changing chemical environment can be measured in terms of bioinformatics. Given that the radiation resistant Deinococcus radiodurans is a strong candidate for an extraterrestrial origin and that the cold temperature Psychrobacter cryohalolentis K5 can function in Siberian permafrost, the fractal dimension comparison in this study suggests that a chemical resistant methanogen could exist in extremely cold conditions (such as that which existed on early

Destruction of Raman biosignatures by ionising radiation and the implications for life detection on Mars.

Science.gov (United States)

Dartnell, Lewis R; Page, Kristian; Jorge-Villar, Susana E; Wright, Gary; Munshi, Tasnim; Scowen, Ian J; Ward, John M; Edwards, Howell G M

2012-04-01

Raman spectroscopy has proven to be a very effective approach for the detection of microorganisms colonising hostile environments on Earth. The ExoMars rover, due for launch in 2018, will carry a Raman laser spectrometer to analyse samples of the martian subsurface collected by the probe's 2-m drill in a search for similar biosignatures. The martian surface is unprotected from the flux of cosmic rays, an ionising radiation field that will degrade organic molecules and so diminish and distort the detectable Raman signature of potential martian microbial life. This study employs Raman spectroscopy to analyse samples of two model organisms, the cyanobacterium Synechocystis sp. PCC 6803 and the extremely radiation resistant polyextremophile Deinococcus radiodurans, that have been exposed to increasing doses of ionising radiation. The three most prominent peaks in the Raman spectra are from cellular carotenoids: deinoxanthin in D. radiodurans and β-carotene in Synechocystis. The degradative effect of ionising radiation is clearly seen, with significant diminishment of carotenoid spectral peak heights after 15 kGy and complete erasure of Raman biosignatures by 150 kGy of ionising radiation. The Raman signal of carotenoid in D. radiodurans diminishes more rapidly than that of Synechocystis, believed to be due to deinoxanthin acting as a superior scavenger of radiolytically produced reactive oxygen species, and so being destroyed more quickly than the less efficient antioxidant β-carotene. This study highlights the necessity for further experimental work on the manner and rate of degradation of Raman biosignatures by ionising radiation, as this is of prime importance for the successful detection of microbial life in the martian near subsurface.

Identification and Characterization of uvrA, a DNA Repair Gene of Deinococcus radiodurans

Science.gov (United States)

1996-01-01

alkylating agents , such as methyl-N-nitro~N~nitrosoguanidine(MNNG), N-methyl-N~ nitrosourea (MNU), and to a lesser extent methyl methanesulfonate (MMS...6,4) Photoproduct 17 c. Thymine Glycols and Cross-links 17 3. Ionizing Radiation Damage " 17 4. Chemical Damage 20 a. Alkylating Agents .20 b. Cross...Examples of base damage induced by ionizing radiation 19 6. Nucleotide centers in DNA that are most reactive to alkylating agents 21 7. Schematic

Involvement of hydroxyl radicals in the release by ionizing radiation of a cell surface nuclease from Micorcoccus radiodurans

International Nuclear Information System (INIS)

Mitchel, R.E.J.

1975-01-01

The ionizing radiation-induced release of a surface exonuclease from Micrococcus radiodurans is to a large extent inhibited by the removal of water. Irradiation of a cell suspension saturated with O 2 (an effective aqueous electron and hydrogen atom scavenger) allows the same release as irradiation in the presence of N 2 . Ethanol (a good hydroxyl radical scavenger) protects the enzyme from release. These data suggest that hydroxyl radicals produced by the radiolysis of water are important releasing agents. Hydroxyl radicals produced by the ultraviolet decomposition of H 2 O 2 were effective in releasing the enzyme

Epigenetic changes of DNA repair genes in cancer.

Science.gov (United States)

Lahtz, Christoph; Pfeifer, Gerd P

2011-02-01

'Every Hour Hurts, The Last One Kills'. That is an old saying about getting old. Every day, thousands of DNA damaging events take place in each cell of our body, but efficient DNA repair systems have evolved to prevent that. However, our DNA repair system and that of most other organisms are not as perfect as that of Deinococcus radiodurans, for example, which is able to repair massive amounts of DNA damage at one time. In many instances, accumulation of DNA damage has been linked to cancer, and genetic deficiencies in specific DNA repair genes are associated with tumor-prone phenotypes. In addition to mutations, which can be either inherited or somatically acquired, epigenetic silencing of DNA repair genes may promote tumorigenesis. This review will summarize current knowledge of the epigenetic inactivation of different DNA repair components in human cancer.

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

Energy Technology Data Exchange (ETDEWEB)

Daly, Michael J.

2005-06-01

Natural selection in highly radioactive waste sites may yield bacteria with favorable bioremediating characteristics. However, until recently the microbial ecology of such environments has remained unexplored because of the high costs and technical complexities associated with extracting and characterizing samples from such sites. We have examined the bacterial ecology within radioactive sediments from a high-level nuclear waste plume in the vadose zone on the DOE?s Hanford Site in south-central Washington state (Fredrickson et al, 2004). Manganese-dependent, radiation resistant bacteria have been isolated from this contaminated site including the highly Mn-dependent Deinococcus and Arthrobacter spp.

Construction and characterization of novel stress-responsive Deinococcal biosensors

International Nuclear Information System (INIS)

Joe, Min Ho; Lim, Sang Youg

2012-01-01

In this research, we constructed a recombinant whole-cell biosensor to detect mutagens (H2O2, mitomycin C, MNNG, bleomycin) using Deinococcus radiodurans and evaluated its possibility for actual application. We performed DNA microarray analysis and selected 10 candidate genes for biosensor recombinant plasmid construction. The expression of ddrA, ddrB, DR 0 161, DR 0 589, and pprA was highly increased after treatment of the target mutagens. Putative promoter region of the genes were used for LacZ-based biosensor plasmid construction by replacing groESL promoter of pRADZ3. Pormoter activity and specificity of the five recombinant LacZ-based biosensor strains harboring the recombinant plasmids was measured. The result indicated that the promoter region of ddrA is the most suitable promoter for the biosensor development. Red pigment-based biosensor plasmid was constructed by displacing lacZ with crtI. The sensor strain was constructed by transforming the sensor plasmid into crtI deleted mutant D. radiodurans strain. Finally, macroscopic detection of the target mutagens by the biosensor strain was evaluated. The strength of red pigment biosynthesis by this recombinant strain in response to the target mutagens was weaker than our expectation. Continuous damage to the sensor strain by the mutagens in the medium might be the main reason for this low red-pigment biosynthesis. Therefore, we propose that the LacZ-based biosensor is more effective than the biosensor using red pigment as indicator for the mutagen detection

The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction

Science.gov (United States)

Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.

1989-01-01

Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

Molecular identification of phosphate solubilizing bacterium ...

African Journals Online (AJOL)

A phosphate solubilizing bacterium was isolated from the rhizosphere soil of upland rice and identified by 16S rRNA gene sequencing. The gene sequence showed 99% homology with Alcaligenes faecalis. Based on the gene sequence homology, it was identified as A. faecalis. Interaction effect of this bacterium on growth ...

Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics

Energy Technology Data Exchange (ETDEWEB)

Callister, Stephen J.; Barry, Richard C.; Adkins, Joshua N.; Johnson, Ethan T.; Qian, Weijun; Webb-Robertson, Bobbie-Jo M.; Smith, Richard D.; Lipton, Mary S.

2006-02-01

Central tendency, linear regression, locally weighted regression, and quantile techniques were investigated for normalization of peptide abundance measurements obtained from high-throughput liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS). Arbitrary abundances of peptides were obtained from three sample sets, including a standard protein sample, two Deinococcus radiodurans samples taken from different growth phases, and two mouse striatum samples from control and methamphetamine-stressed mice (strain C57BL/6). The selected normalization techniques were evaluated in both the absence and presence of biological variability by estimating extraneous variability prior to and following normalization. Prior to normalization, replicate runs from each sample set were observed to be statistically different, while following normalization replicate runs were no longer statistically different. Although all techniques reduced systematic bias, assigned ranks among the techniques revealed significant trends. For most LC-FTICR MS analyses, linear regression normalization ranked either first or second among the four techniques, suggesting that this technique was more generally suitable for reducing systematic biases.

Bacterial and archaeal resistance to ionizing radiation

Energy Technology Data Exchange (ETDEWEB)

Confalonieri, F; Sommer, S, E-mail: fabrice.confalonieri@u-psud.fr, E-mail: suzanne.sommer@u-psud.fr [University Paris-Sud, CNRS UMR8621, Institut de Genetique et Microbiologie, Batiments 400-409, Universite Paris-Sud, 91405 Orsay (France)

2011-01-01

Organisms living in extreme environments must cope with large fluctuations of temperature, high levels of radiation and/or desiccation, conditions that can induce DNA damage ranging from base modifications to DNA double-strand breaks. The bacterium Deinococcus radiodurans is known for its resistance to extremely high doses of ionizing radiation and for its ability to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Recently, extreme ionizing radiation resistance was also generated by directed evolution of an apparently radiation-sensitive bacterial species, Escherichia coli. Radioresistant organisms are not only found among the Eubacteria but also among the Archaea that represent the third kingdom of life. They present a set of particular features that differentiate them from the Eubacteria and eukaryotes. Moreover, Archaea are often isolated from extreme environments where they live under severe conditions of temperature, pressure, pH, salts or toxic compounds that are lethal for the large majority of living organisms. Thus, Archaea offer the opportunity to understand how cells are able to cope with such harsh conditions. Among them, the halophilic archaeon Halobacterium sp and several Pyrococcus or Thermococcus species, such as Thermococcus gammatolerans, were also shown to display high level of radiation resistance. The dispersion, in the phylogenetic tree, of radioresistant prokaryotes suggests that they have independently acquired radioresistance. Different strategies were selected during evolution including several mechanisms of radiation byproduct detoxification and subtle cellular metabolism modifications to help cells recover from radiation-induced injuries, protection of proteins against oxidation, an efficient DNA repair tool box, an original pathway of DNA double-strand break repair, a condensed nucleoid that may prevent the dispersion of the DNA fragments and specific radiation-induced proteins involved in

Bacterium oxidizing carbon monoxide

Energy Technology Data Exchange (ETDEWEB)

Kistner, A

1953-01-01

Present-day knowledge of the microbiological oxidation of carbon monoxide is based on doubtful observations and imperfect experimental procedures. By making use of shake cultures in contact with gas mixtures containing high concentrations of CO and by employing liquid enrichment media with a low content of organic matter and solid media of the same composition with not more than 1.2% agar, it proved possible to isolate a co-oxidizing bacterium of the genus hydrogenomonas from sewage sludge. For the first time irrefutable proof has been given of the oxidation of carbon monoxide by a pure culture of a bacterium, both in growing cultures and in resting cell suspensions. 12 references.

Construction and characterization of novel stress-responsive Deinococcal biosensors

Energy Technology Data Exchange (ETDEWEB)

Joe, Min Ho; Lim, Sang Youg

2012-01-15

In this research, we constructed a recombinant whole-cell biosensor to detect mutagens (H2O2, mitomycin C, MNNG, bleomycin) using Deinococcus radiodurans and evaluated its possibility for actual application. We performed DNA microarray analysis and selected 10 candidate genes for biosensor recombinant plasmid construction. The expression of ddrA, ddrB, DR{sub 0}161, DR{sub 0}589, and pprA was highly increased after treatment of the target mutagens. Putative promoter region of the genes were used for LacZ-based biosensor plasmid construction by replacing groESL promoter of pRADZ3. Pormoter activity and specificity of the five recombinant LacZ-based biosensor strains harboring the recombinant plasmids was measured. The result indicated that the promoter region of ddrA is the most suitable promoter for the biosensor development. Red pigment-based biosensor plasmid was constructed by displacing lacZ with crtI. The sensor strain was constructed by transforming the sensor plasmid into crtI deleted mutant D. radiodurans strain. Finally, macroscopic detection of the target mutagens by the biosensor strain was evaluated. The strength of red pigment biosynthesis by this recombinant strain in response to the target mutagens was weaker than our expectation. Continuous damage to the sensor strain by the mutagens in the medium might be the main reason for this low red-pigment biosynthesis. Therefore, we propose that the LacZ-based biosensor is more effective than the biosensor using red pigment as indicator for the mutagen detection.

Biofilms and planktonic cells of Deinococcus geothermalis in extreme environments

Science.gov (United States)

Panitz, Corinna; Reitz, Guenther; Rabbow, Elke; Rettberg, Petra; Flemming, Hans-Curt; Wingender, Jost; Froesler, Jan

In addition to the several extreme environments on Earth, Space can be considered as just another exceptional environment with a unique mixture of stress factors comprising UV radiation, vacuum, desiccation, temperature, ionizing radiation and microgravity. Life that processes in these environments can depend on the life forms and their state of living. The question is whether there are different strategies for individual microorganisms compared to communities of the same organisms to cope with the different factors of their surroundings. Comparative studies of the survi-val of these communities called biofilms and planktonic cell samples of Deinococcus geothermalis stand at the focal point of the presented investigations. A biofilm is a structured community of microorganisms that live encapsulated in a matrix of extracellular polymeric substances on a surface. Microorganisms living in a biofilm usually have significantly different properties to cooperate than individually living microorganisms of the same species. An advantage of the biofilm is increased resistance to various chemical and physical effects, while the dense extracellular matrix and the outer layer of the cells protect the interior of the microbial consortium. The space experiment BOSS (Biofilm organisms surfing Space) as part the ESA experimental unit EXPOSE R-2 with a planned launch date in July 2014 will be subsequently mounted on the Russian Svesda module outside the ISS. An international team of scientists coordinated by Dr. P. Rettberg will investigate the hypothesis whether microorganisms organized as biofilm outmatch the same microorganisms exposed individually in the long-term survival of the harsh environmental conditions as they occur in space and on Mars. Another protective function in the samples could be dust par-ticles for instance Mars regolith simulant contained inside the biofilms or mixed with the planktonic cells, as additional shelter especially against the extraterrestrial UV

Synthesis of Hyperbranched Glycoconjugates by the Combined Action of Potato Phosphorylase and Glycogen Branching Enzyme from Deinococcus geothermalis

Directory of Open Access Journals (Sweden)

Katja Loos

2012-02-01

Full Text Available Potato phosphorylase is able to synthesize linear polyglucans from maltoheptaose primers. By coupling maltoheptaose to butane diamine, tris(2-aminoethylamine and amine functionalized amine functionalized poly ethyleneglycol (PEG, new primer molecules became available. The resulting di-, tri- and macro-primers were incubated with potato phosphorylase and glycogen branching enzyme from Deinococcus geothermalis. Due to the action of both enzymes, hyperbranched polyglucan arms were grown from the maltoheptaose derivatives with a maximum degree of branching of 11%. The size of the synthesized hyperbranched polyglucans could be controlled by the ratio monomer over primer. About 60%–80% of the monomers were incorporated in the glycoconjugates. The resulting hyperbranched glycoconjugates were subjected to Dynamic Light Scattering (DLS measurements in order to determine the hydrodynamic radius and it became obvious that the structures formed agglomerates in the range of 14–32 nm.

MODELING OF MIXED CHEMOSTAT CULTURES OF AN AEROBIC BACTERIUM, COMAMONAS-TESTOSTERONI, AND AN ANAEROBIC BACTERIUM, VEILLONELLA-ALCALESCENS - COMPARISON WITH EXPERIMENTAL-DATA

NARCIS (Netherlands)

GERRITSE, J; SCHUT, F; GOTTSCHAL, JC

A mathematical model of mixed chemostat cultures of the obligately aerobic bacterium Comamonas testosteroni and the anaerobic bacterium Veillonella alcalescens grown under dual limitation Of L-lactate and oxygen was constructed. The model was based on Michaelis-Menten-type kinetics for the

Engineering a wild fast-growing Mycoplasma bacterium to generate ...

International Development Research Centre (IDRC) Digital Library (Canada)

2018-01-12

Jan 12, 2018 ... The CCPP bacterium causes sick animals to experience severe symptoms ... because antibiotic treatment does not eliminate the responsible bacterium. ... To develop a fast growing CCPP vaccine for cheaper production and ...

Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria-A Challenge for Life on Mars.

Science.gov (United States)

Bak, Ebbe N; Larsen, Michael G; Moeller, Ralf; Nissen, Silas B; Jensen, Lasse R; Nørnberg, Per; Jensen, Svend J K; Finster, Kai

2017-01-01

The habitability of Mars is determined by the physical and chemical environment. The effect of low water availability, temperature, low atmospheric pressure and strong UV radiation has been extensively studied in relation to the survival of microorganisms. In addition to these stress factors, it was recently found that silicates exposed to simulated saltation in a Mars-like atmosphere can lead to a production of reactive oxygen species. Here, we have investigated the stress effect induced by quartz and basalt abraded in Mars-like atmospheres by examining the survivability of the three microbial model organisms Pseudomonas putida, Bacillus subtilis , and Deinococcus radiodurans upon exposure to the abraded silicates. We found that abraded basalt that had not been in contact with oxygen after abrasion killed more than 99% of the vegetative cells while endospores were largely unaffected. Exposure of the basalt samples to oxygen after abrasion led to a significant reduction in the stress effect. Abraded quartz was generally less toxic than abraded basalt. We suggest that the stress effect of abraded silicates may be caused by a production of reactive oxygen species and enhanced by transition metal ions in the basalt leading to hydroxyl radicals through Fenton-like reactions. The low survivability of the usually highly resistant D. radiodurans indicates that the effect of abraded silicates, as is ubiquitous on the Martian surface, would limit the habitability of Mars as well as the risk of forward contamination. Furthermore, the reactivity of abraded silicates could have implications for future manned missions, although the lower effect of abraded silicates exposed to oxygen suggests that the effects would be reduced in human habitats.

Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria—A Challenge for Life on Mars

Directory of Open Access Journals (Sweden)

Ebbe N. Bak

2017-09-01

Full Text Available The habitability of Mars is determined by the physical and chemical environment. The effect of low water availability, temperature, low atmospheric pressure and strong UV radiation has been extensively studied in relation to the survival of microorganisms. In addition to these stress factors, it was recently found that silicates exposed to simulated saltation in a Mars-like atmosphere can lead to a production of reactive oxygen species. Here, we have investigated the stress effect induced by quartz and basalt abraded in Mars-like atmospheres by examining the survivability of the three microbial model organisms Pseudomonas putida, Bacillus subtilis, and Deinococcus radiodurans upon exposure to the abraded silicates. We found that abraded basalt that had not been in contact with oxygen after abrasion killed more than 99% of the vegetative cells while endospores were largely unaffected. Exposure of the basalt samples to oxygen after abrasion led to a significant reduction in the stress effect. Abraded quartz was generally less toxic than abraded basalt. We suggest that the stress effect of abraded silicates may be caused by a production of reactive oxygen species and enhanced by transition metal ions in the basalt leading to hydroxyl radicals through Fenton-like reactions. The low survivability of the usually highly resistant D. radiodurans indicates that the effect of abraded silicates, as is ubiquitous on the Martian surface, would limit the habitability of Mars as well as the risk of forward contamination. Furthermore, the reactivity of abraded silicates could have implications for future manned missions, although the lower effect of abraded silicates exposed to oxygen suggests that the effects would be reduced in human habitats.

Zymomonas mobilis: a bacterium for ethanol production

Energy Technology Data Exchange (ETDEWEB)

Baratti, J.C.; Bu' Lock, J.D.

1986-01-01

Zymomonas mobilis is a facultative anaerobic gram negative bacterium first isolated in tropical countries from alcoholic beverages like the African palm wine, the Mexican pulque and also as a contaminant of cider (cider sickness) or beer in the European countries. It is one of the few facultative anaerobic bacteria degrading glucose by the Entner-Doudoroff pathway usually found in strictly aerobic microorganisms. Some work was devoted to this bacterium in the 50s and 60s and was reviewed by Swings and De Ley in their classical paper published in 1977. During the 70s there was very little work on the bacterium until 1979 and the first report by the Australian group of P.L. Rogers on the great potentialities of Z. mobilis for ethanol production. At that time the petroleum crisis had led the developed countries to search for alternative fuel from renewable resources. The Australian group clearly demonstrated the advantages of the bacterium compared to the yeasts traditionally used for the alcoholic fermentation. As a result, there was a considerable burst in the Zymomonas literature which started from nearly zero in the late 70s to attain 70 papers published in the field in 1984. In this article, papers published from 1982 to 1986 are reviewed.

Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

Energy Technology Data Exchange (ETDEWEB)

Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

1994-06-01

The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

Spectroscopic investigation of ionizing-radiation tolerance of a Chlorophyceae green micro-alga

Energy Technology Data Exchange (ETDEWEB)

Farhi, E; Compagnon, E; Marzloff, V; Ollivier, J; Boisson, A M; Natali, F; Russo, D [Institut Laue-Langevin, BP 156, 38042 Grenoble cedex 9 (France); Rivasseau, C; Gromova, M; Bligny, R [CEA, Laboratoire de Physiologie Cellulaire Vegetale, 17 rue des Martyrs, 38054 Grenoble cedex 9 (France); Coute, A [Museum National d' Histoire Naturelle, Laboratoire de Cryptogamie, 2 rue Buffon, 75005 Paris (France)

2008-03-12

Micro-organisms living in extreme environments are captivating in the peculiar survival processes they have developed. Deinococcus radiodurans is probably the most famous radio-resistant bacteria. Similarly, a specific ecosystem has grown in a research reactor storage pool, and has selected organisms which may sustain radiative stress. An original green micro-alga which was never studied for its high tolerance to radiations has been isolated. It is the only autotrophic eukaryote that develops in this pool, although contamination possibilities coming from outside are not unusual. Studying what could explain this irradiation tolerance is consequently very interesting. An integrative study of the effects of irradiation on the micro-algae physiology, metabolism, internal dynamics, and genomics was initiated. In the work presented here, micro-algae were stressed with irradiation doses up to 20 kGy (2 Mrad), and studied by means of nuclear magnetic resonance, looking for modifications in the metabolism, and on the IN13 neutron backscattering instrument at the ILL, looking for both dynamics and structural macromolecular changes in the cells.

Manganese(II) induces cell division and increases in superoxide dismutase and catalase activities in an aging deinococcal culture

International Nuclear Information System (INIS)

Chou, F.I.; Tan, S.T.

1990-01-01

Addition of Mn(II) at 2.5 microM or higher to stationary-phase cultures of Deinococcus radiodurans IR was found to trigger at least three rounds of cell division. This Mn(II)-induced cell division (Mn-CD) did not occur when the culture was in the exponential or death phase. The Mn-CD effect produced daughter cells proportionally reduced in size, pigmentation, and radioresistance but proportionally increased in activity and amount of the oxygen toxicity defense enzymes superoxide dismutase and catalase. In addition, the concentration of an Mn-CD-induced protein was found to remain high throughout the entire Mn-CD phase. It was also found that an untreated culture exhibited a growth curve characterized by a very rapid exponential-stationary transition and that cells which had just reached the early stationary phase were synchronous. Our results suggest the presence of an Mn(II)-sensitive mechanism for controlling cell division. The Mn-CD effect appears to be specific to the cation Mn(II) and the radioresistant bacteria, deinococci

Spectroscopic investigation of ionizing-radiation tolerance of a Chlorophyceae green micro-alga

International Nuclear Information System (INIS)

Farhi, E; Compagnon, E; Marzloff, V; Ollivier, J; Boisson, A M; Natali, F; Russo, D; Rivasseau, C; Gromova, M; Bligny, R; Coute, A

2008-01-01

Micro-organisms living in extreme environments are captivating in the peculiar survival processes they have developed. Deinococcus radiodurans is probably the most famous radio-resistant bacteria. Similarly, a specific ecosystem has grown in a research reactor storage pool, and has selected organisms which may sustain radiative stress. An original green micro-alga which was never studied for its high tolerance to radiations has been isolated. It is the only autotrophic eukaryote that develops in this pool, although contamination possibilities coming from outside are not unusual. Studying what could explain this irradiation tolerance is consequently very interesting. An integrative study of the effects of irradiation on the micro-algae physiology, metabolism, internal dynamics, and genomics was initiated. In the work presented here, micro-algae were stressed with irradiation doses up to 20 kGy (2 Mrad), and studied by means of nuclear magnetic resonance, looking for modifications in the metabolism, and on the IN13 neutron backscattering instrument at the ILL, looking for both dynamics and structural macromolecular changes in the cells

Plant breeding by using radiation mutation - Development of radiation indicator plants by molecular breeding

Energy Technology Data Exchange (ETDEWEB)

Liu, Jang Ryol; Kwak, Sang Soo; Kwon, Seok Yoon [Korea Research Institute of Bioscience and Biotechnology, Taejon (Korea)

2000-04-01

- tSOD1, cytosolic CuZnSOD cDNA was cloned from tobacco cDNA library by PCR. To develop the under-producing the transgenic plants, the vectors were constructed using by antisense and co-supressing technology. The transgenic tobacco plants were confirmed that over 60% of kanamycin-resistant plants were introduced the foreign gene by PCR and transformed one copy through Southern blot analysis. - In an attempt to identify marker genes for gamma irradiation of plants, expression patterns of diverse genes upon gamma irradiation of young tobacco plants were investigated. With the knowledge of distinctive expression patterns of diverse genes, irradiation-indicating marker plants could be developed by engineering and monitoring multiple radiation-responsive genes. Additionally, a gamma irradiation-responsive NtTMK1 receptor-like kinase gene was molecular biologically characterized. -Uranium reductase gene (Cytochrome C3) and radiation resistance gene (recA) have been cloned from Desulfovibrio and Deinococcus radiodurans. -Two plant transformation vectors (pCYC3 and pDrecA) have been constructed. - Tobacco transgenic plants of have been obtained. 52 refs., 5 figs. (Author)

Microflora of urogenital tract in pregnancy with asymptomatic bacterium

International Nuclear Information System (INIS)

Abdullaeva, R.A.

2006-01-01

The article contains results of research interrelationship from colonization of vagina and urinary tract diseases. E.coli one of the main factors in development asymptomatic bacterium. Presented high effects of penicillin medicaments and nitrofurans in treatment of asymptomatic bacterium

Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

NARCIS (Netherlands)

Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

1998-01-01

The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a

Loss of covalently linked lipid as the mechanism for radiation-induced release of membrane-bound polysaccharide and exonuclease from Micrococcus radiodurans

International Nuclear Information System (INIS)

Mitchel, R.E.J.

1981-01-01

The mechanism of γ-radiation-induced release of polysaccharide and exonuclease from the midwall membrane of Micrococcus radiodurans has been examined. These two components appear to be released independently, but by very similar processes. Direct analysis of radiation-released polysaccharide indicated the absence of an alkali-labile neutral lipid normally present in the native material. Radiation-induced release therefore probably results from the radiolytic cleavage of a covalently linked lipid which normally serves to anchor these substances to the membrane. The absence of a natural membrane-bound carotenoid had no effect on the rate of release of these components. Likewise, the absence of exonuclease in an exonuclease minus mutant did not influence the release of polysaccharide. It is suggested that the major pathway of radical transfer from the initiating .OH and culminating in the cleavage of the neutral lipid anchor may not be via the membrane

A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions

Directory of Open Access Journals (Sweden)

Lamparter Tilman

2006-03-01

Full Text Available Abstract Background Phytochromes are photoreceptors, discovered in plants, that control a wide variety of developmental processes. They have also been found in bacteria and fungi, but for many species their biological role remains obscure. This work concentrates on the phytochrome system of Agrobacterium tumefaciens, a non-photosynthetic soil bacterium with two phytochromes. To identify proteins that might share common functions with phytochromes, a co-distribution analysis was performed on the basis of protein sequences from 138 bacteria. Results A database of protein sequences from 138 bacteria was generated. Each sequence was BLASTed against the entire database. The homolog distribution of each query protein was then compared with the homolog distribution of every other protein (target protein of the same species, and the target proteins were sorted according to their probability of co-distribution under random conditions. As query proteins, phytochromes from Agrobacterium tumefaciens, Pseudomonas aeruginosa, Deinococcus radiodurans and Synechocystis PCC 6803 were chosen along with several phytochrome-related proteins from A. tumefaciens. The Synechocystis photosynthesis protein D1 was selected as a control. In the D1 analyses, the ratio between photosynthesis-related proteins and those not related to photosynthesis among the top 150 in the co-distribution tables was > 3:1, showing that the method is appropriate for finding partner proteins with common functions. The co-distribution of phytochromes with other histidine kinases was remarkably high, although most co-distributed histidine kinases were not direct BLAST homologs of the query protein. This finding implies that phytochromes and other histidine kinases share common functions as parts of signalling networks. All phytochromes tested, with one exception, also revealed a remarkably high co-distribution with glutamate synthase and methionine synthase. This result implies a general role of

Assessing fluctuating evolutionary pressure in yeast and mammal evolutionary rate covariation using bioinformatics of meiotic protein genetic sequences

Science.gov (United States)

Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Holden, T.; Lieberman, D.; Cheung, T.

2013-09-01

The evolutionary rate co-variation in meiotic proteins has been reported for yeast and mammal using phylogenic branch lengths which assess retention, duplication and mutation. The bioinformatics of the corresponding DNA sequences could be classified as a diagram of fractal dimension and Shannon entropy. Results from biomedical gene research provide examples on the diagram methodology. The identification of adaptive selection using entropy marker and functional-structural diversity using fractal dimension would support a regression analysis where the coefficient of determination would serve as evolutionary pathway marker for DNA sequences and be an important component in the astrobiology community. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, clinical trial targeted cancer gene CD47, SIRT6 in spermatogenesis, and HLA-C in mosquito bite immunology demonstrate the diagram classification methodology. Comparisons to the SEPT4-XIAP pair in stem cell apoptosis, testesexpressed taste genes TAS1R3-GNAT3 pair, and amyloid beta APLP1-APLP2 pair with the yeast-mammal DNA sequences for meiotic proteins RAD50-MRE11 pair and NCAPD2-ICK pair have accounted for the observed fluctuating evolutionary pressure systematically. Regression with high R-sq values or a triangular-like cluster pattern for concordant pairs in co-variation among the studied species could serve as evidences for the possible location of common ancestors in the entropy-fractal dimension diagram, consistent with an example of the human-chimp common ancestor study using the FOXP2 regulated genes reported in human fetal brain study. The Deinococcus radiodurans R1 Rad-A could be viewed as an outlier in the RAD50 diagram and also in the free energy versus fractal dimension regression Cook's distance, consistent with a non-Earth source for this radiation resistant bacterium. Convergent and divergent fluctuating evolutionary

[Unique properties of highly radioresistant bacteria].

Science.gov (United States)

Romanovskaia, V A; Rokitko, P V; Malashenko, Iu R

2000-01-01

In connection with the Chernobyl Nuclear Power Plant (ChNPP) accident and the negative ecological after-effects for biota in this zone the interest has arisen to radioresistant bacteria, as to the most dynamic model of the given ecosystem, and to mechanisms which provide resistance of bacteria to ionizing radiation. The analysis of published data has shown that the radioresistant bacteria are not interrelated taxonomically and phylogenetically. The extreme radioresistant bacteria are represented by the Deinococcus species, which form a group phylogenetically close to the line Thermus-Meiothermus. Other radioresistant bacteria are the representatives of the genera Rubrobacter, Methylobacterium, Kocuria, Bacillus and some archebacteria. Data on natural habitats, of radioresistant bacteria are not numerous. In a number of cases it is difficult to distinguish their natural habitats, as they were isolated from the samples which were previously exposed to X-ray or gamma-irradiation, or from the ecosystems with the naturally raised radioactivity. To understand the strategy of survival of radioresistant bacteria, we briefly reviewed the mechanism of action of various species of radiation on cells and macromolecules; physiological signs of the cell damage caused by radiation; mechanisms eliminating (repairing) these damages. More details on mechanisms of the DNA repair in D. radiodurans are described. The extreme resistance of D. radiodurans to the DNA damaging factors is defined by 1) repair mechanisms which fundamentally differ from those in other procaryotes; 2) ability to increase the efficiency of a standard set of the DNA repairing proteins. Literary and own data on the effect of radiation on survival of various groups of bacteria in natural ecosystems are summarized. The ecological consequences of the ChNPP accident for soil bacteria in this region were estimated. The reduction of the number of soil bacteria and recession of microbial diversity under the effect of

Limit for the Survivability from Potassium Decay of Bacterial Spores in Halite Fluid Inclusions

Science.gov (United States)

Kminek, G.; Bada, J. L.

2001-12-01

DNA damage-tolerant organism known today is Deinococcus radiodurans. The viability of D. radiodurans falls to undetectable levels6 at about 18 kGy. The survival curve of dry Bacillus megaterium spores shows a 4-log reduction at about 8-10 kGy7,8. These numbers can be compared to the 87 kGy in the case for a Permian fluid inclusion. The ability to tolerate radiation induced damage lies in the efficient repair mechanism employed by D. radiodurans, which is not operative in a dormant spore. It would thus be highly unusual for a bacterial spore to survive intact for 100's of millions of years unless these bacteria are extremely radiation tolerant. Based on these considerations and without active DNA repair mechanisms, viability of a dormant bacterial spore and the survival of viable genetic material over extended periods of geologic time is probably limited by exposure to natural background radiation. 1. Vreeland, R. H., Rosenzweig, W. D., Powers, D. W. Nature 407, 897-900 (2000) 2. Cano, P. J., Borucki, M. K. Science 268, 1060-1064 (1995) 3. Parkes, R. J.Nature, 407, 844-845 (2000) 4. Lindahl, T. Nature 362, 709-715 (1993) 5. Setlow, P. J. Bacteriol., 174 (9), 2737-2741 (1992) 6. Battista, J. R. Annu. Rev. Micriobiol. 51, 203-224 (1997) 7. Powers, E. L., Kaleta, B. F. Science 132, 959-960 (1960) 8. Ewing, D., Powers, E. L. Science 194, 1049-1051 (1976)

A probabilistic framework for microarray data analysis: fundamental probability models and statistical inference.

Science.gov (United States)

Ogunnaike, Babatunde A; Gelmi, Claudio A; Edwards, Jeremy S

2010-05-21

Gene expression studies generate large quantities of data with the defining characteristic that the number of genes (whose expression profiles are to be determined) exceed the number of available replicates by several orders of magnitude. Standard spot-by-spot analysis still seeks to extract useful information for each gene on the basis of the number of available replicates, and thus plays to the weakness of microarrays. On the other hand, because of the data volume, treating the entire data set as an ensemble, and developing theoretical distributions for these ensembles provides a framework that plays instead to the strength of microarrays. We present theoretical results that under reasonable assumptions, the distribution of microarray intensities follows the Gamma model, with the biological interpretations of the model parameters emerging naturally. We subsequently establish that for each microarray data set, the fractional intensities can be represented as a mixture of Beta densities, and develop a procedure for using these results to draw statistical inference regarding differential gene expression. We illustrate the results with experimental data from gene expression studies on Deinococcus radiodurans following DNA damage using cDNA microarrays. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Effect of pulsed electron beam on cell killing

International Nuclear Information System (INIS)

Acharya, Santhosh; Joseph, Praveen; Sanjeev, Ganesh; Narayana, Y.; Bhat, N.N.

2009-01-01

The extent of repairable and irreparable damage in a living cell produced by ionizing radiation depends on the quality of the radiation. In the case of sparsely ionizing radiation, the dose rate and the pattern of energy deposition of the radiation are the important physical factors which can affect the amount of damage in living cells. In the present study, radio-sensitive and radioresistive bacteria cells were exposed to 8 MeV pulsed electron beam and the efficiency of cell-killing was investigated to evaluate the Do, the mean lethal dose. The dose to the cell was delivered in micro-second pulses at an instantaneous dose rate of 2.6 x 10 5 Gy s -1 . Fricke dosimeter was used to measure the absorbed dose of electron beam. The results were compared with those of gamma rays. The survival curve of radio-resistive Deinococcus-radiodurans (DR) is found to be sigmoidal and the survival response for radio-sensitive Escherichia-coli (E-coli) is found to be exponential without any shoulder. Comparison of Do values indicate that irradiation with pulsed electron beam resulted in more cell-killing than was observed for gamma irradiation. (author)

Dense populations of a giant sulfur bacterium in Namibian shelf sediments

DEFF Research Database (Denmark)

Schulz, HN; Brinkhoff, T.; Ferdelman, TG

1999-01-01

A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA...

Moritella viscosa, a pathogenic bacterium affecting the fillet quality in fish

DEFF Research Database (Denmark)

Ingerslev, Hans-Christian; Nielsen, Michael Engelbrecht

2011-01-01

Moritella viscosa is a bacterium belonging to the family Moritellaceae and was formerly known as Vibrio viscosus. The name ‘viscosa’ originates from the slimy nature of the bacterium. M. viscosa is considered to be the main causative agent of the phenomenon ‘winter ulcer’ or ‘cold-water ulcer......’ which affects various fish species in seawater during cold periods (Lunder et al. 1995). The bacterium is mainly a problem for farmed salmonid species, such as Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but has also been isolated from other fish species, including Atlantic...... market price because of a quality downgrade caused by textural changes in the fillet....

Lactococcus lactis - a diploid bacterium

DEFF Research Database (Denmark)

Michelsen, Ole; Hansen, Flemming G.; Jensen, Peter Ruhdal

the next division. Thus, the regions of the chromosome that are the last to be replicated are haploid even in fast-growing bacteria. In contrast to this general rule for bacteria, we found that Lactococcus lactis, a bacterium which has been exploited for thousands of years for the production of fermented...... milk products, is born with two complete non-replicating chromosomes. L. lactis therefore remain diploid throughout its entire life cycle....

The role of cellular catalase on the radiosensitization of bacterial vegetative cells by N2O

International Nuclear Information System (INIS)

Watanabe, H.; Takehisa, M.

1983-01-01

The radiosensitizing effect of N 2 O on eight strains of bacteria was measured in dilute suspensions. The dose-modifying factors (DMF) of N 2 O on M. radiodurans R 1 , P. radiora O-1, M. lysodeikticus and B. pumilus E601 (vegetative cells) were 3.4, 2.9, 2.4 and 1.7, respectively. But P. radiora RP-C, P. fluorescens B3-1, E. coli B/r and E. coli K-12 were hardly sensitized by N 2 O. From measurements of catalase activity of each bacterium, it was found that the DMF increases with increased catalase activity, suggesting that cellular catalase promotes the sensitizing action of N 2 O. (author)

Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte.

Directory of Open Access Journals (Sweden)

Michele T Hoffman

Full Text Available Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA, often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales, but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales. Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions.

Expression and purification of PprI protein from D.radiodurans R1 in escherichia coli

International Nuclear Information System (INIS)

Zhang Yongqin; Zhou Hui; Chen Jie; Yang Zhanshan

2011-01-01

In order to express and purify PprI protein from D.radiodurans R1 in E. coli, the full length of pprI gene was gained by PCR amplification using pCMV-HA-pprI as a template. The gene segment was inserted into vector pET-28a after digested by two restriction endonucleases Nco I and EcoR I. Then the recombinant vector pET-28a-His-pprI was transfected into E. coli BL21(DE3) RP. The PprI protein expression was induced by IPTG and the fusion protein was confirmed by SDS-PAGE and Western blotting. The expressive conditions of the protein such as E. coli' A 600 , concentration of IPTG, time and temperature of culture, were optimized. Finally the fusion protein was purified by Ni-NTA His Bind Resins and molecule boult. The experimental results show the fusion protein confirmed by Western blotting is 6 x His-PprI and its molecular weight is 37 kDa. The ladders of PprI protein at molecular weight 37 kDa were different due to difference of the PprI protein expression conditions if E. coli. The PprI protein exists both in supernatant and precipitation. The concentration of purified protein is about 0.15 mg/mL which was measured by BCA method. It is concluded that the recombinant plasmid pET-28a-His-pprI is constructed and the PprI fusion protein is expressed and purified. The results lay a solid foundation for studying the radio-resistance and immunity of PprI protein. (authors)

Micrococcus radiodurans surface exonuclease. Dimer to monomer conversion by ionizing radiation-generated aqueous free radicals

Energy Technology Data Exchange (ETDEWEB)

Mitchel, R E.J.

1980-01-01

Micrococcus radiodurans possesses an exonuclease firmly bound to a middle cell wall membrane layer. Aqueous OH/sup -/ radicals generated chemically or by ionizing radiation cause the immediate release of this enzyme into the surrounding medium. The enzyme is located in a hydrophobic site and can also be released by aqueous n-butanol. When extracted by this solvent it is a non-covalently linked dimer and has a molecular weight of 260,000 as determined by gel filtration. When released by radiation generated OH/sup -/ radicals, the enzyme initially appears in solution as the dimer but is rapidly split by further aqueous radical attack into two 130,000 molecular weight subunits. Hydroxyl radicals are most effective but reducing radicals are also able to monomerize the enzyme. Only the released dimer enzyme is subject to free radical monomerization. Bound dimer enzyme is not split prior to release. No detectable loss of activity or change in catalytic properties accompanies the free radical cleavage of the enzyme. Both subunits of the dimer enzyme possess a tightly bound metal ion (probably Ca/sup 2 +/) required for activity. The monomer but not the dimer enzyme will bind to an anion exchanger. The monomer is susceptible to loss of its metal ion, and consequent inactivation, when exposed to the exchanger in the absence of Ca/sup 2 +/. Besides providing information on some of the immediate non-lethal effects of ionizing radiation, the behavior of this enzyme system demonstrates a potential cellular mechanism by which internally or externally generated free radicals could be utilized by the cell to control various enzymic reactions.

Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus

Directory of Open Access Journals (Sweden)

Lukasz Makowski

2016-11-01

Full Text Available Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase and replicating cells (the intracellular-growth phase. The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box (5’-NN(A/TTCCACA-3’. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus. We compared the architecture of the DnaA–oriC complexes (orisomes in homologous (oriC and DnaA from B. bacteriovorus and heterologous (BdoriC and DnaA from prey, E. coli or P. aeruginosa systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium.

Survival of thermophilic and hyper-thermophilic microorganisms after exposure to UV-C, ionizing radiation and desiccation

International Nuclear Information System (INIS)

Beblo, K.; Wirth, R.; Huber, H.; Douki, T.; Schmalz, G.; Rachel, R.

2011-01-01

In this study, we investigated the ability of several (hyper-) thermophilic Archaea and phylo-genetically deep-branching thermophilic Bacteria to survive high fluences of monochromatic UV-C (254 nm) and high doses of ionizing radiation, respectively. Nine out of fourteen tested microorganisms showed a surprisingly high tolerance against ionizing radiation, and two species (Aquifex pyrophilus and Ignicoccus hospitalis) were even able to survive 20 kGy. Therefore, these species had a comparable survivability after exposure to ionizing radiation such as Deinococcus radiodurans. In contrast, there was nearly no difference in survival of the tested strains after exposure to UV-C under anoxic conditions. If the cells had been dried in advance of UV-C irradiation, they were more sensitive to UV-C radiation compared with cells irradiated in liquid suspension; this effect could be reversed by the addition of protective material like sulfidic ores before irradiation. By exposure to UV-C, photoproducts were formed in the DNA of irradiated Archaea and Bacteria. The distribution of the main photoproducts was species specific, but the amount of the photoproducts was only partly dependent on the applied fluence. Overall, our results show that tolerance to radiation seems to be a common phenomenon among thermophilic and hyper-thermophilic microorganisms. (authors)

Survival of thermophilic and hyperthermophilic microorganisms after exposure to UV-C, ionizing radiation and desiccation.

Science.gov (United States)

Beblo, Kristina; Douki, Thierry; Schmalz, Gottfried; Rachel, Reinhard; Wirth, Reinhard; Huber, Harald; Reitz, Günther; Rettberg, Petra

2011-11-01

In this study, we investigated the ability of several (hyper-) thermophilic Archaea and phylogenetically deep-branching thermophilic Bacteria to survive high fluences of monochromatic UV-C (254 nm) and high doses of ionizing radiation, respectively. Nine out of fourteen tested microorganisms showed a surprisingly high tolerance against ionizing radiation, and two species (Aquifex pyrophilus and Ignicoccus hospitalis) were even able to survive 20 kGy. Therefore, these species had a comparable survivability after exposure to ionizing radiation such as Deinococcus radiodurans. In contrast, there was nearly no difference in survival of the tested strains after exposure to UV-C under anoxic conditions. If the cells had been dried in advance of UV-C irradiation, they were more sensitive to UV-C radiation compared with cells irradiated in liquid suspension; this effect could be reversed by the addition of protective material like sulfidic ores before irradiation. By exposure to UV-C, photoproducts were formed in the DNA of irradiated Archaea and Bacteria. The distribution of the main photoproducts was species specific, but the amount of the photoproducts was only partly dependent on the applied fluence. Overall, our results show that tolerance to radiation seems to be a common phenomenon among thermophilic and hyperthermophilic microorganisms.

Studies on the pathogenic bacterium of ulcer disease in Epinephelus awoara

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

Studies were conducted to determine the cause of the acute mortality of cage-cultured Epinephelus awoara in the Tong'an Bay of Xiamen, China during the summer of 2002. Predominant bacteria strain TS-628 was isolated from the diseased grouper. The virulence test confirmed that TS-628 was the pathogenic bacterium. Biochemical characteristics of the isolates were determined using the automatic bacterial identification system and standard tube tests. To further confirm the identification, a 1 121 bp 16S rRNA gene sequence of the isolate was amplified by PCR, which had been deposited into Genbank (accession number: AY747308). According to the biochemical characteristics and by comparing the 16S rRNA gene homology of the isolate, the pathogenic bacterium was identified as Vibrio harveyi. Drug sensitivity tests showed that this pathogenic bacterium was sensitive to 16 antibacterials, especially to chloramphenicol and actinospectacin, but completely resistant to antibacterials likes vancomycin, penicillin, lincomycin, and so on.

The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.

Science.gov (United States)

Woo, Patrick C Y; Lau, Susanna K P; Tse, Herman; Teng, Jade L L; Curreem, Shirly O T; Tsang, Alan K L; Fan, Rachel Y Y; Wong, Gilman K M; Huang, Yi; Loman, Nicholas J; Snyder, Lori A S; Cai, James J; Huang, Jian-Dong; Mak, William; Pallen, Mark J; Lok, Si; Yuen, Kwok-Yung

2009-03-01

Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish intestines and freshwater environments. The gene contents support its phenotypic properties and suggest that amino acids and fatty acids can be used as carbon sources. The extensive variety of transporters, including multidrug efflux and heavy metal transporters as well as genes involved in chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase, superoxide dismutase, and other putative virulence factors-such as hemolysins, RTX toxins, patatin-like proteins, phospholipase A1, and collagenases-are present. Proteomes of L. hongkongensis HLHK9 cultured at 37 degrees C (human body temperature) and 20 degrees C (freshwater habitat temperature) showed differential gene expression, including two homologous copies of argB, argB-20, and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)-NAGK-20 and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37 degrees C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similar duplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that similar mechanisms for temperature adaptation may be employed by other

The physiology of the filamentous bacterium Microthrix parvicella

NARCIS (Netherlands)

Slijkhuis, H.

1983-01-01

A study has been made of the physiology of Microthrix parvicella. This filamentous bacterium often causes poor settleability of activated sludge in oxidation ditches supplied with domestic sewage. The organism was found to utilize only long chain fatty acids (preferably in

Comparative studies on the effect of ionizing and nonionizing radiations on the kinetics of DNA synthesis and postirradiation degradation in Micrococcus radiodurans R115

International Nuclear Information System (INIS)

Auda, H.; Khalef, Z.

1982-01-01

The kinetics of degradation and synthesis of DNA and the nature of radioactive substances released from M. radiodurans R 11 5 labeled with thymidine-methyl- 3 H after UV and gamma irradiations were investigated. The release of labeled material from the DNA began immediately upon incubation and terminated in due time 90 min and 180 min for UV and gamma irradiations, respectively. When acriflavine was added to the medium, post-irradiation degradation process did not terminate even after 9 h in the case of UV exposure. However, it terminated after 6 h in the case of gamma irradiation. In the presence of acriflavine, DNA synthesis resumed after termination of DNA degradation in the case of gamma irradiation and this was not observed in the case of UV irradiation. Degradation products were chromatographed and it was found that they were located in one major radioactive peak. However their locations were different for UV and gamma radiations. For UV irradiation, the peak fell in the thymine region, while for gamma irradiation it fell in the thymidine region. (author)

Isolation and characterization of Caldicellulosiruptor lactoaceticus sp. nov., an extremely thermophilic, cellulolytic, anaerobic bacterium

DEFF Research Database (Denmark)

Mladenovska, Zuzana; Mathrani, Indra M.; Ahring, Birgitte Kiær

1995-01-01

An anaerobic, extremely thermophilic, cellulolytic, non-spore-forming bacterium, strain 6A, was isolated from an alkaline hot spring in Hverageroi, Iceland. The bacterium was non-motile, rod-shaped (1.5-3.5 x 0.7 mu m) and occurred singly, in pairs or in chains and stained gram-negative. The growth...

Isolation, identification, and biocontrol of antagonistic bacterium against Botrytis cinerea after tomato harvest

Directory of Open Access Journals (Sweden)

Jun-Feng Shi

Full Text Available ABSTRACT Tomato is one of the most important vegetables in the world. Decay after harvest is a major issue in the development of tomato industry. Currently, the most effective method for controlling decay after harvest is storage of tomato at low temperature combined with usage of chemical bactericide; however, long-term usage of chemical bactericide not only causes pathogen resistance but also is harmful for human health and environment. Biocontrol method for the management of disease after tomato harvest has great practical significance. In this study, antagonistic bacterium B-6-1 strain was isolated from the surface of tomato and identified as Enterobacter cowanii based on morphological characteristics and physiological and biochemical features combined with sequence analysis of 16SrDNA and ropB gene and construction of dendrogram. Effects of different concentrations of antagonistic bacterium E. cowanii suspension on antifungal activity after tomato harvest were analyzed by mycelium growth rate method. Results revealed that antifungal activity was also enhanced with increasing concentrations of antagonistic bacterium; inhibitory rates of 1 × 105 colony-forming units (cfu/mL antagonistic bacterial solution on Fusarium verticillioides, Alternaria tenuissima, and Botrytis cinerea were 46.31%, 67.48%, and 75.67%, respectively. By using in vivo inoculation method, it was further confirmed that antagonistic bacterium could effectively inhibit the occurrence of B. cinerae after tomato harvest, biocontrol effect of 1 × 109 cfu/mL zymotic fluid reached up to 95.24%, and antagonistic bacterium E. cowanii has biocontrol potential against B. cinerea after harvest of fruits and vegetables.

Monitoring of a novel bacterium, Lactobacillus thermotolerans , in ...

African Journals Online (AJOL)

Abstract. We successfully established fluorescence in situ hybridization (FISH) method for specific detection and enumeration of a novel bacterium, Lactobacillus thermotolerans, in chicken feces. The specific FISH probes were designed based on the L. thermotolerans 16S rRNA gene sequences, and these sequences were ...

Hydrogen production by co-cultures of Lactobacillus and a photosynthetic bacterium, Rhodobacter sphaeroides RV

Energy Technology Data Exchange (ETDEWEB)

Asada, Yasuo; Ishimi, Katsuhiro [Department of General Education, College of Science and Technology, Nihon University, Narashinodai, Chiba 274-8501 (Japan); Tokumoto, Masaru; Aihara, Yasuyuki; Oku, Masayo; Kohno, Hideki [Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Izumi-cho, Chiba 275-8575 (Japan); Wakayama, Tatsuki; Miyake, Jun [Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology, Nakoji, Amagasaki, Hyogo 661-0974 (Japan); Tomiyama, Masamitsu [Genetic Diversity Department, National Institute of Agrobiological Science, Tsukuba, Ibaraki 305-8602 (Japan)

2006-09-15

Hydrogen production with glucose by using co-immobilized cultures of a lactic acid bacterium, Lactobacillus delbrueckii NBRC13953, and a photosynthetic bacterium, Rhodobacter sphaeroides RV, in agar gels was studied. Glucose was converted to hydrogen gas in a yield of 7.1mol of hydrogen per mole of glucose at a maximum under illuminated conditions. (author)

Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

Science.gov (United States)

Idogawa, Nao; Amamoto, Ryuta; Murata, Kousaku; Kawai, Shigeyuki

2014-01-01

Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotrophicus Pal5, a wild type strain that showed a stronger mucous phenotype on solid medium containing 28 mM phosphate than on solid medium containing 7 mM phosphate. A G. diazotrophicus Pal5 levansucrase disruptant showed only a weak mucous phenotype regardless of the phosphate concentration, indicating that the mucous phenotype observed on 28 mM phosphate medium was caused by levan. To our knowledge, this is the first report of the effect of a high concentration of phosphate on exopolysaccharide production. PMID:24717418

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...

New recombinant bacterium comprises a heterologous gene encoding glycerol dehydrogenase and/or an up-regulated native gene encoding glycerol dehydrogenase, useful for producing ethanol

DEFF Research Database (Denmark)

2010-01-01

dehydrogenase encoding region of the bacterium, or is inserted into a phosphotransacetylase encoding region of the bacterium, or is inserted into an acetate kinase encoding region of the bacterium. It is operably linked to an inducible, a regulated or a constitutive promoter. The up-regulated glycerol......TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preparation (claimed): Producing recombinant bacterium having enhanced ethanol production characteristics when cultivated in growth medium comprising glycerol comprises: (a) transforming a parental bacterium by (i) the insertion of a heterologous gene encoding...... glycerol dehydrogenase; and/or (ii) up-regulating a native gene encoding glycerol dehydrogenase; and (b) obtaining the recombinant bacterium. Preferred Bacterium: In the recombinant bacterium above, the inserted heterologous gene and/or the up-regulated native gene is encoding a glycerol dehydrogenase...

Antagonistic bioactivity of an endophytic bacterium isolated from ...

African Journals Online (AJOL)

Antagonistic bioactivity of an endophytic bacterium isolated from Epimedium brevicornu Maxim. R He, G Wang, X Liu, C Zhang, F Lin. Abstract. Endophytic bacteria are one of the most potential biological control agents in plant disease protection. The aim of this work was to evaluate the antimicrobial activities of a strain of ...

Comparative studies on the effect of ionizing and nonionizing radiations on the kinetics of DNA synthesis and postirradiation degradation in Micrococcus radiodurans R/sub 11/5

Energy Technology Data Exchange (ETDEWEB)

Auda, H; Khalef, Z [Nuclear Centre Tuwaitha, Baghdad (Iraq)

1982-06-01

The kinetics of degradation and synthesis of DNA and the nature of radioactive substances released from M. radiodurans R/sub 11/5 labeled with thymidine-methyl-/sup 3/H after UV and gamma irradiations were investigated. The release of labeled material from the DNA began immediately upon incubation and terminated in due time 90 min and 180 min for UV and gamma irradiations, respectively. When acriflavine was added to the medium, post-irradiation degradation process did not terminate even after 9 h in the case of UV exposure. However, it terminated after 6 h in the case of gamma irradiation. In the presence of acriflavine, DNA synthesis resumed after termination of DNA degradation in the case of gamma irradiation and this was not observed in the case of UV irradiation. Degradation products were chromatographed and it was found that they were located in one major radioactive peak. However their locations were different for UV and gamma radiations. For UV irradiation, the peak fell in the thymine region, while for gamma irradiation it fell in the thymidine region.

methoxyethanol by a new bacterium isolate Pseudomonas sp. Strain

African Journals Online (AJOL)

Michael Horsfall

A 2-methoxyethanol degrading bacterium was isolated from anaerobic sludge of a municipal sewage from ... Stoichiometrically, the strain utilized one mole of oxygen per one mole of 2-methoxyethanol instead of ... physiological and biochemical characterization of the .... observed with acetate and the intact resting cells.

Biology Branch

Energy Technology Data Exchange (ETDEWEB)

Baldwin, W F

1974-12-31

Progress is reported on the following studies in biochemistry and molecular biology: study of long pyrimidine polynucleotides in DNA; isolation of thymine dimers from Schizosaccharomyces pombe; thermal stability of high molecular weight RNA; nucleases of Micrococcus radiodurans; effect of ionizing radiation on M. radiodurans cell walls and cell membranes; chemical modification of nucleotides; exonucleases of M. radiodurans; and enzymatic basis of repair of radioinduced damage in M. radiodurans. Genetics, development, and population studies include repair pathways and mutation induction in yeast; induction of pure mutant clones in yeast; radiosensitivity of bacteriophage T4; polyacrylamide gel electrophoresis of bacteriophage T4; radiation genetics of Dahibominus; and radiation studies on bitting flies. (HLW)

Halomonas maura is a physiologically versatile bacterium of both ecological and biotechnological interest.

Science.gov (United States)

Llamas, Inmaculada; del Moral, Ana; Martínez-Checa, Fernando; Arco, Yolanda; Arias, Soledad; Quesada, Emilia

2006-01-01

Halomonas maura is a bacterium of great metabolic versatility. We summarise in this work some of the properties that make it a very interesting microorganism both from an ecological and biotechnological point of view. It plays an active role in the nitrogen cycle, is capable of anaerobic respiration in the presence of nitrate and has recently been identified as a diazotrophic bacterium. Of equal interest is mauran, the exopolysaccharide produced by H. maura, which contributes to the formation of biofilms and thus affords the bacterium advantages in the colonisation of its saline niches. Mauran is highly viscous, shows thixotropic and pseudoplastic behaviour, has the capacity to capture heavy metals and exerts a certain immunomodulator effect in medicine. All these attributes have prompted us to make further investigations into its molecular characteristics. To date we have described 15 open reading frames (ORF's) related to exopolysaccharide production, nitrogen fixation and nitrate reductase activity among others.

From Genome to Function: Systematic Analysis of the Soil Bacterium Bacillus Subtilis

Science.gov (United States)

Crawshaw, Samuel G.; Wipat, Anil

2001-01-01

Bacillus subtilis is a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression of Bacillus genes in situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere. PMID:18628943

Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

KAUST Repository

Narita, Yuko; Zhang, Lei; Kimura, Zen-ichiro; Ali, Muhammad; Fujii, Takao; Okabe, Satoshi

2017-01-01

Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

KAUST Repository

Narita, Yuko

2017-08-18

Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Energy Technology Data Exchange (ETDEWEB)

Xie, Gary [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Ethanologenic potential of the bacterium Bacillus cereus NB-19 in ...

African Journals Online (AJOL)

STORAGESEVER

2009-12-01

Dec 1, 2009 ... Ethanologenic bacterium was cultivated in a suspension of sugarcane ... bagasse is very useful for obtaining yields of the different products including cell mass and ethanol as ... the resources for the green fuel generation.

Genetic engineering microbes for bioremediation/ biorecovery of uranium

International Nuclear Information System (INIS)

Apte, S.K.; Rao, A.S.; Appukuttan, D.; Nilgiriwala, K.S.; Acharya, C.

2005-01-01

Bioremediation (both bioremoval and biorecovery) of metals is considered a feasible, economic and eco-friendly alternative to chemical methods of metal extraction, particularly when the metal concentration is very low. Scanty distribution along with poor ore quality makes biomining of uranium an attractive preposition. Biosorption, bioprecipitation or bioaccumulation of uranium, aided by recombinant DNA technology, offer a promising technology for recovery of uranium from acidic or alkaline nuclear waste, tailings or from sea-water. Genetic engineering of bacteria, with a gene encoding an acid phosphatase, has yielded strains that can bioprecipitate uranium from very low concentrations at acidic-neutral pH, in a relatively short time. Organisms overproducing alkaline phosphatase have been selected for uranium precipitation from alkaline waste. Such abilities have now been transferred to the radioresistant microbe Deinococcus radiodurans to facilitate in situ bioremediation of nuclear waste, with some success. Sulfate-reducing bacteria are being characterized for bioremediation of uranium in tailings with the dual objective of uranium precipitation and reduction of sulfate to sulphide. Certain marine cyanobacteria have shown promise for uranium biosorption to extracellular polysaccharides, and intracellular accumulation involving metal sequestering metallothionin proteins. Future work is aimed at understanding the genetic basis of these abilities and to engineer them into suitable organisms subsequently. As photosynthetic, nitrogen-fixing microbes, which are considerably resistant to ionizing radiations, cyanobacteria hold considerable potential for bioremediation of nuclear waste. (author)

Irradiation of Microbes from Spent Nuclear Fuel Storage Pool Environments

International Nuclear Information System (INIS)

Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.; Roberto, F.F.; Tsang, M.N.; Pinhero, P.J.; Brey, R.F.; Wright, R.N.; Windes, W.F.

1999-01-01

Microbes have been isolated and identified from spent nuclear fuel storage pools at the Idaho National Engineering and Environmental Laboratory (INEEL). Included among these are Corynebacterium aquaticum, Pseudomonas putida, Comamonas acidovorans, Gluconobacter cerinus, Micrococcus diversus, Rhodococcus rhodochrous, and two strains of sulfate-reducing bacteria (SRB). We examined the sensitivity of these microbes to a variety of total exposures of radiation generated by a 6-MeV linear accelerator (LINAC). The advantage of using a LINAC is that it provides a relatively quick screen of radiation tolerance. In the first set of experiments, we exposed each of the aforementioned microbes along with four additional microbes, pseudomonas aeruginosa, Micrococcus luteus, Escherchia coli, and Deinococcus radiodurans to exposures of 5 x 10 3 and 6 x 10 4 rad. All microbial specimens withstood the lower exposure with little or no reduction in cell population. Upon exposing the microbes to the larger dose of 6 x 10 4 rad, we observed two distinct groupings: microbes that demonstrate resistance to radiation, and microbes that display intolerance through a dramatic reduction from their initial population. Microbes in the radiation tolerant grouping were exposed to 1.1 x 10 5 rad to examine the extent of their resistance. We observe a correlation between radiation resistance and gram stain. The gram-positive species we examined seem to demonstrate a greater radiation resistance

Urate is a ligand for the transcriptional regulator PecS.

Science.gov (United States)

Perera, Inoka C; Grove, Anne

2010-09-24

PecS is a member of the MarR (multiple antibiotic resistance regulator) family, which has been shown in Erwinia to regulate the expression of virulence genes. MarR homologs typically bind a small molecule ligand, resulting in attenuated DNA binding. For PecS, the natural ligand has not been identified. We have previously shown that urate is a ligand for the Deinococcus radiodurans-encoded MarR homolog HucR (hypothetical uricase regulator) and identified residues responsible for ligand binding. We show here that all four residues involved in urate binding and propagation of conformational changes to DNA recognition helices are conserved in PecS homologs, suggesting that urate is the ligand for PecS. Consistent with this prediction, Agrobacterium tumefaciens PecS specifically binds urate, and urate attenuates DNA binding in vitro. PecS binds two operator sites in the intergenic region between the divergent pecS gene and pecM genes, one of which features two partially overlapping repeats to which PecS binds as a dimer on opposite faces of the duplex. Notably, urate dissociates PecS from cognate DNA, allowing transcription of both genes in vivo. Taken together, our data show that urate is a ligand for PecS and suggest that urate serves a novel function in signaling the colonization of a host plant. Copyright © 2010 Elsevier Ltd. All rights reserved.

Protein function prediction involved on radio-resistant bacteria

International Nuclear Information System (INIS)

Mezhoud, Karim; Mankai, Houda; Sghaier, Haitham; Barkallah, Insaf

2009-01-01

Previously, we identified 58 proteins under positive selection in ionizing-radiation-resistant bacteria (IRRB) but absent in all ionizing-radiation-sensitive bacteria (IRSB). These are good reasons to believe these 58 proteins with their interactions with other proteins (interactomes) are a part of the answer to the question as to how IRRB resist to radiation, because our knowledge of interactomes of positively selected orphan proteins in IRRB might allow us to define cellular pathways important to ionizing-radiation resistance. Using the Database of Interacting Proteins and the PSIbase, we have predicted interactions of orthologs of the 58 proteins under positive selection in IRRB but absent in all IRSB. We used integrate experimental data sets with molecular interaction networks and protein structure prediction from databases. Among these, 18 proteins with their interactomes were identified in Deinococcus radiodurans R1. DNA checkpoint and repair, kinases pathways, energetic and nucleotide metabolisms were the important biological process that found. We predicted the interactomes of 58 proteins under positive selection in IRRB. It is hoped our data will provide new clues as to the cellular pathways that are important for ionizing-radiation resistance. We have identified news proteins involved on DNA management which were not previously mentioned. It is an important input in addition to protein that studied. It does still work to deepen our study on these new proteins

Irradiation of Microbes from Spent Nuclear Fuel Storage Pool Environments

Energy Technology Data Exchange (ETDEWEB)

Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.; Roberto, F.F.; Tsang, M.N.; Pinhero, P.J. [INEEL (US); Brey, R.F. [ISU (US); Wright, R.N.; Windes, W.F.

1999-09-03

Microbes have been isolated and identified from spent nuclear fuel storage pools at the Idaho National Engineering and Environmental Laboratory (INEEL). Included among these are Corynebacterium aquaticum, Pseudomonas putida, Comamonas acidovorans, Gluconobacter cerinus, Micrococcus diversus, Rhodococcus rhodochrous, and two strains of sulfate-reducing bacteria (SRB). We examined the sensitivity of these microbes to a variety of total exposures of radiation generated by a 6-MeV linear accelerator (LINAC). The advantage of using a LINAC is that it provides a relatively quick screen of radiation tolerance. In the first set of experiments, we exposed each of the aforementioned microbes along with four additional microbes, pseudomonas aeruginosa, Micrococcus luteus, Escherchia coli, and Deinococcus radiodurans to exposures of 5 x 10{sup 3} and 6 x 10{sup 4} rad. All microbial specimens withstood the lower exposure with little or no reduction in cell population. Upon exposing the microbes to the larger dose of 6 x 10{sup 4} rad, we observed two distinct groupings: microbes that demonstrate resistance to radiation, and microbes that display intolerance through a dramatic reduction from their initial population. Microbes in the radiation tolerant grouping were exposed to 1.1 x 10{sup 5} rad to examine the extent of their resistance. We observe a correlation between radiation resistance and gram stain. The gram-positive species we examined seem to demonstrate a greater radiation resistance.

Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.

Science.gov (United States)

Van Puyvelde, Sandra; Cloots, Lore; Engelen, Kristof; Das, Frederik; Marchal, Kathleen; Vanderleyden, Jos; Spaepen, Stijn

2011-05-01

The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.

Understanding the interaction between an obligate hyperparasitic bacterium, Pasteuria penetrans and its obligate plant-parasitic nematode host, Meloidogyne spp.

Science.gov (United States)

Davies, Keith G

2009-01-01

Pasteuria penetrans is an endospore-forming bacterium, which is a hyperparasite of root-knot nematodes Meloidogyne spp. that are economically important pests of a wide range of crops. The life cycle of the bacterium and nematode are described with emphasis on the bacterium's potential as a biocontrol agent. Two aspects that currently prohibit the commercial development of the bacterium as a biocontrol agent are the inability to culture it outside its host and its host specificity. Vegetative growth of the bacterium is possible in vitro; however, getting the vegetative stages of the bacterium to enter sporogenesis has been problematic. Insights from genomic survey sequences regarding the role of cation concentration and the phosphorylation of Spo0F have proved useful in inducing vegetative bacteria to sporulate. Similarly, genomic data have also proved useful in understanding the attachment of endospores to the cuticle of infective nematode juveniles, and a Velcro-like model of spore attachment is proposed that involves collagen-like fibres on the surface of the endospore interacting with mucins on the nematode cuticle. Ecological studies of the interactions between Daphnia and Pasteuria ramosa are examined and similarities are drawn between the co-evolution of virulence in the Daphnia system and that of plant-parasitic nematodes.

Description of a bacterium associated with redmouth disease of rainbow trout (Salmo gairdneri)

Science.gov (United States)

Ross, A.J.; Rucker, R.R.; Ewing, W.H.

1966-01-01

A description was given of a gram-negative, peritrichously flagellated, fermentative bacterium that was isolated on numerous occasions from kidney tissues of rainbow trout (Salmo gairdneri) afflicted with redmouth disease. Although the bacteria apparently were members of the family Enterobacteriaceae, it was impossible to determine their taxonomic position within the family with certainty. Hence it was recommended that their taxonomic position remain sub judice for the present. As a temporary designation RM bacterium was used. Redmouth disease was transmitted from infected to normal fish through the medium of water.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Energy Technology Data Exchange (ETDEWEB)

Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

Science.gov (United States)

Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

Inactivation of bacterial spores by combination processes: ultraviolet plus gamma radiation. [Streptococcus faecium, micrococcus radiodurans, clostridium botulinum

Energy Technology Data Exchange (ETDEWEB)

Grecz, N; Durban, E

1973-01-01

Bacterial spores, viruses and some vegetative bacteria such as Streptococcus faecium and Micrococcus radiodurans are distinguished by high radiation resistance. In order to lay a theoretical basis for biomedical sterilization applications, we have investigated the combined action of uv and gamma rays. Spores of two strains of C. botulinum were selected, a highly radiation resistant strain, 33A having a D/sub 10/-value of 0.32 Mrad, and a relatively radiation sensitive strain, 51B having a D/sub 10/-value of 0.12 Mrad. Strain 33A exhibits an extensive initial ''shoulder'' in its uv as well as gamma ray survival curves; strain 51B shows only a slight shoulder. The shoulder in the gamma ray survival curve of spores of strain 33A could be reduced or completely eliminated by preirradiation with uv. Simultaneously the D/sub 10/-value for gamma inactivation of spores of 33A was reduced substantially. For example, the gamma resistance was reduced almost to half of its original D/sub 10/-value by uv-preirradiation for only one minute under an 8 watt GE germicidal lamp. The effect of uv-preirradiation on the radiation sensitive strain 51B was less pronounced. In fact, there was about seven fold higher positive interaction (synergism) between uv and gamma radiation in 33A spores than in 51B spores. The experiments suggest that interference with DNA repair enzymes in the radiation resistant strain are responsible for lethal synergism between uv and gamma radiation. A hypothesis is developed attempting to explain the combined effect of these two radiations in terms of a special summation of known DNA lesions in the cell. These observations emphasize the potential practical advantages of combining uv and gamma rays for effective sterilization of certain biomedical devices, drugs and biologicals.

Complete genome sequence of the photoautotrophic and bacteriochlorophyll e-synthesizing green sulfur bacterium Chlorobaculum limnaeum DSM 1677T

DEFF Research Database (Denmark)

Tank, Marcus; Liu, Zhenfeng; Frigaard, Niels-Ulrik

2017-01-01

Chlorobaculum limnaeum DSM 1677T is a mesophilic, brown-colored, chlorophototrophic green sulfur bacterium that produces bacteriochlorophyll e and the carotenoid isorenieratene as major pigments. This bacterium serves as a model organism in molecular research on photosynthesis, sulfur metabolism...

Non-obligate predatory bacterium burkholderia casidaeand uses thereof

OpenAIRE

1998-01-01

A novel predator bacterium Burkholderia casidae is disclosed. The invention is directed to the isolation and use of Burkholderia casidae to control microbial diseases of plants. The genetic, biochemical and physiological characteristics of Burkholderia casidae are described. Biocontrol compositions comprising Burkholderia casidae, and antimicrobial compounds and antimicrobial preparations prepared from Burkholderia casidae are also disclosed, as are methods for accomplishing all of the forego...

Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

KAUST Repository

Wang, Yong

2016-07-01

Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.

Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties.

Science.gov (United States)

El Kafsi, Hela; Binesse, Johan; Loux, Valentin; Buratti, Julien; Boudebbouze, Samira; Dervyn, Rozenn; Hammani, Amal; Maguin, Emmanuelle; van de Guchte, Maarten

2014-07-17

Lactobacillus delbrueckii subsp. lactis CNRZ327 is a dairy bacterium with anti-inflammatory properties both in vitro and in vivo. Here, we report the genome sequence of this bacterium, which appears to contain no less than 215 insertion sequence (IS) elements, an exceptionally high number regarding the small genome size of the strain. Copyright © 2014 El Kafsi et al.

Chitin utilization by the insect-transmitted bacterium Xylella fastidiosa.

Science.gov (United States)

Killiny, Nabil; Prado, Simone S; Almeida, Rodrigo P P

2010-09-01

Xylella fastidiosa is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of X. fastidiosa and may serve as a carbon source for this bacterium. Biological assays showed that X. fastidiosa reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by X. fastidiosa. An ortholog of the chitinase A gene (chiA) was identified in the X. fastidiosa genome. The in silico analysis revealed that the open reading frame of chiA encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa. chiA is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus Xanthomonas, which are plant but not insect associated. X. fastidiosa degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into Escherichia coli, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that X. fastidiosa may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger X. fastidiosa's gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in X. fastidiosa.

Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

International Nuclear Information System (INIS)

Aguayo, S; Bozec, L; Donos, N; Spratt, D

2015-01-01

The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine. (topical review)

Physiological and molecular studies of the resistance to ionizing radiations of hyper-thermophilic archaea isolated from deep ocean hydrothermal sources

International Nuclear Information System (INIS)

Jolivet, E.

2002-10-01

In this study, we have first tested in vivo the effect of gamma irradiation on Pyrococcus abyssi, a hyper-thermophilic archaeon, isolated from a deep-sea hydrothermal vent. We have shown that this strain was as radioresistant as P. furiosus but less than Deinococcus radiodurans. The rates of double stranded breaks provoked into DNA following irradiation were monitored by the pulsed-field gel electrophoresis technique (P.F.G.E.) with P. abyssi, P. furiosus, D. radiodurans and Escherichia coli. Results clearly showed that all these rates were similar suggesting that no specific DNA protection system exits in Pyrococcus species. The growth of P. abyssi was efficiently recovered within two hours following the exposure to 2.5 kGy of gamma irradiation. As revealed by P.F.G.E., genomic DNA of P. abyssi totally fragmented after irradiation was efficiently restored within two hours presumably by inter chromosomal homologous recombination. The DNA replication in P. abyssi cells following irradiation at 2.5 kGy was blocked for 90 minutes that corresponds to the decay for repairing damaged DNA. Moreover, following irradiation P. abyssi actively expulse damaged DNA material before DNA replication resumes, preventing the amplification of genetic mutations. We have also showed that at least a subset cf P. abyssi DNA repair and replication proteins, such as RadA, RPA-41 and RFC-S. were constitutively expressed in chromatin bound forms in stationary phase cells. Our results were in agreement with the view that P. abyssi contains a very efficient DNA repair system, which is continuously ready to counteract the DNA damaged caused by the high temperature and/or ionizing radiation. For the first time, three novel hyper-thermophilic archaea species from deep-sea hydrothermal vents more radioresistant than P. abyssi were isolated and characterized, after 'y-irradiation exposures of some enrichment cultures. Thermococcus marinus, Thermococcus radiophilus and Thermococcus gammafolerans

Complete genome of Martelella sp. AD-3, a moderately halophilic polycyclic aromatic hydrocarbons-degrading bacterium.

Science.gov (United States)

Cui, Changzheng; Li, Zhijie; Qian, Jiangchao; Shi, Jie; Huang, Ling; Tang, Hongzhi; Chen, Xin; Lin, Kuangfei; Xu, Ping; Liu, Yongdi

2016-05-10

Martelella sp. strain AD-3, a moderate halophilic bacterium, was isolated from a petroleum-contaminated soil with high salinity in China. Here, we report the complete genome of strain AD-3, which contains one circular chromosome and two circular plasmids. An array of genes related to metabolism of polycyclic aromatic hydrocarbons and halophilic mechanism in this bacterium was identified by the whole genome analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

The Bacterium That Got Infected by a Cow! - Horizontal Gene

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 1. The Bacterium That Got Infected by a Cow! - Horizontal Gene Transfer and Evolution. Saurabh Dhawan Tomás John Ryan. General Article Volume 12 Issue 1 January 2007 pp 49-59 ...

Biosorption of heavy metals by a marine bacterium

Energy Technology Data Exchange (ETDEWEB)

Iyer, Anita [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India); Mody, Kalpana [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India)]. E-mail: khmody@csmcri.org; Jha, Bhavanath [Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat (India)

2005-03-01

Heavy metal chelation property of exopolysaccharide produced by Enterobacter cloaceae, a marine bacterium, isolated from the West Coast of India, is reported in this paper. The exopolysaccharide demonstrated excellent chelating properties with respect to cadmium (65%) followed by copper (20%) and cobalt (8%) at 100 mg/l heavy metal concentration. However, it could not chelate mercury. A comparative study of the percentage biosorption of the above mentioned metals is presented here.

Biosorption of heavy metals by a marine bacterium

International Nuclear Information System (INIS)

Iyer, Anita; Mody, Kalpana; Jha, Bhavanath

2005-01-01

Heavy metal chelation property of exopolysaccharide produced by Enterobacter cloaceae, a marine bacterium, isolated from the West Coast of India, is reported in this paper. The exopolysaccharide demonstrated excellent chelating properties with respect to cadmium (65%) followed by copper (20%) and cobalt (8%) at 100 mg/l heavy metal concentration. However, it could not chelate mercury. A comparative study of the percentage biosorption of the above mentioned metals is presented here

Antimicrobial polyketide furanoterpenoids from seaweed-associated heterotrophic bacterium Bacillus subtilis MTCC 10403.

Science.gov (United States)

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

2017-10-01

Brown seaweed Anthophycus longifolius (Turner) Kützing (family Sargassaceae) associated heterotrophic bacterium Bacillus subtilis MTCC 10403 was found to be a potent isolate with broad range of antibacterial activity against important perceptive food pathogens Vibrio parahaemolyticus, V. vulnificus, and Aeromonas hydrophila. This bacterium was positive for polyketide synthetase gene (KC589397), and therefore, was selected to bioprospect specialized metabolites bearing polyketide backbone. Bioactivity-guided chromatographic fractionation of the ethyl acetate extract of the seaweed-associated bacterium segregated four homologous polyketide furanoterpenoids with potential antibacterial activities against clinically important pathogens. The minimum inhibitory concentration (MIC) assay showed that the referral antibiotics tetracycline and ampicillin were active at 25 μg/mL against the test pathogens, whereas the previously undescribed (4E)-methyl 13-((16-(furan-2-yl) ethyl)-octahydro-7-hydroxy-4-((E)-23-methylbut-21-enyl)-2H-chromen-6-yl)-4-methylpent-4-enoate (compound 1) and methyl 3-(hexahydro-9-((E)-3-methylpent-1-enyl)-4H-furo[3,2-g]isochromen-6-yl) propanoate (compound 3) displayed antibacterial activities against the test pathogens at a lesser concentration (MIC subtilis MTCC 10403 demonstrated to represent a potential source of antimicrobial polyketides for pharmaceutical applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study

Directory of Open Access Journals (Sweden)

OCKY KARNA RADJASA

2005-06-01

Full Text Available 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 signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity, a multifunctional peptide synthetase from Nostoc sp. GSV224, and NdaB (44% identity, a peptide synthetase module of Nodularia spumigena.

Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study

Directory of Open Access Journals (Sweden)

OCKY KARNA RADJASA

2005-06-01

Full Text Available 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 signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity, a multifunctional peptide synthetase from Nostoc sp. GSV224, and NdaB (44% identity, a peptide synthetase module of Nodularia spumigena

Bacterial biodiversity analysis of a contaminated soil from the Chernobyl exclusion zone and characterization of the committed interaction of a Microbacterium strain with uranium

International Nuclear Information System (INIS)

Theodorakopoulos, Nicolas

2013-01-01

The nuclear power plants accidents of Chernobyl and Fukushima demonstrate the importance of the understanding of the transfer of the radioactive contamination in the environment and its ecological consequences. Although certain studies have been realized on superior organisms of the food chain, studies on telluric bacterial communities are scarce. The latter play nevertheless an essential role in the mobility of contaminants in soils by decreasing or improving their transfer towards other compartments (water, vegetables and animals). Moreover radionuclides (RNs) can have toxic effects on bacteria, leading to an inhibition of their participation in such transfer. The objectives of this study were (1) to estimate the impact of the radioactive contamination on bacterial communities belonging to a soil of the Chernobyl exclusion zone (trench T22) and (2) to study the uranium-bacteria interactions of a resistant strain, isolated from this soil. The various techniques used to characterize the bacterial diversity (culture of bacteria, DGGE, 454 pyro-sequencing) all testified of the multiplicity and the abundance of the bacterial communities in spite of the contamination. An impact on the community structure was difficult to assess by DGGE or cultural approach, but was nevertheless highlighted by the use of pyro-sequencing, suggesting the presence of species more adapted to the contaminated soil conditions. A specific molecular tool dedicated to the search of bacteria affiliated to the known radiation resistant Deinococcus-Thermus phylum (for example the Deinococcus radiodurans specie survives after an irradiation of several kGy) was developed. However it did not reveal the presence of bacteria affiliated to such a phylum in the studied soil. In parallel to the study of the bacterial biodiversity, about fifty culturable bacteria were isolated from this site and were used as a support to select a species (Microbacterium) capable to survive strong U(VI) concentrations. The

Agrobacterium tumefaciens is a diazotrophic bacterium

International Nuclear Information System (INIS)

Kanvinde, L.; Sastry, G.R.K.

1990-01-01

This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate 15 N supplied as 15 N 2 . As with most other well-characterized diazotrophic bacteria, the presence of NH 4 + in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship

Non-obligate predatory bacterium Burkholderia casidae and uses thereof

OpenAIRE

2001-01-01

A novel predator bacterium Burkholderia casidae is disclosed. The invention is directed to the isolation and use of Burkholderia casidae to control microbial diseases of plants. The genetic, biochemical and physiological characteristics of Burkholderia casidae are described. Biocontrol compositions comprising Burkholderia casidae, and antimicrobial compounds and antimicrobial preparations prepared from Burkholderia casidae are also disclosed, as are methods for accomplishing all of the forego...

Thermophilic Anaerobic Degradation of Butyrate by a Butyrate-Utilizing Bacterium in Coculture and Triculture with Methanogenic Bacteria

OpenAIRE

Ahring, Birgitte K.; Westermann, Peter

1987-01-01

We studied syntrophic butyrate degradation in thermophilic mixed cultures containing a butyrate-degrading bacterium isolated in coculture with Methanobacterium thermoautotrophicum or in triculture with M. thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic bacterium. Butyrate was β-oxidized to acetate with protons as the electron acceptors. Acetate was used concurrently with its production in the triculture. We found a higher butyrate degradation rate in th...

The atherogenic bacterium Porphyromonas gingivalis evades circulating phagocytes by adhering to erythrocytes

DEFF Research Database (Denmark)

Belstrøm, Daniel; Holmstrup, Palle; Damgaard, Christian

2011-01-01

A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows...... the bacterium to adhere to human red blood cells (RBCs) and thereby evade attack by circulating phagocytes. On incubation with normal human serum, the P. gingivalis strain efficiently fixed complement component 3 (C3). Incubation of bacteria with washed whole blood cells suspended in autologous serum resulted...... in a dose- and time-dependent adherence to RBCs. The adherence required functionally intact complement receptor 1 (CR1; also called CD35) on the RBCs and significantly inhibited the uptake of P. gingivalis by neutrophils and B cells within 1 min of incubation (by 64% and 51%, respectively...

Mitigation of membrane biofouling by a quorum quenching bacterium for membrane bioreactors.

Science.gov (United States)

Ham, So-Young; Kim, Han-Shin; Cha, Eunji; Park, Jeong-Hoon; Park, Hee-Deung

2018-06-01

In this study, a quorum-quenching (QQ) bacterium named HEMM-1 was isolated at a membrane bioreactor (MBR) plant. HEMM-1 has diplococcal morphology and 99% sequence identity to Enterococcus species. The HEMM-1 cell-free supernatant (CFS) showed higher QQ activities than the CFS of other QQ bacteria, mostly by degrading N-acyl homoserine lactones (AHLs) with short acyl chains. Instrumental analyses revealed that HEMM-1 CFS degraded AHLs via lactonase activity. Under static, flow, and shear conditions, the HEMM-1 CFS was effective in reducing bacterial and activated-sludge biofilms formed on membrane surfaces. In conclusion, the HEMM-1 isolate is a QQ bacterium applicable to the control of biofouling in MBRs via inhibition of biofilm formation on membrane surfaces. Copyright © 2018 Elsevier Ltd. All rights reserved.

Agrobacterium tumefaciens is a diazotrophic bacterium

Energy Technology Data Exchange (ETDEWEB)

Kanvinde, L.; Sastry, G.R.K. (Univ. of Leeds (England))

1990-07-01

This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate {sup 15}N supplied as {sup 15}N{sub 2}. As with most other well-characterized diazotrophic bacteria, the presence of NH{sub 4}{sup +} in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship.

The 2015 Nobel Prize in Physiology or Medicine: A Soil Bacterium ...

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 4. The 2015 Nobel Prize in Physiology or Medicine: A Soil Bacterium and a Chinese Herb Steal the Show. Pundi N Rangarajan. General Article Volume 21 Issue 4 April 2016 pp 315-326 ...

Exo- and surface proteomes of the probiotic bacterium Lactobacillus acidophilus NCFM

DEFF Research Database (Denmark)

Celebioglu, Hasan Ufuk; Svensson, Birte

2017-01-01

Lactobacillus acidophilus NCFM is a well-known probiotic bacterium extensively studied for its beneficial health effects. Exoproteome (proteins exported into culture medium) and surface proteome (proteins attached to S-layer) of this probiotic were identified by using 2DE followed by MALDI TOF MS...

Antibacterial marine bacterium deter luminous vibriosis in shrimp larvae

OpenAIRE

Abraham, T.J.

2004-01-01

Inhibitory activity of a marine pigmented bacterium - Alteromonas sp. - isolated from Penaeus monodon Fabricius larva against pathogenic and environmental isolates of Vibrio harveyi was studied. All the isolates were inhibited to varying degrees by Alteromonas sp. in vitro. The antibacterial substance produced by the Alteromonas sp. was soluble in organic solvent and closely bound to the external surface of bacterial cells. The antibacterial Alteromonas sp., when allowed to colonize on shrimp...

Application of agglomerative clustering for analyzing phylogenetically on bacterium of saliva

Science.gov (United States)

Bustamam, A.; Fitria, I.; Umam, K.

2017-07-01

Analyzing population of Streptococcus bacteria is important since these species can cause dental caries, periodontal, halitosis (bad breath) and more problems. This paper will discuss the phylogenetically relation between the bacterium Streptococcus in saliva using a phylogenetic tree of agglomerative clustering methods. Starting with the bacterium Streptococcus DNA sequence obtained from the GenBank, then performed characteristic extraction of DNA sequences. The characteristic extraction result is matrix form, then performed normalization using min-max normalization and calculate genetic distance using Manhattan distance. Agglomerative clustering technique consisting of single linkage, complete linkage and average linkage. In this agglomerative algorithm number of group is started with the number of individual species. The most similar species is grouped until the similarity decreases and then formed a single group. Results of grouping is a phylogenetic tree and branches that join an established level of distance, that the smaller the distance the more the similarity of the larger species implementation is using R, an open source program.

Melanin from the nitrogen-fixing bacterium Azotobacter chroococcum: a spectroscopic characterization.

Directory of Open Access Journals (Sweden)

Aulie Banerjee

Full Text Available Melanins, the ubiquitous hetero-polymer pigments found widely dispersed among various life forms, are usually dark brown/black in colour. Although melanins have variety of biological functions, including protection against ultraviolet radiation of sunlight and are used in medicine, cosmetics, extraction of melanin from the animal and plant kingdoms is not an easy task. Using complementary physicochemical techniques (i.e. MALDI-TOF, FTIR absorption and cross-polarization magic angle spinning solid-state (13C NMR, we report here the characterization of melanins extracted from the nitrogen-fixing non-virulent bacterium Azotobacter chroococcum, a safe viable source. Moreover, considering dihydroxyindole moiety as the main constituent, an effort is made to propose the putative molecular structure of the melanin hetero-polymer extracted from the bacterium. Characterization of the melanin obtained from Azotobacter chroococcum would provide an inspiration in extending research activities on these hetero-polymers and their use as protective agent against UV radiation.

Preparation of monoclonal antibodies against radiation-induced protein

International Nuclear Information System (INIS)

Nozawa, R.; Tanaka, A.; Watanabe, H.; Kitayama, S.

1992-01-01

We obtained the 6 monoclonal antibodies against gamma-induced proteins of Deinococcus radiodurans, and these antibodies were designated as Mab-3F, 4B, 4D, 4F, 4G and 12G. Using these antibodies, we investigated the relations between gamma-induced proteins and other stress protein in strain R1, and the induction of proteins were compared among strain R1, resistant mutant (rec1) and radiosensitive mutant (rec30). We found new 6 proteins recognized by these monoclonal antibodies which were induced after gamma-irradiation especially in strain R1 and rec 1, but not induced in strain rec30. We suppose that these proteins participate in repair of DNA damages including double strand breaks caused by gamma-irradiation. One of them was around 46kDa protein band recognized by Mab-12G, and this protein was so induced in a large quantity after irradiation that the protein could detect by gold staining. In addition to this observation, we found some proteins which were induced in R1 and rec 1 by gamma-irradiation and other stress, but not in strain rec30, such as 31kDa protein band recognized by Mab-3F, 4B and 4G, and other 11 proteins which were especially induced in irradiated strain R1. The latter proteins might be reinforcement factor to radioresistance such as GroE and DnaK, or participant in repair of damage by gamma-irradiation in strain R1. (author)

Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.

Directory of Open Access Journals (Sweden)

Zhiping Wang

Full Text Available Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere.

Photoproduction of hydrogen by a non-sulphur bacterium isolated from root zones of water fern Azolla pinnata

Energy Technology Data Exchange (ETDEWEB)

Singh, S.P.; Srivastava, S.C.; Pandey, K.D. (Banaras Hindu Univ., Varanasi (IN). Centre of Advanced Study in Botany)

1990-01-01

A photosynthetic bacterium Rhodopseudomonas sp. BHU strain 1 was isolated from the root zone of water fern Azolla pinnata. The bacterium was found to produce hydrogen with potato starch under phototrophic conditions. The immobilized bacterial cells showed sustained hydrogen production with a more than 4-fold difference over free cell suspensions. The data have been discussed in the light of possible utilization of relatively cheaper raw materials by non-sulphur bacteria to evolve hydrogen. (author).

["Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum].

Science.gov (United States)

Zhilina, T N; Zavarzina, D G; Kolganova, T V; Turova, T P; Zavarzin, G A

2005-01-01

From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum."

Aliidiomarina haloalkalitolerans sp. nov., a marine bacterium isolated from coastal surface seawater

Digital Repository Service at National Institute of Oceanography (India)

Srinivas, T.N.R.; Nupur; AnilKumar, P.

A novel Gram-negative, rod shaped, motile, non-sporing strictly aerobic bacterium, designated strain AK5 sup(T), was isolated from a sea water sample collected near Visakhapatnam coast, Bay of Bengal, India. Colonies on marine agar were circular, 3...

NCBI nr-aa BLAST: CBRC-GACU-09-0002 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-GACU-09-0002 ref|YP_594114.1| amidohydrolase [Deinococcus geothermalis DSM 113...00] gb|ABF44040.1| amidohydrolase [Deinococcus geothermalis DSM 11300] YP_594114.1 5.5 28% ...

Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

International Nuclear Information System (INIS)

Imam, S.H.; Greene, R.V.; Griffin, H.L.

1990-01-01

Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. 35 S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA [ethylene hlycol-bis(β-aminoethyl ether)-N,N,N'N'-tetraacetic acid] had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction

Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

Directory of Open Access Journals (Sweden)

Bhagwan N. Rekadwad

2016-01-01

Full Text Available A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713. Genome-to-Genome Distance (GGDC showed high similarity to Pseudoalteromonas haloplanktis (X67024. The generated unique Quick Response (QR codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates using MEGA6 software. Principal Component Analysis (PCA was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin.

Science.gov (United States)

Svitil, A L; Chadhain, S; Moore, J A; Kirchman, D L

1997-02-01

Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), probably because of the more open structure of (beta)-chitin. When exposed to different types of chitin, V. harveyi excreted several chitin-degrading proteins into the culture media. Some chitinases were present with all of the tested chitins, while others were unique to a particular chitin. We cloned and identified six separate chitinase genes from V. harveyi. These chitinases appear to be unique based on DNA restriction patterns, immunological data, and enzyme activity. This marine bacterium and probably others appear to synthesize separate chitinases for efficient utilization of different forms of chitin and chitin by-products.

Sexual transmission of a plant pathogenic bacterium, Candidatus Liberibacter asiaticus, between conspecific insect vectors during mating.

Directory of Open Access Journals (Sweden)

Rajinder S Mann

Full Text Available Candidatus Liberibacter asiaticus is a fastidious, phloem-inhabiting, gram-negative bacterium transmitted by Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae. The bacterium is the presumed causal agent of huanglongbing (HLB, one of the most destructive and economically important diseases of citrus. We investigated whether Las is transmitted between infected and uninfected D. citri adults during courtship. Our results indicate that Las was sexually transmitted from Las-infected male D. citri to uninfected females at a low rate (<4% during mating. Sexual transmission was not observed following mating of infected females and uninfected males or among adult pairs of the same sex. Las was detected in genitalia of both sexes and also in eggs of infected females. A latent period of 7 days or more was required to detect the bacterium in recipient females. Rod shaped as well as spherical structures resembling Las were observed in ovaries of Las-infected females with transmission electron microscopy, but were absent in ovaries from uninfected D. citri females. The size of the rod shaped structures varied from 0.39 to 0.67 µm in length and 0.19 to 0.39 µm in width. The spherical structures measured from 0.61 to 0.80 µm in diameter. This investigation provides convincing evidence that a plant pathogenic bacterium is sexually transmitted from male to female insects during courtship and established evidence that bacteria persist in reproductive organs. Moreover, these findings provide an alternative sexually horizontal mechanism for the spread of Las within populations of D. citri, even in the absence of infected host trees.

The chemical formula of a magnetotactic bacterium.

Science.gov (United States)

Naresh, Mohit; Das, Sayoni; Mishra, Prashant; Mittal, Aditya

2012-05-01

Elucidation of the chemical logic of life is one of the grand challenges in biology, and essential to the progress of the upcoming field of synthetic biology. Treatment of microbial cells explicitly as a "chemical" species in controlled reaction (growth) environments has allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views on compositions of a living cell. Application of mass and energy balances on living cells has proved to be useful in modeling of bioengineering systems, particularly in deriving optimized media compositions for growing microorganisms to maximize yields of desired bio-derived products by regulating intra-cellular metabolic networks. In this work, application of elemental mass balance during growth of Magnetospirillum gryphiswaldense in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By developing a stoichiometric equation characterizing the formation of a magnetotactic bacterial cell, coupled with rigorous experimental measurements and robust calculations, we report the elemental formula of M. gryphiswaldense cell as CH(2.06)O(0.13)N(0.28)Fe(1.74×10(-3)). Remarkably, we find that iron metabolism during growth of this magnetotactic bacterium is much more correlated individually with carbon and nitrogen, compared to carbon and nitrogen with each other, indicating that iron serves more as a nutrient during bacterial growth rather than just a mineral. Magnetotactic bacteria have not only invoked some interest in the field of astrobiology for the last two decades, but are also prokaryotes having the unique ability of synthesizing membrane bound intracellular organelles. Our findings on these unique prokaryotes are a strong addition to the limited repertoire, of elemental compositions of living cells, aimed at exploring the chemical logic of life. Copyright © 2011 Wiley Periodicals, Inc.

A pathway closely related to the (D)-tagatose pathway of gram-negative enterobacteria identified in the gram-positive bacterium Bacillus licheniformis.

Science.gov (United States)

Van der Heiden, Edwige; Delmarcelle, Michaël; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M; Galleni, Moreno; Joris, Bernard

2013-06-01

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

OpenAIRE

Van der Heiden, Edwige; Delmarcelle, Michaël; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

2013-01-01

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus.

Magnetic guidance of the magnetotactic bacterium Magnetospirillum gryphiswaldense.

Science.gov (United States)

Loehr, Johannes; Pfeiffer, Daniel; Schüler, Dirk; Fischer, Thomas M

2016-04-21

Magnetospirillum gryphiswaldense is a magnetotactic bacterium with a permanent magnetic moment capable of swimming using two bipolarly located flagella. In their natural environment these bacteria swim along the field lines of the homogeneous geomagnetic field in a typical run and reversal pattern and thereby create non-differentiable trajectories with sharp edges. In the current work we nevertheless achieve stable guidance along curved lines of mechanical instability by using a heterogeneous magnetic field of a garnet film. The successful guidance of the bacteria depends on the right balance between motility and the magnetic moment of the magnetosome chain.

NCBI nr-aa BLAST: CBRC-PTRO-15-0056 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-PTRO-15-0056 ref|YP_605216.1| hypothetical protein Dgeo_1752 [Deinococcus geothermal...is DSM 11300] gb|ABF46047.1| hypothetical protein Dgeo_1752 [Deinococcus geothermalis DSM 11300] YP_605216.1 0.001 28% ...

NCBI nr-aa BLAST: CBRC-OANA-01-0785 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OANA-01-0785 ref|YP_603809.1| hypothetical protein Dgeo_0337 [Deinococcus geothermal...is DSM 11300] gb|ABF44640.1| hypothetical protein Dgeo_0337 [Deinococcus geothermalis DSM 11300] YP_603809.1 1.8 32% ...

NCBI nr-aa BLAST: CBRC-LAFR-01-1366 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-LAFR-01-1366 ref|YP_604712.1| cytochrome c assembly protein [Deinococcus geothermal...is DSM 11300] gb|ABF45543.1| cytochrome c assembly protein [Deinococcus geothermalis DSM 11300] YP_604712.1 2.0 30% ...

NCBI nr-aa BLAST: CBRC-ACAR-01-0712 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-ACAR-01-0712 ref|YP_604712.1| cytochrome c assembly protein [Deinococcus geothermal...is DSM 11300] gb|ABF45543.1| cytochrome c assembly protein [Deinococcus geothermalis DSM 11300] YP_604712.1 7.8 32% ...

NCBI nr-aa BLAST: CBRC-LAFR-01-2025 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-LAFR-01-2025 ref|YP_605433.1| hypothetical protein Dgeo_1970 [Deinococcus geothermal...is DSM 11300] gb|ABF46264.1| hypothetical protein Dgeo_1970 [Deinococcus geothermalis DSM 11300] YP_605433.1 0.15 38% ...

NCBI nr-aa BLAST: CBRC-LAFR-01-0180 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-LAFR-01-0180 ref|YP_605433.1| hypothetical protein Dgeo_1970 [Deinococcus geothermal...is DSM 11300] gb|ABF46264.1| hypothetical protein Dgeo_1970 [Deinococcus geothermalis DSM 11300] YP_605433.1 0.15 38% ...

Reclassification of Clostridium proteoclasticum as Butyrivibrio proteoclasticus comb. nov., a butyrate-producing ruminal bacterium

Czech Academy of Sciences Publication Activity Database

Moon, C. D.; Pacheco, D. M.; Kelly, W. J.; Leahy, S. C.; Li, D.; Kopečný, Jan; Attwood, G. T.

2008-01-01

Roč. 58, - (2008), s. 2041-2045 ISSN 1466-5026 Institutional research plan: CEZ:AV0Z50450515 Keywords : Butyrivibrio * ruminal bacterium Subject RIV: EE - Microbiology, Virology Impact factor: 2.222, year: 2008

A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

Science.gov (United States)

Van der Heiden, Edwige; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

2013-01-01

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. PMID:23524682

[Identification and function test of an alkali-tolerant denitrifying bacterium].

Science.gov (United States)

Wang, Ru; Zheng, Ping; Li, Wei; Chen, Hui; Chen, Tingting; Ghulam, Abbas

2013-04-04

We obtained an alkali-tolerant denitrifying bacterium, and determined its denitrifying activity and alkali-tolerance. An alkali-tolerant denitrifying bacterial strain was obtained by isolation and purification. We identified the bacterial strain by morphological observation, physiological test and 16S rRNA analysis. We determined the denitrifying activity and alkali-tolerance by effects of initial nitrate concentration and initial pH on denitrification. An alkali-tolerant denitrifier strain R9 was isolated from the lab-scale high-rate denitrifying reactor, and it was identified as Diaphorobater nitroreducens. The strain R9 grew heterotrophically with methanol as the electron donor and nitrate as the electron acceptor. The nitrate conversion was 93.25% when strain R9 was cultivated for 288 h with initial nitrate concentration 50 mg/L and initial pH 9.0. The denitrification activity could be inhibited at high nitrate concentration with a half inhibition constant of 202.73 mg N/L. Strain R9 showed a good alkali tolerance with the nitrate removal rate at pH 11.0 remained 86% of that at pH 9.0. Strain R9 was identified as Diaphorobater nitroreducens, and it was an alkali-tolerant denitrifying bacterium with optimum pH value of 9.0.

NCBI nr-aa BLAST: CBRC-CJAC-01-0283 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-CJAC-01-0283 ref|YP_593975.1| hypothetical protein Dgeo_2467 [Deinococcus geothermal...is DSM 11300] gb|ABF43901.1| hypothetical protein Dgeo_2467 [Deinococcus geothermalis DSM 11300] YP_593975.1 5e-10 28% ...

Design of semi industrial radium separator by a new bacterium MGF-48

International Nuclear Information System (INIS)

Ghafourian, H.; Emami, M.R.; Farazmand, A.

1998-01-01

Following of a research work which has been recently published in AEOI scientific Bulletin no. 14, a semi industrial bioreactor has been designed for separation of radium using a new bacterium MGF-48. This bioreactor could be utilized for a high rate separation of radium in semi industrial scale. (author)

Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

KAUST Repository

Li, Yongxin; Xu, Ying; Liu, Lingli; Han, Zhuang; Lai, Pok Yui; Guo, Xiangrong; Zhang, Xixiang; Lin, Wenhan; Qian, Pei-Yuan

2012-01-01

Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.

Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

KAUST Repository

Li, Yongxin

2012-02-03

Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.

Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4

OpenAIRE

Masuda, Shinji; Hori, Koichi; Maruyama, Fumito; Ren, Shukun; Sugimoto, Saori; Yamamoto, Nozomi; Mori, Hiroshi; Yamada, Takuji; Sato, Shusei; Tabata, Satoshi; Ohta, Hiroyuki; Kurokawa, Ken

2013-01-01

We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum. The photosynthesis gene cluster comprises two segments?a unique feature among photosynthesis gene clusters of purple bacteria. The genome information will be useful for further analysis of bacterial photosynthesis.

NCBI nr-aa BLAST: CBRC-LAFR-01-1215 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-LAFR-01-1215 ref|YP_605765.1| major facilitator superfamily MFS_1 [Deinococcus geothermal...is DSM 11300] gb|ABF46596.1| major facilitator superfamily MFS_1 [Deinococcus geothermalis DSM 11300] YP_605765.1 0.67 28% ...

NCBI nr-aa BLAST: CBRC-XTRO-01-2352 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-XTRO-01-2352 ref|YP_605707.1| major facilitator superfamily MFS_1 [Deinococcus geothermal...is DSM 11300] gb|ABF46538.1| major facilitator superfamily MFS_1 [Deinococcus geothermalis DSM 11300] YP_605707.1 0.86 29% ...

Growth of a Strictly Anaerobic Bacterium on Furfural (2-Furaldehyde)

OpenAIRE

Brune, Gerhard; Schoberth, Siegfried M.; Sahm, Hermann

1983-01-01

A strictly anaerobic bacterium was isolated from a continuous fermentor culture which converted the organic constituents of sulfite evaporator condensate to methane and carbon dioxide. Furfural is one of the major components of this condensate. This furfural isolate could degrade furfural as the sole source of carbon and energy in a defined mineral-vitamin-sulfate medium. Acetic acid was the major fermentation product. This organism could also use ethanol, lactate, pyruvate, or fumarate and c...

The effect of Pseudoxanthomonas sp. as manganese oxidizing bacterium on the corrosion behavior of carbon steel

Energy Technology Data Exchange (ETDEWEB)

Ashassi-Sorkhabi, H., E-mail: habib_ashassi@yahoo.com [Electrochemistry Research Laboratory, Physical Chemistry Department, Faculty of Chemistry, University of Tabriz, Tabriz (Iran, Islamic Republic of); Moradi-Haghighi, M. [Electrochemistry Research Laboratory, Physical Chemistry Department, Faculty of Chemistry, University of Tabriz, Tabriz (Iran, Islamic Republic of); Zarrini, G. [Microbiology laboratory, Biology Department, Science Faculty, University of Tabriz, Tabriz (Iran, Islamic Republic of)

2012-02-01

The present study investigated the role of manganese oxidizing bacterium (MOB), namely Pseudoxanthomonas sp. on the corrosion behavior of carbon steel. This bacterium was isolated from sewage treatment plants and identified by biochemical and molecular methods. The electrochemical techniques such as open circuit potentiometry, electrochemical impedance spectroscopy, potentiodynamic and cyclic polarization were used to measure the corrosion rate and observe the corrosion mechanism. Also, scanning electron microscopy and X-ray diffraction studies were applied to surface analysis. This study revealed the strong adhesion of the biofilm on the metal surface in the presence of Pseudoxanthomonas sp. that enhanced the corrosion of carbon steel. X-ray diffraction patterns identified a high content of MnO{sub 2} deposition within these biofilms. This is the first report that discloses the involvement of Pseudoxanthomonas sp. as manganese oxidizing bacteria on the corrosion of carbon steel. - Highlights: Black-Right-Pointing-Pointer A new type of manganese oxidizing bacteria, namely Pseudoxanthomonas sp. was indicated. Black-Right-Pointing-Pointer This bacterium can create a biofilm on the part of metal surface and affect localized corrosion. Black-Right-Pointing-Pointer In the presence of biofilm, the diffusion of oxygen vacancies and manganese ions has occurred.

The effect of Pseudoxanthomonas sp. as manganese oxidizing bacterium on the corrosion behavior of carbon steel

International Nuclear Information System (INIS)

Ashassi-Sorkhabi, H.; Moradi-Haghighi, M.; Zarrini, G.

2012-01-01

The present study investigated the role of manganese oxidizing bacterium (MOB), namely Pseudoxanthomonas sp. on the corrosion behavior of carbon steel. This bacterium was isolated from sewage treatment plants and identified by biochemical and molecular methods. The electrochemical techniques such as open circuit potentiometry, electrochemical impedance spectroscopy, potentiodynamic and cyclic polarization were used to measure the corrosion rate and observe the corrosion mechanism. Also, scanning electron microscopy and X-ray diffraction studies were applied to surface analysis. This study revealed the strong adhesion of the biofilm on the metal surface in the presence of Pseudoxanthomonas sp. that enhanced the corrosion of carbon steel. X-ray diffraction patterns identified a high content of MnO 2 deposition within these biofilms. This is the first report that discloses the involvement of Pseudoxanthomonas sp. as manganese oxidizing bacteria on the corrosion of carbon steel. - Highlights: ► A new type of manganese oxidizing bacteria, namely Pseudoxanthomonas sp. was indicated. ► This bacterium can create a biofilm on the part of metal surface and affect localized corrosion. ► In the presence of biofilm, the diffusion of oxygen vacancies and manganese ions has occurred.

Biological Control of Meloidogyne hapla Using an Antagonistic Bacterium

Directory of Open Access Journals (Sweden)

Jiyeong Park

2014-09-01

Full Text Available We examined the efficacy of a bacterium for biocontrol of the root-knot nematode (RKN Meloidogyne hapla in carrot (Daucus carota subsp. sativus and tomato (Solanum lycopersicum. Among 542 bacterial isolates from various soils and plants, the highest nematode mortality was observed for treatments with isolate C1-7, which was identified as Bacillus cereus based on cultural and morphological characteristics, the Biolog program, and 16S rRNA sequencing analyses. The population density and the nematicidal activity of B. cereus C1-7 remained high until the end of culture in brain heart infusion broth, suggesting that it may have sustainable biocontrol potential. In pot experiments, the biocontrol efficacy of B. cereus C1-7 was high, showing complete inhibition of root gall or egg mass formation by RKN in carrot and tomato plants, and subsequently reducing RKN damage and suppressing nematode population growth, respectively. Light microscopy of RKN-infected carrot root tissues treated with C1-7 showed reduced formation of gall cells and fully developed giant cells, while extensive gall cells and fully mature giant cells with prominent cell wall ingrowths formed in the untreated control plants infected with RKNs. These histopathological characteristics may be the result of residual or systemic biocontrol activity of the bacterium, which may coincide with the biocontrol efficacies of nematodes in pots. These results suggest that B. cereus C1-7 can be used as a biocontrol agent for M. hapla.

Extreme furfural tolerance of a soil bacterium Enterobacter cloacae GGT036.

Science.gov (United States)

Choi, Sun Young; Gong, Gyeongtaek; Park, Hong-Sil; Um, Youngsoon; Sim, Sang Jun; Woo, Han Min

2015-01-10

Detoxification process of cellular inhibitors including furfural is essential for production of bio-based chemicals from lignocellulosic biomass. Here we isolated an extreme furfural-tolerant bacterium Enterobacter cloacae GGT036 from soil sample collected in Mt. Gwanak, Republic of Korea. Among isolated bacteria, only E. cloacae GGT036 showed cell growth with 35 mM furfural under aerobic culture. Compared to the maximal half inhibitory concentration (IC50) of well-known industrial strains Escherichia coli (24.9 mM furfural) and Corynebacterium glutamicum (10 mM furfural) based on the cell density, IC50 of E. cloacae GGT036 (47.7 mM) was significantly higher after 24 h, compared to E. coli and C. glutamicum. Since bacterial cell growth was exponentially inhibited depending on linearly increased furfural concentrations in the medium, we concluded that E. cloacae GGT036 is an extreme furfural-tolerant bacterium. Recently, the complete genome sequence of E. cloacae GGT036 was announced and this could provide an insight for engineering of E. cloacae GGT036 itself or other industrially relevant bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater

Science.gov (United States)

A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50**T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rDNA sequences revealed that the novel isolate represented...

NCBI nr-aa BLAST: CBRC-OANA-01-0840 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OANA-01-0840 ref|YP_605770.1| protein of unknown function DUF422 [Deinococcus geothermal...is DSM 11300] gb|ABF46601.1| protein of unknown function DUF422 [Deinococcus geothermalis DSM 11300] YP_605770.1 3.6 34% ...

NCBI nr-aa BLAST: CBRC-LAFR-01-0684 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-LAFR-01-0684 ref|YP_605770.1| protein of unknown function DUF422 [Deinococcus geothermal...is DSM 11300] gb|ABF46601.1| protein of unknown function DUF422 [Deinococcus geothermalis DSM 11300] YP_605770.1 3.2 25% ...

Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)".

Science.gov (United States)

Yang, Yu; Yang, Jun; Jiang, Lei

2016-08-19

Yoshida et al (Report, 11 March 2016, p. 1196) reported that the bacterium Ideonella sakaiensis 201-F6 can degrade and assimilate poly(ethylene terephthalate) (PET). However, the authors exaggerated degradation efficiency using a low-crystallinity PET and presented no straightforward experiments to verify depolymerization and assimilation of PET. Thus, the authors' conclusions are rather misleading. Copyright © 2016, American Association for the Advancement of Science.

Bacterium-like Particles for efficient immune stimulation of existing vaccines and new subunit vaccines in mucosal applications

Directory of Open Access Journals (Sweden)

Natalija eVan Braeckel-Budimir

2013-09-01

Full Text Available The successful development of a mucosal vaccine critically depends on the use of a safe and effective immunostimulant and/or carrier system. This review describes the effectiveness and mode of action of an immunostimulating particle derived from bacteria in mucosal subunit vaccines. The non-living particles, designated Bacterium-like Particles (BLPs are based on the food-grade bacterium Lactococcus lactis. The focus of the overview is on the development of intranasal BLP-based vaccines to prevent diseases caused by influenza and respiratory syncytial virus, and includes a selection of Phase I clinical data for the intranasal FluGEM vaccine.

Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides.

Science.gov (United States)

Devendran, Saravanan; Abdel-Hamid, Ahmed M; Evans, Anton F; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I; Cann, Isaac

2016-10-17

Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.

A newly discovered bacterium associated with parthenogenesis and a change in host selection behavior in parasitoid wasps.

Science.gov (United States)

Zchori-Fein, E; Gottlieb, Y; Kelly, S E; Brown, J K; Wilson, J M; Karr, T L; Hunter, M S

2001-10-23

The symbiotic bacterium Wolbachia pipientis has been considered unique in its ability to cause multiple reproductive anomalies in its arthropod hosts. Here we report that an undescribed bacterium is vertically transmitted and associated with thelytokous parthenogenetic reproduction in Encarsia, a genus of parasitoid wasps. Although Wolbachia was found in only one of seven parthenogenetic Encarsia populations examined, the "Encarsia bacterium" (EB) was found in the other six. Among seven sexually reproducing populations screened, EB was present in one, and none harbored Wolbachia. Antibiotic treatment did not induce male production in Encarsia pergandiella but changed the oviposition behavior of females. Cured females accepted one host type at the same rate as control females but parasitized significantly fewer of the other host type. Phylogenetic analysis based on the 16S rDNA gene sequence places the EB in a unique clade within the Cytophaga-Flexibacter-Bacteroid group and shows EB is unrelated to the Proteobacteria, where Wolbachia and most other insect symbionts are found. These results imply evolution of the induction of parthenogenesis in a lineage other than Wolbachia. Importantly, these results also suggest that EB may modify the behavior of its wasp carrier in a way that enhances its transmission.

Framing in the Spanish press about the health crisis because of the E. coli bacterium

Directory of Open Access Journals (Sweden)

Paloma López Villafranca

2013-12-01

Full Text Available This research article analyses  the approach made by press media and other institutional advertising about the E. coli bacterium, most commonly known as cucumber crisis in Spain. While in the rest of Europe this crisis receives the same treatment as A Flu or mad cow disease in this country it is treated as a crisis that affects to the spanish economy and not to the health of the citizen. Economic interests prevail over public health and this is due to official information given. An analysis of contents of the most popular journals in Spain, according to OJD, is made to prove this hypothesis, El Pais, El Mundo and ABC, as well as a study of the main institutional advertising made about E. coli bacterium by official spanish organizations and the media.

Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age.

Science.gov (United States)

Murfin, Kristen E; Dillman, Adler R; Foster, Jeremy M; Bulgheresi, Silvia; Slatko, Barton E; Sternberg, Paul W; Goodrich-Blair, Heidi

2012-08-01

Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.

Enhanced Cadmium (Cd Phytoextraction from Contaminated Soil using Cd-Resistant Bacterium

Directory of Open Access Journals (Sweden)

Kunchaya Setkit

2014-01-01

Full Text Available A cadmium (Cd-resistant bacterium, Micrococcus sp. MU1, is able to produce indole-3-acetic acid and promotes root elongation and plant growth. The potential of this bacterium on enhancement of Cd uptake and bioaccumulation of Cd in Helianthus annuus L. planted in Cd-contaminated soil was evaluated in greenhouse condition. The results showed that Micrococcus sp. MU1promoted the growth of H. annuus L. by increasing the root length, stem height, dry biomass, root to shoot ratio and also significantly increased Cd accumulation in the root and above-ground tissues of H. annuus L. compared to uninoculated control. Re-inoculation with Micrococcus sp. MU1in contaminated soil helped in promoting plant growth and Cd phytoextraction throughout the cultivation period. In addition, phytoextraction coefficient and translocation factor (TF of H. annuus L. inoculated with Micrococcus sp. MU1were higher than that of uninoculated control and TF continuously increased with time. Our results suggested that Micrococcus sp. MU1 has an ability to enhance plant growth and Cd uptake in H. annuus L. Synergistic interaction between Micrococcus sp. MU1 and H. annuus L. could be further applied for Cd phytoextraction in polluted areas.

Septicemia caused by the gram-negative bacterium CDC IV c-2 in an immunocompromised human.

OpenAIRE

Dan, M; Berger, S A; Aderka, D; Levo, Y

1986-01-01

A 37-year-old man with plasma cell leukemia developed nonfatal septicemia caused by the gram-negative bacterium CDC IV c-2. Recovery followed appropriate treatment with antibiotics. The biochemical features of this organism are reviewed.

Characterization of a Neochlamydia-like Bacterium Associated with Epitheliocystis in Cultured Artic Char Salvelinus alpinus

Science.gov (United States)

Infections of branchial epithelium by intracellular gram-negative bacteria, termed epitheliocystis, have limited culture of Arctic char (Salvelinus alpinus). To characterize a bacterium associated with epitheliocystis in cultured char, gills were sampled for histopathologic examination, conventional...

Removal of zinc from aqueous solution by metal resistant symbiotic bacterium Mesorhizobium amorphae

DEFF Research Database (Denmark)

Hao, Xiuli; Mohamad, Osama Abdalla; Xie, Pin

2014-01-01

Biosorption of zinc by living biomasses of metal resistant symbiotic bacterium Mesorhizobium amorphae CCNWGS0123 was investigated under optimal conditions at pH 5.0, initial metal concentrations of 100 mg L-1, and a dose of 1.0 g L-1. M. amorphae exhibited an efficient removal of Zn2+ from aqueous...

Two-dimensional gel-based alkaline proteome of the probiotic bacterium Lactobacillus acidophilus NCFM

DEFF Research Database (Denmark)

Majumder, Avishek; Cai, Liyang; Ejby, Morten

2012-01-01

Lactobacillus acidophilus NCFM (NCFM) is a well‐documented probiotic bacterium isolated from human gut. Detailed 2D gel‐based NCFM proteomics addressed the so‐called alkaline range, i.e., pH 6–11. Proteins were identified in 150 of the 202 spots picked from the Coomassie Brilliant Blue stained 2D...

Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens

Energy Technology Data Exchange (ETDEWEB)

Daniel P. Molloy

2004-02-24

The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

A Comparative biochemical study on two marine endophytes, Bacterium SRCnm and Bacillus sp. JS, Isolated from red sea algae.

Science.gov (United States)

Ahmed, Eman Fadl; Hassan, Hossam Mokhtar; Rateb, Mostafa Ezzat; Abdel-Wahab, Noha; Sameer, Somayah; Aly Taie, Hanan Anwar; Abdel-Hameed, Mohammed Sayed; Hammouda, Ola

2016-01-01

Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS.

Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water

Digital Repository Service at National Institute of Oceanography (India)

Bhumika, V.; Ravinder, K.; Korpole, S.; Srinivas, T.N.R.; AnilKumar, P.

A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21^T , was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, L-proline arylamidase...

A highly infective plant-associated bacterium influences reproductive rates in pea aphids.

Science.gov (United States)

Hendry, Tory A; Clark, Kelley J; Baltrus, David A

2016-02-01

Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction.

A highly infective plant-associated bacterium influences reproductive rates in pea aphids

Science.gov (United States)

Hendry, Tory A.; Clark, Kelley J.; Baltrus, David A.

2016-01-01

Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction. PMID:26998321

Purification and Characterization of Haloalkaline, Organic Solvent Stable Xylanase from Newly Isolated Halophilic Bacterium-OKH

Science.gov (United States)

Sanghvi, Gaurav; Jivrajani, Mehul; Patel, Nirav; Jivrajani, Heta; Bhaskara, Govinal Badiger; Patel, Shivani

2014-01-01

A novel, alkali-tolerant halophilic bacterium-OKH with an ability to produce extracellular halophilic, alkali-tolerant, organic solvent stable, and moderately thermostable xylanase was isolated from salt salterns of Mithapur region, Gujarat, India. Identification of the bacterium was done based upon biochemical tests and 16S rRNA sequence. Maximum xylanase production was achieved at pH 9.0 and 37°C temperature in the medium containing 15% NaCl and 1% (w/v) corn cobs. Sugarcane bagasse and wheat straw also induce xylanase production when used as carbon source. The enzyme was active over a range of 0–25% sodium chloride examined in culture broth. The optimum xylanase activity was observed at 5% sodium chloride. Xylanase was purified with 25.81%-fold purification and 17.1% yield. Kinetic properties such as Km and Vmax were 4.2 mg/mL and 0.31 μmol/min/mL, respectively. The enzyme was stable at pH 6.0 and 50°C with 60% activity after 8 hours of incubation. Enzyme activity was enhanced by Ca2+, Mn2+, and Mg2+ but strongly inhibited by heavy metals such as Hg2+, Fe3+, Ni2+, and Zn2+. Xylanase was found to be stable in organic solvents like glutaraldehyde and isopropanol. The purified enzyme hydrolysed lignocellulosic substrates. Xylanase, purified from the halophilic bacterium-OKH, has potential biotechnological applications. PMID:27350996

Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences

NARCIS (Netherlands)

Vanfossen, A.L.; Verhaart, M.R.A.; Kengen, S.W.M.; Kelly, R.M.

2009-01-01

Co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on

Optimization of liquid media and biosafety assessment for algae-lysing bacterium NP23.

Science.gov (United States)

Liao, Chunli; Liu, Xiaobo; Shan, Linna

2014-09-01

To control algal bloom caused by nutrient pollution, a wild-type algae-lysing bacterium was isolated from the Baiguishan reservoir in Henan province of China and identified as Enterobacter sp. strain NP23. Algal culture medium was optimized by applying a Placket-Burman design to obtain a high cell concentration of NP23. Three minerals (i.e., 0.6% KNO3, 0.001% MnSO4·H2O, and 0.3% K2HPO4) were found to be independent factors critical for obtaining the highest cell concentration of 10(13) CFU/mL, which was 10(4) times that of the control. In the algae-lysing experiment, the strain exhibited a high lysis rate for the 4 algae test species, namely, Chlorella vulgari, Scenedesmus, Microcystis wesenbergii, and Chlorella pyrenoidosa. Acute toxicity and mutagenicity tests showed that the bacterium NP23 had no toxic and mutagenic effects on fish, even in large doses such as 10(7) or 10(9) CFU/mL. Thus, Enterobacter sp. strain NP23 has strong potential application in the microbial algae-lysing project.

Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.

Science.gov (United States)

Boutard, Magali; Cerisy, Tristan; Nogue, Pierre-Yves; Alberti, Adriana; Weissenbach, Jean; Salanoubat, Marcel; Tolonen, Andrew C

2014-11-01

Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.

Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium.

Science.gov (United States)

Tago, Damian; Meyer, Damien F

2016-01-01

Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria.

The impact of a pathogenic bacterium on a social carnivore population.

Science.gov (United States)

Höner, Oliver P; Wachter, Bettina; Goller, Katja V; Hofer, Heribert; Runyoro, Victor; Thierer, Dagmar; Fyumagwa, Robert D; Müller, Thomas; East, Marion L

2012-01-01

1. The long-term ecological impact of pathogens on group-living, large mammal populations is largely unknown. We evaluated the impact of a pathogenic bacterium, Streptococcus equi ruminatorum, and other key ecological factors on the dynamics of the spotted hyena Crocuta crocuta population in the Ngorongoro Crater, Tanzania. 2. We compared key demographic parameters during two years when external signs of bacterial infection were prevalent ('outbreak') and periods of five years before and after the outbreak when such signs were absent or rare. We also tested for density dependence and calculated the basic reproductive rate R(0) of the bacterium. 3. During the five pre-outbreak years, the mean annual hyena mortality rate was 0.088, and annual population growth was relatively high (13.6%). During the outbreak, mortality increased by 78% to a rate of 0.156, resulting in an annual population decline of 4.3%. After the outbreak, population size increased moderately (5.1%) during the first three post-outbreak years before resuming a growth similar to pre-outbreak levels (13.9%). We found no evidence that these demographic changes were driven by density dependence or other ecological factors. 4. Most hyenas showed signs of infection when prey abundance in their territory was low. During the outbreak, mortality increased among adult males and yearlings, but not among adult females - the socially dominant group members. These results suggest that infection and mortality were modulated by factors linked to low social status and poor nutrition. During the outbreak, we estimated R(0) for the bacterium to be 2.7, indicating relatively fast transmission. 5. Our results suggest that the short-term 'top-down' impact of S. equi ruminatorum during the outbreak was driven by 'bottom-up' effects on nutritionally disadvantaged age-sex classes, whereas the longer-term post-outbreak reduction in population growth was caused by poor survival of juveniles during the outbreak and subsequent

Isolation and Characterization of a Human Intestinal Bacterium Eggerthella sp. AUH-JLD49s for the Conversion of (-)-3'-Desmethylarctigenin.

Science.gov (United States)

Wang, Ye; Yu, Fei; Liu, Ming-Yue; Zhao, Yi-Kai; Wang, Dong-Ming; Hao, Qing-Hong; Wang, Xiu-Ling

2017-05-24

Arctiin is the most abundant bioactive compound contained in the Arctium lappa plant. In our previous study, we isolated one single bacterium capable of bioconverting arctigenin, an aglycone of arctiin, to 3'-desmethylarctigenin (3'-DMAG) solely. However, to date, a specific bacterium capable of producing other arctiin metabolites has not been reported. In this study, we isolated one single bacterium, which we named Eggerthella sp. AUH-JLD49s, capable of bioconverting 3'-DMAG under anaerobic conditions. The metabolite of 3'-DMAG by strain AUH-JLD49s was identified as 3'-desmethyl-4'-dehydroxyarctigenin (DMDH-AG) based on electrospray ionization mass spectrometry (ESI-MS) and 1 H and 13 C nuclear magnetic resonance spectroscopy. The bioconversion kinetics and bioconversion capacity of strain AUH-JLD49s were investigated. In addition, the metabolite DMDH-AG showed an inhibitory effect on cell growth of human colon cancer cell line HCT116 and human breast cancer cell line MDA-MB-231.

Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium

KAUST Repository

Katuri, Krishna

2017-03-03

Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was originally isolated from digester sludge from a sewage treatment plant in Germany. This bacterium is capable of anode respiration with high electrochemical activity in microbial electrochemical systems. The draft genome contains 3,376 predicted protein-coding genes and putative multiheme c-type cytochromes.

Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium

KAUST Repository

Katuri, Krishna; Albertsen, Mads; Saikaly, Pascal

2017-01-01

Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was originally isolated from digester sludge from a sewage treatment plant in Germany. This bacterium is capable of anode respiration with high electrochemical activity in microbial electrochemical systems. The draft genome contains 3,376 predicted protein-coding genes and putative multiheme c-type cytochromes.

Draft genome sequence of Bacillus okhensis Kh10-101T, a halo-alkali tolerant bacterium from Indian saltpan

Directory of Open Access Journals (Sweden)

Pilla Sankara Krishna

2015-12-01

Full Text Available We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.

Directory of Open Access Journals (Sweden)

Ronald M Weiner

2008-05-01

Full Text Available The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40 is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.

Oceanospirillum nioense sp. nov., a marine bacterium isolated from sediment sample of Palk bay, India

Digital Repository Service at National Institute of Oceanography (India)

Krishna, K.K.; Bhumika, V.; Thomas, M.; AnilKumar, P.; Srinivas, T.N.R.

A novel Gram-negative, spiral shaped, motile bacterium, designated strain NIO-S6T, was isolated from a sediment sample collected from Offshore Rameswaram, Tamilnadu, India. Strain NIO-S6 sup(T) was found to be positive for oxidase, DNase and lysine...

A fatal endocarditis case due to an emerging bacterium: Moraxella nonliquefaciens

Directory of Open Access Journals (Sweden)

C. Duployez

2017-01-01

Full Text Available Moraxella nonliquefaciens is a Gram-negative coccobacillus considered as a commensal organism from the upper respiratory tract, with low pathogenic potential. The phenotypical conventional identification is difficult and the matrix-assisted laser desorption/ionization time-of-flight technology has increased the resolution of identification of this bacterium. We report a fatal case of endocarditis due to M. nonliquefaciens whose identification was confirmed by 16S rRNA, and we review the literature on this pathogen in endocarditis.

Isolation of an unidentified pink-pigmented bacterium in a clinical specimen.

OpenAIRE

Odugbemi, T; Nwofor, C; Joiner, K T

1988-01-01

An unidentified pink-pigmented bacterium isolated from a clinical specimen is reported. The organism was oxidase, urease, and catalase positive; it grew on Thayer-Martin and MacConkey media. The isolate is possibly similar to an unnamed taxon (G.L. Gilardi and Y.C. Faur, J. Clin. Microbiol. 20:626-629, 1984); however, it had unique characteristics of nonmotility with no flagellum detectable and was a gram-negative coccoid with a few rods in pairs and negative for starch hydrolysis.

Isolation of an unidentified pink-pigmented bacterium in a clinical specimen.

Science.gov (United States)

Odugbemi, T; Nwofor, C; Joiner, K T

1988-05-01

An unidentified pink-pigmented bacterium isolated from a clinical specimen is reported. The organism was oxidase, urease, and catalase positive; it grew on Thayer-Martin and MacConkey media. The isolate is possibly similar to an unnamed taxon (G.L. Gilardi and Y.C. Faur, J. Clin. Microbiol. 20:626-629, 1984); however, it had unique characteristics of nonmotility with no flagellum detectable and was a gram-negative coccoid with a few rods in pairs and negative for starch hydrolysis.

Echinicola shivajiensis sp. nov., a novel bacterium of the family "Cyclobacteriaceae" isolated from brackish water pond

Digital Repository Service at National Institute of Oceanography (India)

Srinivas, T.N.R.; Tryambak, B.K.; AnilKumar, P.

Strain AK12 sup(T), an orange pigmented Gramnegative, rod shaped, non-motile bacterium, was isolated fromamud sample collected froma brackishwater pond at Rampur of West Bengal, India. The strain was positive for oxidase, catalase and phosphatase...

Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9

Science.gov (United States)

Liu, Jin-liang; Hu, Xiao-min

2013-01-01

Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus. PMID:23618713

Dissolution of Fe(III)(hydr)oxides by an Aerobic Bacterium

International Nuclear Information System (INIS)

Maurice, P.

2004-01-01

This project investigated the effects of an aerobic Pseudomonas mendocina bacterium on the dissolution of Fe(III)(hydr)oxides. The research is important because metals and radionuclides that adsorb to Fe(III)(hydr)oxides could potentially be remobilized by dissolving bacteria. We showed that P. mendocina is capable of dissolving Fe-bearing minerals by a variety of mechanisms, including production of siderophores, pH changes, and formation of reductants. The production of siderophores by P. mendocina was quantified under a variety of growth conditions. Finally, we demonstrated that microbial siderophores may adsorb to and enhance dissolution of clay minerals

Removal of arsenic from groundwater by using a native isolated arsenite-oxidizing bacterium.

Science.gov (United States)

Kao, An-Chieh; Chu, Yu-Ju; Hsu, Fu-Lan; Liao, Vivian Hsiu-Chuan

2013-12-01

Arsenic (As) contamination of groundwater is a significant public health concern. In this study, the removal of arsenic from groundwater using biological processes was investigated. The efficiency of arsenite (As(III)) bacterial oxidation and subsequent arsenate (As(V)) removal from contaminated groundwater using bacterial biomass was examined. A novel As(III)-oxidizing bacterium (As7325) was isolated from the aquifer in the blackfoot disease (BFD) endemic area in Taiwan. As7325 oxidized 2300μg/l As(III) using in situ As(III)-contaminated groundwater under aerobic conditions within 1d. After the oxidation of As(III) to As(V), As(V) removal was further examined using As7325 cell pellets. The results showed that As(V) could be adsorbed efficiently by lyophilized As7325 cell pellets, the efficiency of which was related to lyophilized cell pellet concentration. Our study conducted the examination of an alternative technology for the removal of As(III) and As(V) from groundwater, indicating that the oxidation of As(III)-contaminated groundwater by native isolated bacterium, followed by As(V) removal using bacterial biomass is a potentially effective technology for the treatment of As(III)-contaminated groundwater. © 2013.

Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila

OpenAIRE

Hammer, Austin J.; Walters, Amber; Carroll, Courtney; Newell, Peter D.; Chaston, John M.

2017-01-01

ABSTRACT The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429?bp, with 3,454 predicted genes.

Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

Science.gov (United States)

Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

2016-03-20

We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments. Copyright © 2016 Elsevier B.V. All rights reserved.

'Cand. Actinochlamydia clariae' gen. nov., sp. nov., a unique intracellular bacterium causing epitheliocystis in catfish (Clarias gariepinus in Uganda.

Directory of Open Access Journals (Sweden)

Andreas Steigen

Full Text Available BACKGROUND AND OBJECTIVES: Epitheliocystis, caused by bacteria infecting gill epithelial cells in fish, is common among a large range of fish species in both fresh- and seawater. The aquaculture industry considers epitheliocystis an important problem. It affects the welfare of the fish and the resulting gill disease may lead to mortalities. In a culture facility in Kampala, Uganda, juveniles of the African sharptooth catfish (Clarias gariepinus was observed swimming in the surface, sometimes belly up, showing signs of respiratory problems. Histological examination of gill tissues from this fish revealed large amounts of epitheliocysts, and also presence of a few Ichthyobodo sp. and Trichodina sp. METHODS AND RESULTS: Sequencing of the epitheliocystis bacterium 16S rRNA gene shows 86.3% similarity with Candidatus Piscichlamydia salmonis causing epitheliocystis in Atlantic salmon (Salmo salar. Transmission electron microscopy showed that the morphology of the developmental stages of the bacterium is similar to that of members of the family Chlamydiaceae. The similarity of the bacterium rRNA gene sequences compared with other chlamydia-like bacteria ranged between 80.5% and 86.3%. Inclusions containing this new bacterium have tubules/channels (termed actinae that are radiating from the inclusion membrane and opening on the cell surface or in neighbouring cells. CONCLUSIONS: Radiation of tubules/channels (actinae from the inclusion membrane has never been described in any of the other members of Chlamydiales. It seems to be a completely new character and an apomorphy. We propose the name Candidatus Actinochlamydia clariae gen. nov., sp. nov. (Actinochlamydiaceae fam. nov., order Chlamydiales, phylum Chlamydiae for this new agent causing epitheliocystis in African sharptooth catfish.

(Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

KAUST Repository

Balk, Melike

2010-08-03

A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

(Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

KAUST Repository

Balk, Melike; Mehboob, Farrakh; van Gelder, Antonie H; Rijpstra, W Irene C; Damsté , Jaap S Sinninghe; Stams, Alfons J M

2010-01-01

A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater

Digital Repository Service at National Institute of Oceanography (India)

Nupur; Bhumika, V.; Srinivas, T.N.R.; AnilKumar, P.

A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1 sup(T), was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate...

Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

NARCIS (Netherlands)

Sirota-Madi, A.; Olender, T.; Helman, Y.; Ingham, C.; Brainis, I.; Roth, D.; Hagi, E.; Brodsky, L.; Leshkowitz, D.; Galatenko, V.; Nikolaev, V.; Mugasimangalam, R.C.; Bransburg-Zabary, S.; Gutnick, D.L.; Lancet, D.; Ben-Jacob, E.

2010-01-01

Background: The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae)

Two New Cholic Acid Derivatives from the Marine Ascidian-Associated Bacterium Hasllibacter halocynthiae

Directory of Open Access Journals (Sweden)

Sung Hun Kim

2012-10-01

Full Text Available The investigation of secondary metabolites in liquid cultures of a recently discovered marine bacterium, Hasllibacter halocynthiae strain KME 002T, led to the isolation of two new cholic acid derivatives. The structures of these compounds were determined to be 3,3,12-trihydroxy-7-ketocholanic acid (1 and 3,3,12-trihydroxy-7-deoxycholanic acid (2 through HRFABMS and NMR data analyses.

Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium

Science.gov (United States)

Joshi, M. N.; Sharma, A. C.; Pandya, R. V.; Patel, R. P.; Saiyed, Z. M.; Saxena, A. K.

2012-01-01

Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented, menaquinone-7-producing bacterium isolated from sediments of a drilling well. The draft genome sequence of the strain, consisting of one chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin biosynthesis and resistance against various metals and antibiotics. PMID:23105068

Intestinimonas butyriciproducens gen. nov., sp. nov., a novel butyrate-producing bacterium from the mouse intestine

NARCIS (Netherlands)

Kläring, K.; Hanske, L.; Bui, T.P.N.; Charrier, C.; Blaut, M.; Haller, D.; Plugge, C.M.; Clavel, T.

2013-01-01

Whilst creating a bacterial collection of strains from the mouse intestine, we isolated a Gram-negative, spore-forming, non-motile and strictly anaerobic rod-shaped bacterium from the caecal content of a TNFdeltaARE mouse. The isolate, referred to as strain SRB-521-5-IT, was originally cultured on a

Curiously modern DNA for a "250 million-year-old" bacterium.

Science.gov (United States)

Nickle, David C; Learn, Gerald H; Rain, Matthew W; Mullins, James I; Mittler, John E

2002-01-01

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies.

Diversity of 23S rRNA genes within individual prokaryotic genomes.

Directory of Open Access Journals (Sweden)

Anna Pei

Full Text Available BACKGROUND: The concept of ribosomal constraints on rRNA genes is deduced primarily based on the comparison of consensus rRNA sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rRNA operons. METHODOLOGY/PRINCIPAL FINDINGS: Using the 23S rRNA gene as an example, we analyzed the diversity among individual rRNA genes within a genome. Of 184 prokaryotic species containing multiple 23S rRNA genes, diversity was observed in 113 (61.4% genomes (mean 0.40%, range 0.01%-4.04%. Significant (1.17%-4.04% intragenomic variation was found in 8 species. In 5 of the 8 species, the diversity in the primary structure had only minimal effect on the secondary structure (stem versus loop transition. In the remaining 3 species, the diversity significantly altered local secondary structure, but the alteration appears minimized through complex rearrangement. Intervening sequences (IVS, ranging between 9 and 1471 nt in size, were found in 7 species. IVS in Deinococcus radiodurans and Nostoc sp. encode transposases. T. tengcongensis was the only species in which intragenomic diversity >3% was observed among 4 paralogous 23S rRNA genes. CONCLUSIONS/SIGNIFICANCE: These findings indicate tight ribosomal constraints on individual 23S rRNA genes within a genome. Although classification using primary 23S rRNA sequences could be erroneous, significant diversity among paralogous 23S rRNA genes was observed only once in the 184 species analyzed, indicating little overall impact on the mainstream of 23S rRNA gene-based prokaryotic taxonomy.

Geomicrobiology of High Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State

International Nuclear Information System (INIS)

Fredrickson, Jim K.; Zachara, John M.; Balkwill, David L.; Kennedy, David W.; Li, Shu-Mei W.; Kostandarithes, Heather M.; Daly, Michael J.; Romine, Margaret F.; Brockman, Fred J.

2004-01-01

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), 137Cs, and 99Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to ∼104 7 CFU g-1 but viable microorganisms were recovered from 11 of 16 samples including several of the most radioactive ones (e.g., > 10 ?Ci/g 137Cs). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known Gram-positive bacteria. Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples but other high G+C phyla were also represented including Rhodococcus and Nocardia. Two isolates from the second most radioactive sample (>20 ?Ci 137Cs g-1) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20kGy. Many of the Gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that Gram-positive bacteria, predominantly high G+C phyla, are indigenous to Hanford vadose sediments and some are effective at surviving the extreme physical and chemical stress associated with radioactive waste

The fate of a nitrobenzene-degrading bacterium in pharmaceutical wastewater treatment sludge.

Science.gov (United States)

Ren, Yuan; Yang, Juan; Chen, Shaoyi

2015-12-01

This paper describes the fate of a nitrobenzene-degrading bacterium, Klebsiella oxytoca NBA-1, which was isolated from a pharmaceutical wastewater treatment facility. The 90-day survivability of strain NBA-1 after exposure to sludge under anaerobic and aerobic conditions was investigated. The bacterium was inoculated into sludge amended with glucose and p-chloronitrobenzene (p-CNB) to compare the bacterial community variations between the modified sludge and nitrobenzene amendment. The results showed that glucose had no obvious effect on nitrobenzene biodegradation in the co-metabolism process, regardless of the presence/absence of oxygen. When p-CNB was added under anaerobic conditions, the biodegradation rate of nitrobenzene remained unchanged although p-CNB inhibited the production of aniline. The diversity of the microbial community increased and NBA-1 continued to be one of the dominant strains. Under aerobic conditions, the degradation rate of both nitrobenzene and p-CNB was only 20% of that under anaerobic conditions. p-CNB had a toxic effect on the microorganisms in the sludge so that most of the DGGE (denaturing gradient gel electrophoresis) bands, including that of NBA-1, began to disappear under aerobic conditions after 90days of exposure. These data show that the bacterial community was stable under anaerobic conditions and the microorganisms, including NBA-1, were more resistant to the adverse environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Reduction of nitric oxide catalyzed by hydroxylamine oxidoreductase from an anammox bacterium.

Science.gov (United States)

Irisa, Tatsuya; Hira, Daisuke; Furukawa, Kenji; Fujii, Takao

2014-12-01

The hydroxylamine oxidoreductase (HAO) from the anammox bacterium, Candidatus Kuenenia stuttgartiensis has been reported to catalyze the oxidation of hydroxylamine (NH2OH) to nitric oxide (NO) by using bovine cytochrome c as an oxidant. In contrast, we investigated whether the HAO from anammox bacterium strain KSU-1 could catalyze the reduction of NO with reduced benzyl viologen (BVred) and the NO-releasing reagent, NOC 7. The reduction proceeded, resulting in the formation of NH2OH as a product. The oxidation rate of BVred was proportional to the concentration of BVred itself for a short period in each experiment, a situation that was termed quasi-steady state. The analyses of the states at various concentrations of HAO allowed us to determine the rate constant for the catalytic reaction, (2.85 ± 0.19) × 10(5) M(-1) s(-1), governing NO reduction by BVred and HAO, which was comparable to that reported for the HAO from the ammonium oxidizer, Nitrosomonas with reduced methyl viologen. These results suggest that the anammox HAO functions to adjust anammox by inter-conversion of NO and NH2OH depending on the redox potential of the physiological electron transfer protein in anammox bacteria. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

UV-induced variability of the amylolytic thermophilic bacterium Bacillus diastaticus

International Nuclear Information System (INIS)

Murygina, V.P.

1978-01-01

UV-induced variability of a thermophilic bacterium Bacillus diastaticus 13 by amylase formation has been studied. It has been shown, that variability limits in amylase biosynthesis vary from 2.2 to 158.7% under UV irradiation. At 41.8x10 2 erg/mm 2 UV dose a ''plus-variant'' designated as the UV1 mutant has been prepared. Its subsequent selection without using mutagene permitted to select the UV 1-25 variant, exceeding the initial strain in amylase biosynthesis by 43.3%. Under UV irradiation two low-active in biosynthesis amylases of the mutant were prepared. Demands for growth factors of some mutant have been studied as well

UV-induced variability of the amylolytic thermophilic bacterium Bacillus diastaticus

Energy Technology Data Exchange (ETDEWEB)

Murygina, V P

1978-03-01

Ultroviolet-radioinduced variability in analyase biosynthesis of a thermophilic bacterium Bacillus diastaticus 13, has been studied. It has been shown that amylase biosynthesis varies from 2.2 to 158.7% under UV irradiation. At 41.8x10/sup 2/ erg/mm/sup 2/ UV dose, a ''plus-variant'' designated as the UV1 mutant has been prepared. Its subsequent selection without using mutagene permitted to select the UV 1-25 variant, exceeding the initial strain in amylase biosynthesis by 43.3%. Under UV irradiation, two mutants with reduced amylose biosynthesis activity were prepared. Demands for growth factors by some mutants have been studied as well.

Cesium accumulation by bacterium Thermus sp.TibetanG7: hints for biomineralization of cesiumbearing geyserite in hot springs in Tibet, China

Institute of Scientific and Technical Information of China (English)

无

2007-01-01

The bacterium Thermus sp. TibetanG7, isolated from hot springs in Tibet, China, was examined for the ability to accumulate cesium from solutions. Environmental conditions were simulated and the effects of pH, K+, Na+ and K+-regimes were then studied to determine the possible role of the bacterium in the formation of cesium-bearing geyserite around these hot springs. In despite of the inhibition of K+ and Na+, the bacterium Thermus sp. TibetanG7 revealed noticeable accumulation of cesium from solutions, with maximum accumulations of 53.49 and 40.41 μmol Cesium/g cell dry weight in Na+ and K+ inhibition experiments, respectively. The accumulation of cesium by this microorganism is rapid, with 40%―50% accumulated within the first 5 min. K+-deficient cells showed a much higher capacity of cesium accumulation compared with K+-sufficient cells. It is evident that the bacteria within the genus thermus play a significant role in the cesium assembly. The formation of cesium-bearing geyserite is also considered.

Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila.

Science.gov (United States)

Hammer, Austin J; Walters, Amber; Carroll, Courtney; Newell, Peter D; Chaston, John M

2017-07-06

The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429 bp, with 3,454 predicted genes. Copyright © 2017 Hammer et al.

Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group.

Directory of Open Access Journals (Sweden)

Vitaly V Kadnikov

Full Text Available Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2(T. A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi.

Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.

Science.gov (United States)

Han, Yejun; Agarwal, Vinayak; Dodd, Dylan; Kim, Jason; Bae, Brian; Mackie, Roderick I; Nair, Satish K; Cann, Isaac K O

2012-10-12

Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.

Complete genome sequencing of the luminescent bacterium, Vibrio qinghaiensis sp. Q67 using PacBio technology

Science.gov (United States)

Gong, Liang; Wu, Yu; Jian, Qijie; Yin, Chunxiao; Li, Taotao; Gupta, Vijai Kumar; Duan, Xuewu; Jiang, Yueming

2018-01-01

Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands. Our dataset can be useful as a comparative genome for evolution and speciation studies, as well as for the analysis of protein-coding gene families, the pathogenicity of different Vibrio species in fish, the evolution of non-coding RNA and transposon, and the regulation of gene expression in relation to the bioluminescence of Vqin-Q67.

ANALYSIS OF IMMUNE RESPONSES ON TRANSGENIC TIGER SHRIMP (Penaeus monodon AGAINST PATHOGENIC BACTERIUM Vibrio harveyi

Directory of Open Access Journals (Sweden)

Andi Parenrengi

2014-06-01

Full Text Available Vibriosis is one of main diseases of the black tiger shrimp Penaeus monodon infected by pathogenic bioluminous bacterium Vibrio harveyi that can cause mass mortalities in shrimp culture. The bacteria can also trigger the disease white spot syndrome virus (WSSV. An effort to produce shrimp disease-resistant strains has been done through transgenesis technology with antiviral gene transfection. By this technology, it is expected an increase in the immune response of shrimp in a variety of diseasecausing pathogens. This study aimed to determine the immune responses (total haemocytes, haemocyte differentiation, and phenoloxydase activity of transgenic tiger shrimp against pathogenic bacterium V. harveyi. Research using completely randomized design, which consists of two treatments and three replications. Test animals being used were transgenic and non-transgenic shrimp with size, weight 3.93±1.25 g and a total length of 7.59±0.87 cm. Treatments being tested were the injection of bacterium V. harveyi (density of 5x106 cfu/mL of 0.1 mL/individual on transgenic (A and non-transgenic shrimp (B. Immune response parameters such as total haemocytes, haemocyte differentiation, and phenoloxydase activity were observed on day 1, 3, and 6 days after challenging. Data were analyzed using t-test by SPSS software. The results showed that the total haemocyte of transgenic shrimp was not significantly different (P>0.05 from non-transgenic shrimp, but haemocyte differentiation and phenoloxydase activity were significantly different (P<0.05 especially on sixth days after being exposed to the bioluminescent bacteria. The study results implied that transgenic shrimp has a better immune response compared than non-transgenic shrimp.

Host-adaptation of Francisella tularensis alters the bacterium's surface-carbohydrates to hinder effectors of innate and adaptive immunity.

Directory of Open Access Journals (Sweden)

Tiffany M Zarrella

Full Text Available The gram-negative bacterium Francisella tularensis survives in arthropods, fresh water amoeba, and mammals with both intracellular and extracellular phases and could reasonably be expected to express distinct phenotypes in these environments. The presence of a capsule on this bacterium has been controversial with some groups finding such a structure while other groups report that no capsule could be identified. Previously we reported in vitro culture conditions for this bacterium which, in contrast to typical methods, yielded a bacterial phenotype that mimics that of the bacterium's mammalian, extracellular phase.SDS-PAGE and carbohydrate analysis of differentially-cultivated F. tularensis LVS revealed that bacteria displaying the host-adapted phenotype produce both longer polymers of LPS O-antigen (OAg and additional HMW carbohydrates/glycoproteins that are reduced/absent in non-host-adapted bacteria. Analysis of wildtype and OAg-mutant bacteria indicated that the induced changes in surface carbohydrates involved both OAg and non-OAg species. To assess the impact of these HMW carbohydrates on the access of outer membrane constituents to antibody we used differentially-cultivated bacteria in vitro to immunoprecipitate antibodies directed against outer membrane moieties. We observed that the surface-carbohydrates induced during host-adaptation shield many outer membrane antigens from binding by antibody. Similar assays with normal mouse serum indicate that the induced HMW carbohydrates also impede complement deposition. Using an in vitro macrophage infection assay, we find that the bacterial HMW carbohydrate impedes TLR2-dependent, pro-inflammatory cytokine production by macrophages. Lastly we show that upon host-adaptation, the human-virulent strain, F. tularensis SchuS4 also induces capsule production with the effect of reducing macrophage-activation and accelerating tularemia pathogenesis in mice.F. tularensis undergoes host-adaptation which

Cellulosic ethanol production via consolidated bioprocessing by a novel thermophilic anaerobic bacterium isolated from a Himalayan hot spring.

Science.gov (United States)

Singh, Nisha; Mathur, Anshu S; Tuli, Deepak K; Gupta, Ravi P; Barrow, Colin J; Puri, Munish

2017-01-01

Cellulose-degrading thermophilic anaerobic bacterium as a suitable host for consolidated bioprocessing (CBP) has been proposed as an economically suited platform for the production of second-generation biofuels. To recognize the overall objective of CBP, fermentation using co-culture of different cellulolytic and sugar-fermenting thermophilic anaerobic bacteria has been widely studied as an approach to achieving improved ethanol production. We assessed monoculture and co-culture fermentation of novel thermophilic anaerobic bacterium for ethanol production from real substrates under controlled conditions. In this study, Clostridium sp. DBT-IOC-C19, a cellulose-degrading thermophilic anaerobic bacterium, was isolated from the cellulolytic enrichment cultures obtained from a Himalayan hot spring. Strain DBT-IOC-C19 exhibited a broad substrate spectrum and presented single-step conversion of various cellulosic and hemicellulosic substrates to ethanol, acetate, and lactate with ethanol being the major fermentation product. Additionally, the effect of varying cellulose concentrations on the fermentation performance of the strain was studied, indicating a maximum cellulose utilization ability of 10 g L -1 cellulose. Avicel degradation kinetics of the strain DBT-IOC-C19 displayed 94.6% degradation at 5 g L -1 and 82.74% degradation at 10 g L -1 avicel concentration within 96 h of fermentation. In a comparative study with Clostridium thermocellum DSM 1313, the ethanol and total product concentrations were higher by the newly isolated strain on pretreated rice straw at an equivalent substrate loading. Three different co-culture combinations were used on various substrates that presented two-fold yield improvement than the monoculture during batch fermentation. This study demonstrated the direct fermentation ability of the novel thermophilic anaerobic bacteria on various cellulosic and hemicellulosic substrates into ethanol without the aid of any exogenous enzymes

Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

Science.gov (United States)

Jin, Decai; Zhou, Lisha; Wu, Liang; An, Wei; Zhao, Lin

2014-01-01

Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated marine sediments. Here, we report the 4.8-Mb draft genome sequence of this strain, which will provide insights into the diversity of A. kashmirensis and the mechanism of PAH degradation in the marine environment. PMID:24482505

The heterocyclic ring fission and dehydroxylation of catechins and related compounds by Eubacterium sp. strain SDG-2, a human intestinal bacterium.

Science.gov (United States)

Wang, L Q; Meselhy, M R; Li, Y; Nakamura, N; Min, B S; Qin, G W; Hattori, M

2001-12-01

A human intestinal bacterium, Eubacterium (E.) sp. strain SDG-2, was tested for its ability to metabolize various (3R)- and (3S)-flavan-3-ols and their 3-O-gallates. This bacterium cleaved the C-ring of (3R)- and (3S)-flavan-3-ols to give 1,3-diphenylpropan-2-ol derivatives, but not their 3-O-gallates. Furthermore, E. sp. strain SDG-2 had the ability of p-dehydroxylation in the B-ring of (3R)-flavan-3-ols, such as (-)-catechin, (-)-epicatechin, (-)-gallocatechin and (-)-epigallocatechin, but not of (3S)-flavan-3-ols, such as (+)-catechin and (+)-epicatechin.

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

NARCIS (Netherlands)

Bollmann, A.; Sedlacek, C.J.; Norton, J.; Laanbroek, H.J.; Suwa, Y.; Stein, L.Y.; Klotz, M.G.; Arp, D.; Sayavedra-Soto, L.; Lu, M.; Bruce, D.; Detter, C.; Tapia, R.; Han, J.; Woyke, T.; Lucas, S.; Pitluck, S.; Pennacchio, L.; Nolan, M.; Land, M.L.; Huntemann, M.; Deshpande, S.; Han, C.; Chen, A.; Kyrpides, N.; Mavromatis, K.; Markowitz, V.; Szeto, E.; Ivanova, N.; Mikhailova, N.; Pagani, I.; Pati, A.; Peters, L.; Ovchinnikova, G.; Goodwin, L.

2013-01-01

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production

Extracellular polymer substance synthesized by a halophilic bacterium Chromohalobacter canadensis 28.

Science.gov (United States)

Radchenkova, Nadja; Boyadzhieva, Ivanka; Atanasova, Nikolina; Poli, Annarita; Finore, Ilaria; Di Donato, Paola; Nicolaus, Barbara; Panchev, Ivan; Kuncheva, Margarita; Kambourova, Margarita

2018-04-03

Halophilic microorganisms are producers of a lot of new compounds whose properties suggest promising perspectives for their biotechnological exploration. Moderate halophilic bacterium Chromohalobacter canadensis 28 was isolated from Pomorie salterns as an extracellular polymer substance (EP) producer. The best carbon source for extracellular polymer production was found to be lactose, a sugar received as a by-product from the dairy industry. After optimization of the culture medium and physicochemical conditions for cultivation, polymer biosynthesis increased more than 2-fold. The highest level of extracellular polymer synthesis by C. canadensis 28 was observed in an unusually high NaCl concentration (15% w/v). Chemical analysis of the purified polymer revealed the presence of an exopolysaccharide (EPS) fraction (14.3% w/w) and protein fraction (72% w/w). HPLC analysis of the protein fraction showed the main presence of polyglutamic acid (PGA) (75.7% w/w). EPS fraction analysis revealed the following sugar composition (% w/w): glucosamine 36.7, glucose 32.3, rhamnose 25.4, xylose 1.7, and not identified sugar 3.9. The hydrogel formed by PGA and EPS fractions showed high swelling behavior, very good emulsifying and stabilizing properties, and good foaming ability. This is the first report for halophilic bacterium able to synthesize a polymer containing PGA fraction. The synthesized biopolymer shows an extremely high hydrophilicity, due to the simultaneous presence of PGA and EPS. The analysis of its functional properties and the presence of glucosamine in the highest proportion in EPS fraction clearly determine the potential of EP synthesized by C. canadensis 28 for application in the cosmetics industry.

The Purine-Utilizing Bacterium Clostridium acidurici 9a: A Genome-Guided Metabolic Reconsideration

OpenAIRE

Hartwich, Katrin; Poehlein, Anja; Daniel, Rolf

2012-01-01

Clostridium acidurici is an anaerobic, homoacetogenic bacterium, which is able to use purines such as uric acid as sole carbon, nitrogen, and energy source. Together with the two other known purinolytic clostridia C. cylindrosporum and C. purinilyticum, C. acidurici serves as a model organism for investigation of purine fermentation. Here, we present the first complete sequence and analysis of a genome derived from a purinolytic Clostridium. The genome of C. acidurici 9a consists ...

Characterization of carbon dioxide concentrating chemolithotrophic bacterium Serratia sp. ISTD04 for production of biodiesel.

Science.gov (United States)

Kumar, Manish; Morya, Raj; Gnansounou, Edgard; Larroche, Christian; Thakur, Indu Shekhar

2017-11-01

Proteomics and metabolomics analysis has become a powerful tool for characterization of microbial ability for fixation of Carbon dioxide. Bacterial community of palaeoproterozoic metasediments was enriched in the shake flask culture in the presence of NaHCO 3 . One of the isolate showed resistance to NaHCO 3 (100mM) and was identified as Serratia sp. ISTD04 by 16S rRNA sequence analysis. Carbon dioxide fixing ability of the bacterium was established by carbonic anhydrase enzyme assay along with proteomic analysis by LC-MS/MS. In proteomic analysis 96 proteins were identified out of these 6 protein involved in carbon dioxide fixation, 11 in fatty acid metabolism, indicating the carbon dioxide fixing potency of bacterium along with production of biofuel. GC-MS analysis revealed that hydrocarbons and FAMEs produced by bacteria within the range of C 13 -C 24 and C 11 -C 19 respectively. Presence of 59% saturated and 41% unsaturated organic compounds, make it a better fuel composition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque.

Science.gov (United States)

Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan

2016-02-10

Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium.

Menaquinone-7 in the reaction center complex of the green sulfur bacterium Chlorobium vibrioforme functions as the electron acceptor A1

DEFF Research Database (Denmark)

Kjaer, B; Frigaard, N-U; Yang, F

1998-01-01

Photosynthetically active reaction center complexes were prepared from the green sulfur bacterium Chlorobium vibrioforme NCIMB 8327, and the content of quinones was determined by extraction and high-performance liquid chromatography. The analysis showed a stoichiometry of 1.7 molecules of menaqui......Photosynthetically active reaction center complexes were prepared from the green sulfur bacterium Chlorobium vibrioforme NCIMB 8327, and the content of quinones was determined by extraction and high-performance liquid chromatography. The analysis showed a stoichiometry of 1.7 molecules...

Natural Competence of Xylella fastidiosa Occurs at a High Frequency Inside Microfluidic Chambers Mimicking the Bacterium's Natural Habitats.

Science.gov (United States)

Kandel, Prem P; Lopez, Samantha M; Almeida, Rodrigo P P; De La Fuente, Leonardo

2016-09-01

Xylella fastidiosa is a xylem-limited bacterium that is the causal agent of emerging diseases in a number of economically important crops. Genetic diversity studies have demonstrated homologous recombination occurring among X. fastidiosa strains, which has been proposed to contribute to host plant shifts. Moreover, experimental evidence confirmed that X. fastidiosa is naturally competent for recombination in vitro Here, as an approximation of natural habitats (plant xylem vessels and insect mouthparts), recombination was studied in microfluidic chambers (MCs) filled with media amended with grapevine xylem sap. First, different media were screened for recombination in solid agar plates using a pair of X. fastidiosa strains that were previously reported to recombine in coculture. The highest frequency of recombination was obtained with PD3 medium, compared to those with the other two media (X. fastidiosa medium [XFM] and periwinkle wilt [PW] medium) used in previous studies. Dissection of the media components led to the identification of bovine serum albumin as an inhibitor of recombination that was correlated to its previously known effect on inhibition of twitching motility. When recombination was performed in liquid culture, the frequencies were significantly higher under flow conditions (MCs) than under batch conditions (test tubes). The recombination frequencies in MCs and agar plates were not significantly different from each other. Grapevine xylem sap from both susceptible and tolerant varieties allowed high recombination frequency in MCs when mixed with PD3. These results suggest that X. fastidiosa has the ability to be naturally competent in the natural growth environment of liquid flow, and this phenomenon could have implications in X. fastidiosa environmental adaptation. Xylella fastidiosa is a plant pathogen that lives inside xylem vessels (where water and nutrients are transported inside the plant) and the mouthparts of insect vectors. This bacterium

Establishment of an efficient fermentation system of gamma-aminobutyric acid by a lactic acid bacterium, Enterococcus avium G-15, isolated from carrot leaves.

Science.gov (United States)

Tamura, Takayoshi; Noda, Masafumi; Ozaki, Moeko; Maruyama, Masafumi; Matoba, Yasuyuki; Kumagai, Takanori; Sugiyama, Masanori

2010-01-01

In the present study, we successfully isolated a carrot leaf-derived lactic acid bacterium that produces gamma-aminobutyric acid (GABA) from monosodium L-glutamate (L-MSG) at a hyper conversion rate. The GABA-producing bacterium, identified as Enterococcus (E.) avium G-15, produced 115.7±6.4 g/l GABA at a conversion rate of 86.0±5.0% from the added L-MSG under the optimum culture condition by a continuous L-MSG feeding method using a jar-fermentor, suggesting that the bacterium displays a great potential ability for the commercial-level fermentation production of GABA. Using the reverse transcription polymerase chain reaction (RT-PCR) method, we analyzed the expression of genes for the GABA transporter and glutamate decarboxylase, designated gadT and gadG, respectively, which were cloned from the E. avium G-15 chromosome. Both genes were expressed even without the added L-MSG, but their expression was enhanced by the addition of L-MSG.

[Genetic variability of the bacterium Ralstonia solanacearum (Burkholderiales: Burholderiaceae) in the banana-growing region of Uraba (Colombia)].

Science.gov (United States)

Cardozo, Carolina; Rodríguez, Paola; Cotes, José Miguel; Marín, Mauricio

2010-03-01

The banana moko disease, caused by the bacterium Ralstonia solanacearum, is one of the most important phytopathological problems of the banana agribusiness in tropical countries. In Uraba and Magdalena (Colombia), the main exporting regions of banana in Colombia, this disease causes a destruction estimated in 16.5 ha/year. The bacterium presents an extremely high level of genetic variation that affects control measures. This is the first study of its variation in Colombia and was done with AFLP molecular markers on a population of 100 isolates from banana plants, soils and "weeds". The high level of genetic diversity, with Nei and Shannon indexes of h=0.32 and I=0.48, respectively, and the AMOVA, showed that this population is subestructured (Fst=0.66): the host is the main factor of differentiation. Even so, previous tests show that all varieties have pathogenicity on Musa.

Characterization of bornite (Cu5FeS4 electrodes in the presence of the bacterium Acidithiobacillus ferrooxidans

Directory of Open Access Journals (Sweden)

Bevilaqua Denise

2003-01-01

Full Text Available Bornite electrodes were characterized in the absence or in the presence of Acidithiobacillus ferrooxidans, which is an important microorganism involved in metal bioleaching processes. The presence of the bacterium modified the mineral/electrolyte interface, increasing the corrosion rate, as revealed by interferometric, AEM, ICP and EIS analyses. As a consequence of bacterial activity the electrode became porous, increasing its surface heterogeneity. This behavior was correlated with the evolution of impedance diagrams obtained during the time course of experiments. The main difference in these diagrams was the presence of an inductive feature (up to 44 h, which was related to bacterial action on the mineral dissolution, better than to its adhesion on the bornite. The total real impedance measured in presence of the bacterium was about 10 times lower than in its absence, due to the acceleration of the mineral dissolution, because an oxidant environment was maintained.

Roles of dental pulp fibroblasts in the recognition of bacterium-related factors and subsequent development of pulpitis

Directory of Open Access Journals (Sweden)

Tadashi Nakanishi

2011-08-01

Full Text Available As caries-related bacteria invade deeply into dentin and come into close proximity to the pulp, inflammatory cells (such as lymphocytes, macrophages and neutrophils infiltrate into the bacterium-invaded area and consequently pulpitis develops. Many types of cytokines and adhesion molecules are responsible for the initiation and progression of pulpitis. Dental pulp fibroblasts, a major cell type in the dental pulp, also have capacity to produce pro-inflammatory cytokines and express adhesion molecules in response to pathogen-associated molecular patterns (PAMPs, including lipopolysaccharide. The innate immune system senses microbial infection using pattern recognition receptors, such as Toll-like receptors (TLRs and nucleotide-binding oligomerization domain (NOD, for PAMPs. In this review, we summarize the roles of dental pulp fibroblasts in the recognition of invaded bacterium-related factors via TLR and NOD pathways, and the subsequent pulpal immune responses, leading to progressive pulpitis.

The O-antigen structure of bacterium Comamonas aquatica CJG.

Science.gov (United States)

Wang, Xiqian; Kondakova, Anna N; Zhu, Yutong; Knirel, Yuriy A; Han, Aidong

2017-11-01

Genus Comamonas is a group of bacteria that are able to degrade a variety of environmental waste. Comamonas aquatica CJG (C. aquatica) in this genus is able to absorb low-density lipoprotein but not high-density lipoprotein of human serum. Using 1 H and 13 C NMR spectroscopy, we found that the O-polysaccharide (O-antigen) of this bacterium is comprised of a disaccharide repeat (O-unit) of d-glucose and 2-O-acetyl-l-rhamnose, which is shared by Serratia marcescens O6. The O-antigen gene cluster of C. aquatica, which is located between coaX and tnp4 genes, contains rhamnose synthesis genes, glycosyl and acetyl transferase genes, and ATP-binding cassette transporter genes, and therefore is consistent with the O-antigen structure determined here.

Growth of a Strictly Anaerobic Bacterium on Furfural (2-Furaldehyde)

Science.gov (United States)

Brune, Gerhard; Schoberth, Siegfried M.; Sahm, Hermann

1983-01-01

A strictly anaerobic bacterium was isolated from a continuous fermentor culture which converted the organic constituents of sulfite evaporator condensate to methane and carbon dioxide. Furfural is one of the major components of this condensate. This furfural isolate could degrade furfural as the sole source of carbon and energy in a defined mineral-vitamin-sulfate medium. Acetic acid was the major fermentation product. This organism could also use ethanol, lactate, pyruvate, or fumarate and contained cytochrome c3 and desulfoviridin. Except for furfural degradation, the characteristics of the furfural isolate were remarkably similar to those of the sulfate reducer Desulfovibrio gigas. The furfural isolate has been tentatively identified as Desulfovibrio sp. strain F-1. Images PMID:16346423

Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

Science.gov (United States)

Liu, Yang; Wang, Runping; Zeng, Runying

2014-12-01

Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

Complete genome sequences of two strains of the meat spoilage bacterium Brochothrix thermosphacta isolated from ground chicken

Science.gov (United States)

Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT©) technology and are the first complete ...

Characterization of cytochrome P450 monooxygenase CYP154H1 from the thermophilic soil bacterium Thermobifida fusca

NARCIS (Netherlands)

Schallmey, Anett; den Besten, Gijs; Teune, Ite G. P.; Kembaren, Roga F.; Janssen, Dick B.

Cytochrome P450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. We have cloned the gene for a new cytochrome P450 monooxygenase, named CYP154H1, from the moderately thermophilic soil bacterium Thermobifida fusca. The

Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air.

Directory of Open Access Journals (Sweden)

M Tanweer Khan

Full Text Available The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far precluded its clinical application in the treatment of patients with inflammatory bowel diseases. The present studies were therefore aimed at developing a strategy to keep F. prausnitzii alive at ambient air. Our previous research showed that F. prausnitzii can survive in moderately oxygenized environments like the gut mucosa by transfer of electrons to oxygen. For this purpose, the bacterium exploits extracellular antioxidants, such as riboflavin and cysteine, that are abundantly present in the gut. We therefore tested to what extent these antioxidants can sustain the viability of F. prausnitzii at ambient air. The present results show that cysteine can facilitate the survival of F. prausnitzii upon exposure to air, and that this effect is significantly enhanced the by addition of riboflavin and the cryoprotectant inulin. The highly oxygen-sensitive gut bacterium F. prausnitzii can be kept alive at ambient air for 24 h when formulated with the antioxidants cysteine and riboflavin plus the cryoprotectant inulin. Improved formulations were obtained by addition of the bulking agents corn starch and wheat bran. Our present findings pave the way towards the biomedical exploitation of F. prausnitzii in redox-based therapeutics for treatment of dysbiosis-related inflammatory disorders of the human gut.

Illuminating the landscape of host–pathogen interactions with the bacterium Listeria monocytogenes

Science.gov (United States)

Cossart, Pascale

2011-01-01

Listeria monocytogenes has, in 25 y, become a model in infection biology. Through the analysis of both its saprophytic life and infectious process, new concepts in microbiology, cell biology, and pathogenesis have been discovered. This review will update our knowledge on this intracellular pathogen and highlight the most recent breakthroughs. Promising areas of investigation such as the increasingly recognized relevance for the infectious process, of RNA-mediated regulations in the bacterium, and the role of bacterially controlled posttranslational and epigenetic modifications in the host will also be discussed. PMID:22114192

Lactobacillus diolivorans sp nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage

NARCIS (Netherlands)

Krooneman, J; Faber, F; Alderkamp, AC; Elferink, SJHWO; Driehuis, F; Cleenwerck, [No Value; Swings, J; Gottschal, JC; Vancanneyt, M

Inoculation of maize silage with Lactobacillus buchneri (5 x 10(5) c.f.u. g(-1) of maize silage) prior to ensiling results in the formation of aerobically stable silage. After 9 months, lactic acid bacterium counts are approximately 10(10) c.f.u. g(-1) in these treated silages. An important

Thermotoga lettingae sp. nov. : a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor

NARCIS (Netherlands)

Balk, M.; Weijma, J.; Stams, A.J.M.

2002-01-01

A novel, anaerobic, non-spore-forming, mobile, Gram-negative, thermophilic bacterium, strain TMO(T), was isolated from a thermophilic sulfate-reducing bioreactor operated at 65 degrees C with methanol as the sole substrate. The G C content of the DNA of strain TMO(T) was 39.2 molÐThe optimum pH,

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

KAUST Repository

Harjes, Janno; Ryu, Tae Woo; Abdelmohsen, Usama Ramadan; Moitinho-Silva, Lucas; Horn, Hannes; Ravasi, Timothy; Hentschel, Ute

2014-01-01

The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

KAUST Repository

Harjes, Janno

2014-03-06

The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

Isolation and Structure Elucidation of a Novel Yellow Pigment from the Marine Bacterium Pseudoalteromonas tunicata

Directory of Open Access Journals (Sweden)

N. Kumar

2005-10-01

Full Text Available The marine environment is a major source for many novel natural compounds. A new yellow pigment has been isolated from the marine bacterium P. tunicata and identified as a new member of the tambjamine class of compounds. The structural identification was achieved by a combination of 1D and 2D-NMR spectroscopy and high resolution mass spectrometry data.

Isolation, cloning and characterization of an azoreductase from the halophilic bacterium Halomonas elongata.

Science.gov (United States)

Eslami, Maryam; Amoozegar, Mohammad Ali; Asad, Sedigheh

2016-04-01

Azo dyes are a major class of colorants used in various industries including textile, paper and food. These dyes are regarded as pollutant since they are not readily reduced under aerobic conditions. Halomonas elongata, a halophilic bacterium, has the ability to decolorize different mono and di-azo dyes in anoxic conditions. In this study the putative azoreductase gene of H. elongata, formerly annotated as acp, was isolated, heterologously expressed in Escherichia coli, purified and characterized. The gene product, AzoH, was found to have a molecular mass of 22 kDa. The enzyme requires NADH, as an electron donor for its activity. The apparent Km was 63 μM for NADH and 12 μM for methyl red as a mono-azo dye substrate. The specific activity for methyl red was 0.27 μmol min(-1)mg(-1). The optimum enzyme activity was achieved in 50mM sodium phosphate buffer at pH 6. Although increased salinity resulted in reduced activity, AzoH could decolorize azo dye at NaCl concentrations up to 15% (w/v). The enzyme was also shown to be able to decolorize remazol black B as a representative of di-azo dyes. This is the first report describing the sequence and activity of an azo-reducing enzyme from a halophilic bacterium. Copyright © 2015 Elsevier B.V. All rights reserved.

Nonlinear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacterium Dinoroseobacter shibae

Czech Academy of Sciences Publication Activity Database

Piwosz, Kasia; Kaftan, David; Dean, Jason; Šetlík, Jiří; Koblížek, Michal

2018-01-01

Roč. 20, č. 2 (2018), s. 724-733 ISSN 1758-2229 R&D Projects: GA MŠk(CZ) LO1416 Institutional support: RVO:61388971 Keywords : PHOTOSYNTHETIC BACTERIUM * LEUCINE INCORPORATION * SOLAR-RADIATION Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.363, year: 2016

Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria

OpenAIRE

da Silva, F?bio Daniel Flor?ncio; Lima, Alex Ranieri Jer?nimo; Moraes, Pablo Henrique Gon?alves; Siqueira, Andrei Santos; Dall?Agnol, Leonardo Teixeira; Bara?na, Anna Rafaella Ferreira; Martins, Luisa Car?cio; Oliveira, Karol Guimar?es; de Lima, Clayton Pereira Silva; Nunes, M?rcio Roberto Teixeira; Vianez-J?nior, Jo?o L?dio Silva Gon?alves; Gon?alves, Evonnildo Costa

2016-01-01

Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here.

Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24.

Directory of Open Access Journals (Sweden)

Sang-Yeop Lee

Full Text Available Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs, including benzene, toluene, and xylene (BTX, as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.

Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24

Science.gov (United States)

Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

2016-01-01

Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX. PMID:27124467

A bacterium that can grow by using arsenic instead of phosphorus

Energy Technology Data Exchange (ETDEWEB)

Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

2010-11-01

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

A bacterium that can grow by using arsenic instead of phosphorus.

Science.gov (United States)

Wolfe-Simon, Felisa; Switzer Blum, Jodi; Kulp, Thomas R; Gordon, Gwyneth W; Hoeft, Shelley E; Pett-Ridge, Jennifer; Stolz, John F; Webb, Samuel M; Weber, Peter K; Davies, Paul C W; Anbar, Ariel D; Oremland, Ronald S

2011-06-03

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

Science.gov (United States)

Abdoun, Hamid; McMillan, Mary; Pereg, Lily

2016-04-01

Azospirillum brasilense spp. have ecological, scientific and agricultural importance. As model plant growth promoting rhizobacteria they interact with a large variety of plants, including important food and cash crops. Azospirillum strains are known for their production of plant growth hormones that enhance root systems and for their ability to fix nitrogen. Azospirillum cells transform in response to environmental cues. The production of exopolysaccharides and cell aggregation during cellular transformation are important steps in the attachment of Azospirillum to roots. We investigate signals that induce cellular transformation and aggregation in the Azospirillum and report on the importance of oxygen to the process of aggregation in this rhizospheric bacterium.

Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

DEFF Research Database (Denmark)

Tanaka, Reiji; Kawaichi, Satoshi; Nishimura, Hiroshi

2006-01-01

A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52-78°C (optimum, 70°C), pH 5-8 (optimum, pH 7...

First report of a cross-kingdom pathogenic bacterium, Achromobacter xylosoxidans isolated from stipe-rot Coprinus comatus.

Science.gov (United States)

Ye, Luona; Guo, Mengpei; Ren, Pengfei; Wang, Gangzheng; Bian, Yinbing; Xiao, Yang; Zhou, Yan

2018-03-01

Coprinus comatus is an edible mushroom widely cultivated in China as a delicious food. Various diseases have occurred on C. comatus with the cultivated area increasing. In this study, the pathogenic bacterium JTG-B1, identified as Achromobacter xylosoxidans by 16S rDNA and nrdA gene sequencing, was isolated from edible mushroom Coprinus comatus with serious rot disease on its stipe. A. xylosoxidans has been confirmed as an important opportunistic human pathogenic bacterium and has been isolated from respiratory samples from cystic fibrosis. It is widely distributed in the environment. Here, we first report that fungi can also serve as a host for A. xylosoxidans. We confirmed that it can cross-kingdom infect between animals (mice) and fungi (C. comatus). The results of pathogenicity tests, physiological, biochemical and genotyping analysis of A. xylosoxidans from different hosts suggested that different strain of A. xylosoxidans may have pathogenicity differentiation. A. xylosoxidans not only is pathogenic to C. comatus but also may threaten human health. Copyright © 2017 Elsevier GmbH. All rights reserved.

A bacterium that degrades and assimilates poly(ethylene terephthalate).

Science.gov (United States)

Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

2016-03-11

Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. Copyright © 2016, American Association for the Advancement of Science.

Antioxidants keep the potentially probiotic but highly oxygen-sensitive human gut bacterium Faecalibacterium prausnitzii alive at ambient air

NARCIS (Netherlands)

Khan, M. Tanweer; van Dijl, Jan Maarten; Harmsen, Hermie J M

2014-01-01

The beneficial human gut microbe Faecalibacterium prausnitzii is a 'probiotic of the future' since it produces high amounts of butyrate and anti-inflammatory compounds. However, this bacterium is highly oxygen-senstive, making it notoriously difficult to cultivate and preserve. This has so far

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

OpenAIRE

Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T.B.K.; Klenk, Hans-Peter; Spring, Stefan; G?ker, Markus; Reva, Oleg N.; Miroshnichenko, Margarita L.

2017-01-01

© 2017 Kublanov, Sigalova, Gavrilov, Lebedinsky, Rinke, Kovaleva, Chernyh, Ivanova, Daum, Reddy, Klenk, Spring, Göker, Reva, Miroshnichenko, Kyrpides, Woyke, Gelfand, Bonch-Osmolovskaya. The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to impl...

Co-metabolism of DDT by the newly isolated bacterium, Pseudoxanthomonas sp. wax

Directory of Open Access Journals (Sweden)

Guangli Wang

2010-06-01

Full Text Available Microbial degradation of 1,1,1-trichloro-2,2-bis(p-chlorophenylethane (DDT is the most promising way to clean up DDT residues found in the environment. In this paper, a bacterium designated as wax, which was capable of co-metabolizing DDT with other carbon sources, was isolated from a long-term DDT-contaminated soil sample by an enrichment culture technique. The new isolate was identified as a member of the Pseudoxanthomonas sp., based on its morphological, physiological and biochemical properties, as well as by 16S rRNA gene analysis. In the presence of 100 mg l-1 glucose, the wax strain could degrade over 95% of the total DDT, at a concentration of 20 mg l-1, in 72 hours, and could degrade over 60% of the total DDT, at a concentration of 100 mg l-1, in 144 hours. The wax strain had the highest degradation efficiency among all of the documented DDT-degrading bacteria. The wax strain could efficiently degrade DDT at temperatures ranging from 20 to 37ºC, and with initial pH values ranging from 7 to 9. The bacterium could also simultaneously co-metabolize 1,1-dichloro-2,2-bis(p-chlorophenylethane (DDD, 2,2-bis(p-chlorophenyl-1,1-dichlorethylene (DDE, and other organochlorine compounds. The wax strain could also completely remove 20 mg kg-1 of DDT from both sterile and non-sterile soils in 20 days. This study demonstrates the significant potential use of Pseudoxanthomonas sp. wax for the bioremediation of DDT in the environment.

Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1

Directory of Open Access Journals (Sweden)

Yunlong Yang

Full Text Available ABSTRACT Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal.

Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?

Directory of Open Access Journals (Sweden)

Andrew McDowell

2017-12-01

Full Text Available The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the last decade, our knowledge of the intraspecies phylogenetics and taxonomy of this bacterium has increased tremendously due to the introduction of DNA typing schemes based on single and multiple gene loci, as well as whole genomes. Furthermore, this work has led to the identification of specific lineages associated with skin health and human disease. In this review we will look back at the introduction of DNA sequence typing of P. acnes based on recA and tly loci, and then describe how these methods provided a basic understanding of the population genetic structure of the bacterium, and even helped characterize the grapevine-associated lineage of P. acnes, known as P. acnes type Zappe, which appears to have undergone a host switch from humans-to-plants. Particular limitations of recA and tly sequence typing will also be presented, as well as a detailed discussion of more recent, higher resolution, DNA-based methods to type P. acnes and investigate its evolutionary history in greater detail.

Phosphorus uptake of an arbuscular mycorrhizal fungus is not effected by the biocontrol bacterium ¤Burkholderia cepacia¤

DEFF Research Database (Denmark)

Ravnskov, S.; Larsen, J.; Jakobsen, I.

2002-01-01

The biocontrol bacterium Burkholderia cepacia is known to suppress a broad range of root pathogenic fungi, while its impact on other beneficial non-target organisms such as arbuscular mycorrhizal (AM) fungi is unknown. Direct interactions between five B. cepacia strains and the AM fungus, Glomus ...

Locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium Idiomarina loihiensis

NARCIS (Netherlands)

van der Horst, M.A.; Stalcup, T.P.; Kaledhonkar, S.; Kumauchi, M.; Hara, M.; Xie, A.; Hellingwerf, K.J.; Hoff, W.D.

2009-01-01

Idiomarina loihiensis is a heterotrophic deep sea bacterium with no known photobiology. We show that light suppresses biofilm formation in this organism. The genome of I. loihiensis encodes a single photoreceptor protein: a homologue of photoactive yellow protein (PYP), a blue light receptor with

Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures

DEFF Research Database (Denmark)

Nazir, Rashid; Hansen, Martin A.; Sorensen, Soren

2012-01-01

Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately...

Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium

Directory of Open Access Journals (Sweden)

Leong-Keat eChan

2012-05-01

Full Text Available Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC, a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ~50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium Ruegeria pomeroyi (a member of the Roseobacter clade under four element limitation regimes (C, N, P, and S. Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S-limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to 6-fold were measured in R. pomeroyi biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometery in R. pomeroyi may have implications for global carbon cycling. Strong homeostatic responses to N limitation by heterotrophic marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean.

Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium

OpenAIRE

Arif, Mohammad; Busot, Grethel Y.; Mann, Rachel; Rodoni, Brendan; Liu, Sanzhen; Stack, James P.

2016-01-01

Rathayibacter toxicus is a gram-positive bacterium that infects the floral parts of several Poaceae species in Australia. Bacterial ooze is often produced on the surface of infected plants and bacterial galls are produced in place of seed. R. toxicus is a regulated plant pathogen in the U.S. yet reliable detection and diagnostic tools are lacking. To better understand this geographically-isolated plant pathogen, genetic variation as a function of geographic location, host species, and date of...

Expression and surface display of Cellulomonas endoglucanase in the ethanologenic bacterium Zymobacter palmae

Energy Technology Data Exchange (ETDEWEB)

Kojima, Motoki; Akahoshi, Tomohiro; Okamoto, Kenji; Yanase, Hideshi [Tottori Univ. (Japan). Dept. of Chemistry and Biotechnology

2012-11-15

In order to reduce the cost of bioethanol production from lignocellulosic biomass, we developed a tool for cell surface display of cellulolytic enzymes on the ethanologenic bacterium Zymobacter palmae. Z. palmae is a novel ethanol-fermenting bacterium capable of utilizing a broad range of sugar substrates, but not cellulose. Therefore, to express and display heterologous cellulolytic enzymes on the Z. palmae cell surface, we utilized the cell-surface display motif of the Pseudomonas ice nucleation protein Ina. The gene encoding Ina from Pseudomonas syringae IFO3310 was cloned, and its product was comprised of three functional domains: an N-terminal domain, a central domain with repeated amino acid residues, and a C-terminal domain. The N-terminal domain of Ina was shown to function as the anchoring motif for a green fluorescence protein fusion protein in Escherichia coli. To express a heterologous cellulolytic enzyme extracellularly in Z. palmae, we fused the N-terminal coding sequence of Ina to the coding sequence of an N-terminal-truncated Cellulomonas endoglucanase. Z. palmae cells carrying the fusion endoglucanase gene were shown to degrade carboxymethyl cellulose. Although a portion of the expressed fusion endoglucanase was released from Z. palmae cells into the culture broth, we confirmed the display of the protein on the cell surface by immunofluorescence microscopy. The results indicate that the N-terminal anchoring motif of Ina from P. syringae enabled the translocation and display of the heterologous cellulase on the cell surface of Z. palmae. (orig.)

Isolation and characterization of a radiation resistant thermophilic bacterium from radon hot spring

International Nuclear Information System (INIS)

Liang Xinle; Yang Long; Zhang Hong; Zhang Lei

2011-01-01

A radiation resistant and thermophilic bacterium strain R4-33 was isolated from radon hot spring water samples, pretreated with 60 Co γ-rays and UV irradiation. Tests on morphological, physiological and biochemical characters, fatty acid compositions, (G + C) mol% contents, and 16S rDNA sequencing were conducted. The results showed that strain R4-33 was of rod-shape, Gram-negative, atrichous, and endospore-forming. The optimum growth temperature and pH were 60 ℃ and 7.5, respectively. The strain utilized glucose, maltose and trehalose as carbon sources, and hydrolyzed casein and starch. Its catalase positive. The strain was sensitive to penicillin, neomycin, erythromycin, vancomycin, streptomycin, gentamycin, amikacin and ampicillin. The major cellular fatty acids were C 14:1 (48.8%) and C 15:1 (15.2%). The (G + C) mol% content of DNA was 58.2%. Phylogenetic tree based on 16S rDNA sequence showed R4-33 shared highly similarity to those of species in genus Anoxybacillus, especially to that of Anoxybacillus gonensis (99.5%). Based on the above, the strain R4-33 was proposed to the evolution branch of Anoxybacillus and designated as Anoxybacillu sp. R4-33. The UV and γ-radiation tests showed that the strain R4-33 had an ability of resistance to UV of 396 J/m 2 and 60 Co γ-rays irradiation of 14.0 kGy, indicating that the strain was a radiation resistant and thermophilic bacterium. (authors)

Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

Energy Technology Data Exchange (ETDEWEB)

Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Lykidis, Athanasios; Hooper, Sean D.; Sun, Hui; Kunin, Victor; Lapidus, Alla; Hugenholtz, Philip; Patel, Bharat; Kyrpides, Nikos C.

2008-11-03

Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

Complete genome sequence of Klebsiella pneumoniae J1, a protein-based microbial flocculant-producing bacterium.

Science.gov (United States)

Pang, Changlong; Li, Ang; Cui, Di; Yang, Jixian; Ma, Fang; Guo, Haijuan

2016-02-20

Klebsiella pneumoniae J1 is a Gram-negative strain, which belongs to a protein-based microbial flocculant-producing bacterium. However, little genetic information is known about this species. Here we carried out a whole-genome sequence analysis of this strain and report the complete genome sequence of this organism and its genetic basis for carbohydrate metabolism, capsule biosynthesis and transport system. Copyright © 2016 Elsevier B.V. All rights reserved.

Draft genome sequence of Enterobacter sp. Sa187, an endophytic bacterium isolated from the desert plant Indigofera argentea

NARCIS (Netherlands)

Lafi, Feras F.; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged M.

2017-01-01

Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth-promoting activity and

Phosphinothricin Acetyltransferases Identified Using In Vivo, In Vitro, and Bioinformatic Analyses

Science.gov (United States)

VanDrisse, Chelsey M.; Hentchel, Kristy L.

2016-01-01

ABSTRACT Acetylation of small molecules is widespread in nature, and in some cases, cells use this process to detoxify harmful chemicals. Streptomyces species utilize a Gcn5 N-acetyltransferase (GNAT), known as Bar, to acetylate and detoxify a self-produced toxin, phosphinothricin (PPT), a glutamate analogue. Bar homologues, such as MddA from Salmonella enterica, acetylate methionine analogues such as methionine sulfoximine (MSX) and methionine sulfone (MSO), but not PPT, even though Bar homologues are annotated as PPT acetyltransferases. S. enterica was used as a heterologous host to determine whether or not putative PPT acetyltransferases from various sources could acetylate PPT, MSX, and MSO. In vitro and in vivo analyses identified substrates acetylated by putative PPT acetyltransferases from Deinococcus radiodurans (DR_1057 and DR_1182) and Geobacillus kaustophilus (GK0593 and GK2920). In vivo, synthesis of DR_1182, GK0593, and GK2920 blocked the inhibitory effects of PPT, MSX, and MSO. In contrast, DR_1057 did not detoxify any of the above substrates. Results of in vitro studies were consistent with the in vivo results. In addition, phylogenetic analyses were used to predict the functionality of annotated PPT acetyltransferases in Burkholderia xenovorans, Bacillus subtilis, Staphylococcus aureus, Acinetobacter baylyi, and Escherichia coli. IMPORTANCE The work reported here provides an example of the use of a heterologous system for the identification of enzyme function. Many members of this superfamily of proteins do not have a known function, or it has been annotated solely on the basis of sequence homology to previously characterized enzymes. The critical role of Gcn5 N-acetyltransferases (GNATs) in the modulation of central metabolic processes, and in controlling metabolic stress, necessitates approaches that can reveal their physiological role. The combination of in vivo, in vitro, and bioinformatics approaches reported here identified GNATs that can

On the Stability of Deinoxanthin Exposed to Mars Conditions during a Long-Term Space Mission and Implications for Biomarker Detection on Other Planets

Directory of Open Access Journals (Sweden)

Stefan Leuko

2017-09-01

Full Text Available Outer space, the final frontier, is a hostile and unforgiving place for any form of life as we know it. The unique environment of space allows for a close simulation of Mars surface conditions that cannot be simulated as accurately on the Earth. For this experiment, we tested the resistance of Deinococcus radiodurans to survive exposure to simulated Mars-like conditions in low-Earth orbit for a prolonged period of time as part of the Biology and Mars experiment (BIOMEX project. Special focus was placed on the integrity of the carotenoid deinoxanthin, which may serve as a potential biomarker to search for remnants of life on other planets. Survival was investigated by evaluating colony forming units, damage inflicted to the 16S rRNA gene by quantitative PCR, and the integrity and detectability of deinoxanthin by Raman spectroscopy. Exposure to space conditions had a strong detrimental effect on the survival of the strains and the 16S rRNA integrity, yet results show that deinoxanthin survives exposure to conditions as they prevail on Mars. Solar radiation is not only strongly detrimental to the survival and 16S rRNA integrity but also to the Raman signal of deinoxanthin. Samples not exposed to solar radiation showed only minuscule signs of deterioration. To test whether deinoxanthin is able to withstand the tested parameters without the protection of the cell, it was extracted from cell homogenate and exposed to high/low temperatures, vacuum, germicidal UV-C radiation, and simulated solar radiation. Results obtained by Raman investigations showed a strong resistance of deinoxanthin against outer space and Mars conditions, with the only exception of the exposure to simulated solar radiation. Therefore, deinoxanthin proved to be a suitable easily detectable biomarker for the search of Earth-like organic pigment-containing life on other planets.

Study of the impact of environmental bacteria ob uranium speciation in order to engage bioremediation process

International Nuclear Information System (INIS)

Untereiner, G.

2008-11-01

Uranium is both a radiological and a chemical toxic. Its concentration in the environment is low except when human activities have caused pollution. Uranium is a heavy reactive element, and thus it is easily complexed with soil component like minerals or organic molecules. These different complexes can be more or less bioavailable for microorganisms and plants, and then get in the human food chain. The knowledge and the understanding of transfer mechanisms and also the fate of toxic elements in the biosphere are a key issue to estimate health and ecological hazards. The knowledge of the speciation is very important for bioremediation processes. Here, we focused on the microorganisms effects onto uranium speciation in environment. Bacteria can accumulate and/or transform uranium depending on the initial form of the element. Thus, its bioavailability could be changed. The species used in this work are Cupriavidus metallidurans CH34, which is an environmental bacteria with a high resistance to heavy metal, Deinococcus radiodurans R1, which is known for his radiological resistance, and Rhodopseudomonas palustris, which is a purple photo-trophic bacteria capable of degrading aromatic compounds. Two forms of uranium were used with these bacteria, a mineral one, uranyl carbonate, and an organic one, uranyl citrate. In a first step, the growth media were modified in order to stabilize uranium complexes thanks to a simulation program. Then, the capacity of the bacteria to accumulate or transform uranium was studied. We saw a difference between minimal inhibition concentrations of these two speciation which is due to a difference between phosphate bioavailability. No accumulation was observed with environmental pH but uranium precipitation was observed with acidic pH (pH 1). Uranium speciation seemed to be well controlled in the growth media and the precipitates were uranyl phosphate. (author)

Study on human intestinal bacterium Blautia sp. AUH-JLD56 for the conversion of arctigenin to (-)-3'-desmethylarctigenin.

Science.gov (United States)

Liu, Ming-Yue; Li, Meng; Wang, Xiu-Ling; Liu, Peng; Hao, Qing-Hong; Yu, Xiu-Mei

2013-12-11

Arctium lappa L. (A. lappa) is a popularly used vegetable as well as herbal medicine. Human intestinal microflora was reported to convert arctiin, the lignan compound with highest content in the dried fruits of Arctium lappa, to a series of metabolites. However, the specific bacterium responsible for the formation of 3'-desmethylarctigenin (3'-DMAG), the most predominant metabolite of arctiin by rat or human intestinal microflora, has not been isolated yet. In the present study, we isolated one single bacterium, which we named Blautia sp. AUH-JLD56, capable of solely biotransforming arctiin or arctigenin to (-)-3'-DMAG. The structure of the metabolite 3'-DMAG was elucidated by electrospray ionization mass spectrometry (ESI-MS) and (1)H and (13)C nuclear magnetic resonance spectroscopy. The biotransforming kinetics and maximum biotransforming capacity of strain AUH-JLD56 was investigated. In addition, the metabolite 3'-DMAG showed significantly higher 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity than that of the substrate arctigenin at the concentrations tested.

Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria.

Science.gov (United States)

da Silva, Fábio Daniel Florêncio; Lima, Alex Ranieri Jerônimo; Moraes, Pablo Henrique Gonçalves; Siqueira, Andrei Santos; Dall'Agnol, Leonardo Teixeira; Baraúna, Anna Rafaella Ferreira; Martins, Luisa Carício; Oliveira, Karol Guimarães; de Lima, Clayton Pereira Silva; Nunes, Márcio Roberto Teixeira; Vianez-Júnior, João Lídio Silva Gonçalves; Gonçalves, Evonnildo Costa

2016-05-19

Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here. Copyright © 2016 da Silva et al.

Effect of cell immobilization on the treatment of olive mill wastewater by a total phenols, acetic acid and formic acid degrading bacterium strain

Directory of Open Access Journals (Sweden)

Errami, Mohamed

2005-06-01

Full Text Available Olive mill wastewater (OMW is a pure vegetative by-product, containing a high organic and polyphenol content and is resistant to biodegradation. Its disposal lead to major environmental pollution problems in the Mediterranean basin. An aerobic bacterium was isolated from OMW. During three consecutive diluted and supplemented OMW treatment cycles, significant abatement of its phytotoxic substances was observed. In fact, total phenols, acetic and formic acids were reduced between 33 and 64 % when cells of the isolated bacterium were grown free; and between 62 and 78 % when cells of the same isolated bacterium were grown immobilized in a polyurethane sponge. These results suggest that the bacterium culture of the new isolate would decrease the OMW phytotoxicity. Phylogenetic analysis of 16S ribosomal DNA showed that all the related sequences are members of the Enterobacteriaceae family and revealed that the isolated bacterium was characterized as a Klebsiella oxytoca strain.El alpechín (OMW es un residuo puro de la extracción del aceite de oliva, que contiene una elevada carga orgánica y de polifenoles por lo que es resistente a la degradación. Su descarga produce graves problemas de contaminación medioambiental en toda el área mediterránea. Se ha aislado una bacteria anaerobia del OMW, que , durante tres ciclos consecutivos de tratamiento del OMW diluido y suplementado, produjo una disminución significativa de las sustancias fitotóxicas del residuo. De hecho, la concentración en fenoles totales, ácido acético y ácido fórmico se redujeron entre 33 y 64 % cuando las células no estaban inmovilizadas y entre el 62 y 78 % cuando las células bacterianas se inmovilizaron en una esponja de poliuretano. Estos resultados indican que el cultivo de la nueva bacteria aislada puede disminuir la fototoxicidad del alpechín. Análisis filogenético del ribosoma 16S de DNA demostró que todas las secuencias eran miembros de la familia

Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacterium Methylobacterium mesophilicum SR1.6/6.

Science.gov (United States)

Dourado, Manuella Nóbrega; Santos, Daiene Souza; Nunes, Luiz Roberto; Costa de Oliveira, Regina Lúcia Batista da; de Oliveira, Marcus Vinicius; Araújo, Welington Luiz

2015-12-01

Xylella fastidiosa, the causal agent of citrus variegated chlorosis (CVC), colonizes plant xylem, reducing sap flow, and inducing internerval chlorosis, leaf size reduction, necrosis, and harder and smaller fruits. This bacterium may be transmitted from plant to plant by sharpshooter insects, including Bucephalogonia xanthopis. The citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 colonizes citrus xylem and previous studies showed that this strain is also transferred from plant to plant by B. xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta and inside the insect vector during co-transmission by the same insect vector. To better understand the X. fastidiosa behavior in the presence of M. mesophilicum, we evaluated the X. fastidiosa transcriptional profile during in vitro interaction with M. mesophilicum SR1.6/6. The results showed that during co-cultivation, X. fastidiosa down-regulated genes related to growth and up-regulated genes related to energy production, stress, transport, and motility, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adopt a Bacterium - an active and collaborative learning experience in microbiology based on social media.

Science.gov (United States)

Piantola, Marco Aurélio Floriano; Moreno, Ana Carolina Ramos; Matielo, Heloísa Alonso; Taschner, Natalia Pasternak; Cavalcante, Rafael Ciro Marques; Khan, Samia; Ferreira, Rita de Cássia Café

2018-04-24

The "Adopt a Bacterium" project is based on the use of social network as a tool in Microbiology undergraduate education, improving student learning and encouraging students to participate in collaborative learning. The approach involves active participation of both students and teachers, emphasizing knowledge exchange, based on widely used social media. Students were organized in groups and asked to adopt a specific bacterial genus and, subsequently, submit posts about "adopted genus". The formative assessment is based on posting information on Facebook®, and the summative assessment involves presentation of seminars about the adopted theme. To evaluate the project, students filled out three anonymous and voluntary surveys. Most of the students enjoyed the activities and positively evaluated the experience. A large amount of students declared a change in their attitude towards the way they processed information, especially regarding the use of scientific sources. Finally, we evaluated knowledge retention six months after the end of the course and students were able to recall relevant Microbiology concepts. Our results suggest that the "Adopt a Bacterium" project represents a useful strategy in Microbiology learning and may be applied to other academic fields. Copyright © 2018 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Production and characterization of bioemulsifier from a marine bacterium, Acinetobacter calcoaceticus subsp. anitratus SM7

Directory of Open Access Journals (Sweden)

Kulnaree Phetrong

2008-05-01

Full Text Available Marine bacterium strain SM7 was isolated as a bioemulsifier-producing bacterium from oil-spilled seawater in Songkhla lagoon, Thailand. It was identified as Acinetobacter calcoaceticus subsp. anitratus based on morphology, biochemicalcharacteristics and 16S rRNA sequence. A. calcoaceticus subsp. anitratus SM7 produced an extracellular emulsifying agent when grown in a minimal salt medium (pH 7.0 containing 0.3% (v/v n-heptadecane and 0.1% (w/v ammoniumhydrogen carbonate as carbon source and nitrogen source, respectively, at 30oC with agitation rate of 200 rpm. Crude bioemulsifier was recovered from the culture supernatant by ethanol precipitation with a yield of 2.94 g/l and had a criticalemulsifier concentration of 0.04 g/ml. The crude bioemulsifier was capable of emulsifying n-hexadecane in a broad pH range (6-12, temperatures (30-121oC and in the presence of NaCl up to 12% (w/v. The bioemulsifier was stable in saltsolution ranging from 0 to 0.1% (w/v of MgCl2 and CaCl2. The broad range of pH stability, thermostability and salt tolerance suggested that the bioemulsifier from A. calcoaceticus subsp. anitratus SM7 could be useful in environmentalapplication, especially bioremediation of oil-polluted seawater.

Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2017-01-01

Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth–promoting activity and environmental adaption.

Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi

2017-02-17

Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth–promoting activity and environmental adaption.

Differential proteome and cellular adhesion analyses of the probiotic bacterium Lactobacillus acidophilus NCFM grown on raffinose - an emerging prebiotic

DEFF Research Database (Denmark)

Celebioglu, Hasan Ufuk; Hansen, Morten Ejby; Majumder, Avishek

2016-01-01

Whole cell and surface proteomes were analyzed together with adhesive properties of the probiotic bacterium Lactobacillus acidophilus NCFM (NCFM) grown on the emerging prebiotic raffinose, exemplifying a synbiotic. Adhesion of NCFM to mucin and intestinal HT-29 cells increased three-fold after...

Influence of yeast and lactic acid bacterium on the constituent profile of soy sauce during fermentation.

Science.gov (United States)

Harada, Risa; Yuzuki, Masanobu; Ito, Kotaro; Shiga, Kazuki; Bamba, Takeshi; Fukusaki, Eiichiro

2017-02-01

Soy sauce is a Japanese traditional seasoning composed of various constituents that are produced by various microbes during a long-term fermentation process. Due to the complexity of the process, the investigation of the constituent profile during fermentation is difficult. Metabolomics, the comprehensive study of low molecular weight compounds in biological samples, is thought to be a promising strategy for deep understanding of the constituent contribution to food flavor characteristics. Therefore, metabolomics is suitable for the analysis of soy sauce fermentation. Unfortunately, only few and unrefined studies of soy sauce fermentation using metabolomics approach have been reported. Therefore, we investigated changes in low molecular weight hydrophilic and volatile compounds of soy sauce using gas chromatography/mass spectrometry (GC/MS)-based non-targeted metabolic profiling. The data were analyzed by statistical analysis to evaluate influences of yeast and lactic acid bacterium on the constituent profile. Consequently, our results suggested a novel finding that lactic acid bacterium affected the production of several constituents such as cyclotene, furfural, furfuryl alcohol and methional in the soy sauce fermentation process. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A novel enzyme portfolio for red algal polysaccharide degradation in the marine bacterium Paraglaciecola hydrolytica S66T encoded in a sizeable polysaccharide utilization locus

DEFF Research Database (Denmark)

Schultz-Johansen, Mikkel; Bech, Pernille Kjersgaard; Hennessy, Rosanna Catherine

2018-01-01

with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides. A special feature of P. hydrolytica S66T is the presence of a large genomic region harboring an array of carbohydrate-active enzymes (CAZymes) notably agarases...... and carrageenases. Based on a first functional characterization combined with a comparative sequence analysis, we confirmed the enzymatic activities of several enzymes required for red algal polysaccharide degradation by the bacterium. In particular, we report for the first time, the discovery of novel enzyme...

Burkholderia vietnamiensis isolated from root tissues of Nipa Palm (Nypa fruticans) in Sarawak, Malaysia, proved to be its major endophytic nitrogen-fixing bacterium.

Science.gov (United States)

Tang, Sui-Yan; Hara, Shintaro; Melling, Lulie; Goh, Kah-Joo; Hashidoko, Yasuyuki

2010-01-01

Root-associating bacteria of the nipa palm (Nypa fruticans), preferring brackish-water affected mud in Sarawak, Malaysia, were investigated. In a comparison of rhizobacterial microbiota between the nipa and the sago (Metroxylon sagu) palm, it was found that the nipa palm possessed a group of Burkholderia vietnamiensis as its main active nitrogen-fixing endophytic bacterium. Acetylene reduction by the various isolates of B. vietnamiensis was constant (44 to 68 nmol h(-1) in ethylene production rate) in soft gel medium containing 0.2% sucrose as sole carbon source, and the bacterium also showed motility and biofilm-forming capacity. This is the first report of endophytic nitrogen-fixing bacteria from nipa palm.

Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog.

Science.gov (United States)

Dedysh, Svetlana N; Khmelenina, Valentina N; Suzina, Natalia E; Trotsenko, Yuri A; Semrau, Jeremy D; Liesack, Werner; Tiedje, James M

2002-01-01

A novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov., are proposed for a methane-oxidizing bacterium isolated from an acidic Sphagnum peat bog. This bacterium, designated strain B2T, represents aerobic, gram-negative, colourless, non-motile, curved coccoids that form conglomerates covered by an extracellular polysaccharide matrix. The cells use methane and methanol as sole sources of carbon and energy and utilize the serine pathway for carbon assimilation. Strain B2T is a moderately acidophilic organism with growth between pH 4.2 and 7.2 and at temperatures from 10 to 30 degrees C. The cells possess a well-developed system of intracytoplasmic membranes (ICM) packed in parallel on only one side of the cell membrane. This type of ICM structure represents a novel arrangement, which was termed type III. The resting cells are Azotobacter-type cysts. Strain B2T is capable of atmospheric nitrogen fixation; it possesses particulate methane monooxygenase and does not express soluble methane monooxygenase. The major phospholipid fatty acid is 18:1omega7c and the major phospholipids are phosphatidylglycerols. The G+C content of the DNA is 63.1 mol%. This bacterium belongs to the alpha-subclass of the Proteobacteria and is most closely related to the acidophilic methanotroph Methylocella palustris KT (97.3% 16S rDNA sequence similarity). However, the DNA-DNA hybridization value between strain B2T and Methylocella palustris K(T) is only 7%. Thus, strain B2T is proposed to comprise a novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov. Strain B2T (= DSM 13967T = NCIMB 13765T) is the type strain.

Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment

OpenAIRE

Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant?Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, F?bio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M. P.

2015-01-01

Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.

Alteration of the Canine Small-Intestinal Lactic Acid Bacterium Microbiota by Feeding of Potential Probiotics

OpenAIRE

Manninen, Titta J. K.; Rinkinen, Minna L.; Beasley, Shea S.; Saris, Per E. J.

2006-01-01

Five potentially probiotic canine fecal lactic acid bacterium (LAB) strains, Lactobacillus fermentum LAB8, Lactobacillus salivarius LAB9, Weissella confusa LAB10, Lactobacillus rhamnosus LAB11, and Lactobacillus mucosae LAB12, were fed to five permanently fistulated beagles for 7 days. The survival of the strains and their potential effects on the indigenous intestinal LAB microbiota were monitored for 17 days. Denaturing gradient gel electrophoresis (DGGE) demonstrated that the five fed LAB ...

A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium

OpenAIRE

Hoshi, Ayaka; Oshima, Kenro; Kakizawa, Shigeyuki; Ishii, Yoshiko; Ozeki, Johji; Hashimoto, Masayoshi; Komatsu, Ken; Kagiwada, Satoshi; Yamaji, Yasuyuki; Namba, Shigetou

2009-01-01

One of the most important themes in agricultural science is the identification of virulence factors involved in plant disease. Here, we show that a single virulence factor, tengu-su inducer (TENGU), induces witches' broom and dwarfism and is a small secreted protein of the plant-pathogenic bacterium, phytoplasma. When tengu was expressed in Nicotiana benthamiana plants, these plants showed symptoms of witches' broom and dwarfism, which are typical of phytoplasma infection. Transgenic Arabidop...

Global Analysis of Protein Lysine Succinylation Profiles and Their Overlap with Lysine Acetylation in the Marine Bacterium Vibrio parahemolyticus.

Science.gov (United States)

Pan, Jianyi; Chen, Ran; Li, Chuchu; Li, Weiyan; Ye, Zhicang

2015-10-02

Protein lysine acylation, including acetylation and succinylation, has been found to be a major post-translational modification (PTM) and is associated with the regulation of cellular processes that are widespread in bacteria. Vibrio parahemolyticus is a model marine bacterium that causes seafood-borne illness in humans worldwide. The lysine acetylation of V. parahemolyticus has been extensively characterized in our previous work, and here, we report the first global analysis of lysine succinylation and the overlap between the two types of acylation in this bacterium. Using high-accuracy nano liquid chromatography-tandem mass spectrometry combined with affinity purification, we identified 1931 lysine succinylated peptides matched on 642 proteins, with the quantity of the succinyl-proteins accounting for 13.3% of the total proteins in cells. Bioinformatics analysis results showed that these succinylated proteins are involved in almost every cellular process, particularly in protein biosynthesis and metabolism, and are distributed in diverse subcellular compartments. Moreover, several sequence motifs were identified, including succinyl-lysine flanked by a lysine or arginine residue at the -8, -7, or +7 position and without these residues at the -1 or +2 position, and these motifs differ from those found in other bacteria and eukaryotic cells. Furthermore, a total of 517 succinyl-lysine sites (26.7%) on 288 proteins (44.9%) were also found to be acetylated, suggesting extensive overlap between succinylation and acetylation in this bacterium. This systematic analysis provides a promising starting point for further investigations of the physiologic and pathogenic roles of lysine succinylation and acetylation in V. parahemolyticus.

Soil components mitigate the antimicrobial effects of silver nanoparticles towards a beneficial soil bacterium, Pseudomonas chlororaphis O6

Energy Technology Data Exchange (ETDEWEB)

Calder, Alyssa J. [Department of Biological Engineering, Utah State University, Logan, UT 84322 (United States); Dimkpa, Christian O. [Department of Biological Engineering, Utah State University, Logan, UT 84322 (United States); Department of Biology, Utah State University, Logan, UT 84322 (United States); McLean, Joan E. [Utah Water Research Laboratory, Utah State University, Logan, UT 84322 (United States); Britt, David W. [Department of Biological Engineering, Utah State University, Logan, UT 84322 (United States); Johnson, William [Geology and Geophysics, University of Utah, Salt Lake City, UT 84112 (United States); Anderson, Anne J., E-mail: anne.anderson@usu.edu [Department of Biology, Utah State University, Logan, UT 84322 (United States)

2012-07-01

Silver nanoparticles (Ag NPs) are widely used for their antimicrobial activity and consequently the particles will become environmental contaminants. This study evaluated in sand and soil matrices the toxicity of 10 nm spherical Ag NPs (1 and 3 mg Ag/L) toward a beneficial soil bacterium, Pseudomonas chlororaphis O6. In sand, both NP doses resulted in loss in bacterial culturability whereas in a loam soil, no cell death was observed. Amendments of sand with clays (30% v/v kaolinite or bentonite) did not protect the bacterium when challenged with Ag NPs. However, culturability of the bacterium was maintained when the Ag NP-amended sand was mixed with soil pore water or humic acid. Imaging by atomic force microscopy revealed aggregation of single nanoparticles in water, and their embedding into background material when suspended in pore water and humic acids. Zeta potential measurements supported aggregation and surface charge modifications with pore water and humic acids. Measurement of soluble Ag in the microcosms and geochemical modeling to deduce the free ion concentration revealed bacterial culturability was governed by the predicted free Ag ion concentrations. Our study confirmed the importance of Ag NPs as a source of ions and illustrated that processes accounting for protection in soil against Ag NPs involved distinct NP- and ion-effects. Processes affecting NP bioactivity involved surface charge changes due to sorption of Ca{sup 2+} from the pore water leading to agglomeration and coating of the NPs with humic acid and other organic materials. Removal of bioactive ions included the formation of soluble Ag complexes with dissolved organic carbon and precipitation of Ag ions with chloride in pore water. We conclude that mitigation of toxicity of Ag NPs in soils towards a soil bacterium resides in several interactions that differentially involve protection from the Ag NPs or the ions they produce. - Highlights: Black-Right-Pointing-Pointer Silver nanoparticles

Soil components mitigate the antimicrobial effects of silver nanoparticles towards a beneficial soil bacterium, Pseudomonas chlororaphis O6

International Nuclear Information System (INIS)

Calder, Alyssa J.; Dimkpa, Christian O.; McLean, Joan E.; Britt, David W.; Johnson, William; Anderson, Anne J.

2012-01-01

Silver nanoparticles (Ag NPs) are widely used for their antimicrobial activity and consequently the particles will become environmental contaminants. This study evaluated in sand and soil matrices the toxicity of 10 nm spherical Ag NPs (1 and 3 mg Ag/L) toward a beneficial soil bacterium, Pseudomonas chlororaphis O6. In sand, both NP doses resulted in loss in bacterial culturability whereas in a loam soil, no cell death was observed. Amendments of sand with clays (30% v/v kaolinite or bentonite) did not protect the bacterium when challenged with Ag NPs. However, culturability of the bacterium was maintained when the Ag NP-amended sand was mixed with soil pore water or humic acid. Imaging by atomic force microscopy revealed aggregation of single nanoparticles in water, and their embedding into background material when suspended in pore water and humic acids. Zeta potential measurements supported aggregation and surface charge modifications with pore water and humic acids. Measurement of soluble Ag in the microcosms and geochemical modeling to deduce the free ion concentration revealed bacterial culturability was governed by the predicted free Ag ion concentrations. Our study confirmed the importance of Ag NPs as a source of ions and illustrated that processes accounting for protection in soil against Ag NPs involved distinct NP- and ion-effects. Processes affecting NP bioactivity involved surface charge changes due to sorption of Ca 2+ from the pore water leading to agglomeration and coating of the NPs with humic acid and other organic materials. Removal of bioactive ions included the formation of soluble Ag complexes with dissolved organic carbon and precipitation of Ag ions with chloride in pore water. We conclude that mitigation of toxicity of Ag NPs in soils towards a soil bacterium resides in several interactions that differentially involve protection from the Ag NPs or the ions they produce. - Highlights: ► Silver nanoparticles (Ag NPs) are widely used for

Complete genome sequence of Agarivorans gilvus WH0801(T), an agarase-producing bacterium isolated from seaweed.

Science.gov (United States)

Zhang, Pujuan; Rui, Junpeng; Du, Zongjun; Xue, Changhu; Li, Xiangzhen; Mao, Xiangzhao

2016-02-10

Agarivorans gilvus WH0801(T), an agarase-producing bacterium, was isolated from the surface of seaweed. Here, we present the complete genome sequence, which consists of one circular chromosome of 4,416,600 bp with a GC content of 45.9%. This genetic information will provide insight into biotechnological applications of producing agar for food and industry. Copyright © 2015 Elsevier B.V. All rights reserved.

Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii.

Directory of Open Access Journals (Sweden)

Konstantinos Mavromatis

Full Text Available Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

Successful split thickness skin grafting in the presence of heavy colonisation with rare bacterium Aeromonas hydrophila: A case report

Directory of Open Access Journals (Sweden)

S. Koschel

2017-09-01

Discussion: Contemporary literature is yet to make the distinction between colonisation and infection of this bacterium, with clinicians relying solely on the presence of infective stigmata and serum analysis. However, this is a critically important distinction when ascertaining the likelihood of success of wound healing.

Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2016-01-01

Pseudomonas argentinensis strain SA190 is a plant endophytic-inhabiting bacterium that was isolated from root nodules of the desert plant Indigofera argentea collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of SA

A marine bacterium, Micrococcus MCCB 104, antagonistic to vibrios in prawn larval rearing systems.

Science.gov (United States)

Jayaprakash, N S; Pai, S Somnath; Anas, A; Preetha, R; Philip, Rosamma; Singh, I S Bright

2005-12-30

A marine bacterium, Micrococcus MCCB 104, isolated from hatchery water, demonstrated extracellular antagonistic properties against Vibrio alginolyticus, V. parahaemolyticus, V. vulnificus, V. fluviallis, V. nereis, V. proteolyticus, V. mediterranei, V cholerae and Aeromonas sp., bacteria associated with Macrobrachium rosenbergii larval rearing systems. The isolate inhibited the growth of V. alginolyticus during co-culture. The antagonistic component of the extracellular product was heat-stable and insensitive to proteases, lipase, catalase and alpha-amylase. Micrococcus MCCB 104 was demonstrated to be non-pathogenic to M. rosenbergii larvae.

Genome Sequence of the Enterobacter mori Type Strain, LMG 25706, a Pathogenic Bacterium of Morus alba L. ▿

Science.gov (United States)

Zhu, Bo; Zhang, Guo-Qing; Lou, Miao-Miao; Tian, Wen-Xiao; Li, Bin; Zhou, Xue-Ping; Wang, Guo-Feng; Liu, He; Xie, Guan-Lin; Jin, Gu-Lei

2011-01-01

Enterobacter mori is a plant-pathogenic enterobacterium responsible for the bacterial wilt of Morus alba L. Here we present the draft genome sequence of the type strain, LMG 25706. To the best of our knowledge, this is the first genome sequence of a plant-pathogenic bacterium in the genus Enterobacter. PMID:21602328

The FPase properties and morphology changes of a cellulolytic bacterium, Sporocytophaga sp. JL-01, on decomposing filter paper cellulose.

Science.gov (United States)

Wang, Xiuran; Peng, Zhongqi; Sun, Xiaoling; Liu, Dongbo; Chen, Shan; Li, Fan; Xia, Hongmei; Lu, Tiancheng

2012-01-01

Sporocytophaga sp. JL-01 is a sliding cellulose degrading bacterium that can decompose filter paper (FP), carboxymethyl cellulose (CMC) and cellulose CF11. In this paper, the morphological characteristics of S. sp. JL-01 growing in FP liquid medium was studied by Scanning Electron Microscope (SEM), and one of the FPase components of this bacterium was analyzed. The results showed that the cell shapes were variable during the process of filter paper cellulose decomposition and the rod shape might be connected with filter paper decomposing. After incubating for 120 h, the filter paper was decomposed significantly, and it was degraded absolutely within 144 h. An FPase1 was purified from the supernatant and its characteristics were analyzed. The molecular weight of the FPase1 was 55 kDa. The optimum pH was pH 7.2 and optimum temperature was 50°C under experiment conditions. Zn(2+) and Co(2+) enhanced the enzyme activity, but Fe(3+) inhibited it.

Fourier transform infrared spectroscopic study of intact cells of the nitrogen-fixing bacterium Azospirillum brasilense

Science.gov (United States)

Kamnev, A. A.; Ristić, M.; Antonyuk, L. P.; Chernyshev, A. V.; Ignatov, V. V.

1997-06-01

The data of Fourier transform infrared (FTIR) spectroscopic measurements performed on intact cells of the soil nitrogen-fixing bacterium Azospirillum brasilense grown in a standard medium and under the conditions of an increased metal uptake are compared and discussed. The structural FTIR information obtained is considered together with atomic absorption spectrometry (AAS) data on the content of metal cations in the bacterial cells. Some methodological aspects concerning preparation of bacterial cell samples for FTIR measurements are also discussed.

Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site.

Science.gov (United States)

Lim, Yan-Lue; Ee, Robson; Yong, Delicia; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan

2015-11-20

Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

Biofilm and capsule formation of the diatom Achnanthidium minutissimum are affected by a bacterium.

Science.gov (United States)

Windler, Miriam; Leinweber, Katrin; Bartulos, Carolina Rio; Philipp, Bodo; Kroth, Peter G

2015-04-01

Photoautotrophic biofilms play an important role in various aquatic habitats and are composed of prokaryotic and/or eukaryotic organisms embedded in extracellular polymeric substances (EPS). We have isolated diatoms as well as bacteria from freshwater biofilms to study organismal interactions between representative isolates. We found that bacteria have a strong impact on the biofilm formation of the pennate diatom Achnanthidium minutissimum. This alga produces extracellular capsules of insoluble EPS, mostly carbohydrates (CHO), only in the presence of bacteria (xenic culture). The EPS themselves also have a strong impact on the aggregation and attachment of the algae. In the absence of bacteria (axenic culture), A. minutissimum did not form capsules and the cells grew completely suspended. Fractionation and quantification of CHO revealed that the diatom in axenic culture produces large amounts of soluble CHO, whereas in the xenic culture mainly insoluble CHO were detected. For investigation of biofilm formation by A. minutissimum, a bioassay was established using a diatom satellite Bacteroidetes bacterium that had been shown to induce capsule formation of A. minutissimum. Interestingly, capsule and biofilm induction can be achieved by addition of bacterial spent medium, indicating that soluble hydrophobic molecules produced by the bacterium may mediate the diatom/bacteria interaction. With the designed bioassay, a reliable tool is now available to study the chemical interactions between diatoms and bacteria with consequences for biofilm formation. © 2015 Phycological Society of America.

Draft Genome Sequence of Caenibacillus caldisaponilyticus B157T, a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost

Science.gov (United States)

Tsujimoto, Yoshiyuki; Saito, Ryo; Sahara, Takehiko; Kimura, Nobutada; Tsuruoka, Naoki; Shigeri, Yasushi

2017-01-01

ABSTRACT Caenibacillus caldisaponilyticus B157T (= NBRC 111400T = DSM 101100T), in the family Sporolactobacillaceae, was isolated from acidulocompost as a thermophilic and phospholipid-degrading bacterium. Here, we report the 3.36-Mb draft genome sequence, with a G+C content of 51.8%, to provide the genetic information coding for phospholipases. PMID:28360164

Reduction of Mo(VI) by the bacterium Serratia sp. strain DRY5.

Science.gov (United States)

Rahman, M F A; Shukor, M Y; Suhaili, Z; Mustafa, S; Shamaan, N A; Syed, M A

2009-01-01

The need to isolate efficient heavy metal reducers for cost effective bioremediation strategy have resulted in the isolation of a potent molybdenum-reducing bacterium. The isolate was tentatively identified as Serratia sp. strain DRY5 based on the Biolog GN carbon utilization profiles and partial 16S rDNA molecular phylogeny. Strain DRY5 produced 2.3 times the amount of Mo-blue than S. marcescens strain Dr.Y6, 23 times more than E. coli K12 and 7 times more than E. cloacae strain 48. Strain DRY5 required 37 degrees C and pH 7.0 for optimum molybdenum reduction. Carbon sources such as sucrose, maltose, glucose and glycerol, supported cellular growth and molybdate reduction after 24 hr of static incubation. The most optimum carbon source that supported reduction was sucrose at 1.0% (w/v). Ammonium sulphate, ammonium chloride, glutamic acid, cysteine, and valine supported growth and molybdate reduction with ammonium sulphate as the optimum nitrogen source at 0. 2% (w/v). Molybdate reduction was optimally supported by 30 mM molybdate. The optimum concentration of phosphate for molybdate reduction was 5 mM when molybdate concentration was fixed at 30 mM and molybdate reduction was totally inhibited at 100 mM phosphate. Mo-blue produced by this strain shows a unique characteristic absorption profile with a maximum peak at 865 nm and a shoulder at 700 nm, Dialysis tubing experiment showed that 95.42% of Mo-blue was found in the dialysis tubing suggesting that the molybdate reduction seen in this bacterium was catalyzed by enzyme(s). The characteristics of isolate DRY5 suggest that it would be useful in the bioremediation ofmolybdenum-containing waste.

Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

NARCIS (Netherlands)

Berben, T.; Sorokin, D.Y.; Ivanova, N.; Pati, A.; Kyrpides, N.; Goodwin, L.A; Woyke, T.; Muyzer, G.

2015-01-01

Thioalkalivibrio thiocyanodenitrificans strain ARhD 1 T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a

‘Lactobacillus raoultii’ sp. nov., a new bacterium isolated from the vaginal flora of a woman with bacterial vaginosis

Directory of Open Access Journals (Sweden)

B. Nicaise

2018-01-01

Full Text Available We report the isolation of a new bacterium species, ‘Lactobacillus raoultii’ strain Marseille P4006 (CSUR P4006, isolated from a vaginal sample of a 45-year-old woman with bacterial vaginosis. Keywords: Bacterial vaginosis, culturomics, emerging bacteria, human microbiota, Lactobacillus raoultii, vaginal microbiota

Engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery

DEFF Research Database (Denmark)

Martinez, Virginia; Herencias, Cristina; Jurkevitch, Edouard

2016-01-01

This work examines the potential of the predatory bacterium Bdellovibrio bacteriovorus HD100, an obligate predator of other Gram-negative bacteria, as an external cell-lytic agent for recovering valuable intracellular bio-products produced by prey cultures. The bio-product targets to be recovered......% of that accumulated by the prey bacteria, even at high biomass concentrations. This innovative downstream process highlights how B. bacteriovorus can be used as a novel, biological lytic agent for the inexpensive, industrial scale recovery of intracellular products from different Gram-negative prey cultures....

Study on screening of anti-predator rhizosphere bacterium against Caenorhabditis elegans and its anti predation mechanism

Directory of Open Access Journals (Sweden)

HE Qingling

2016-08-01

Full Text Available Althoughmicrobial fertilizer is multi-effect,environmental friendly and long-term efficient,its practical application effect is but decreased for being prey by the other creators living in soil frequently.Many bacterium have developed their mechanisms that expel or kill worms to defend themselves from predators.Screening of anti-predator rhizosphere bacterium helps us to find out competitive plant growth promoting rhizobacteria(PGPR.Using Caenorhabditis elegans as sample,this study roughly observed two strains of biocontrol:Pseudomonas aurantiaca JD37 and Pseudomonas fluorescens P13.Using Escherichia coli OP50 as control group,we find the preference order of worms,from highest to lowest,is P13,OP50 and JD37.In slow killing assay,the death rate of worms for JD37 and P13 are 26.12% and 18.66% respectively.The activity and reproduction rate of C.elegans decrease when it is fed on JD37.The results of chemical and micro-biological study show that JD37 cannot produce any currently studied second metabolites which kill worms,while P13 can produce Hydrogen cyanide (HCN.All these results show that JD37 has the ability of anti-predator,and is more competitive under predation pressure,which suggests its broad application prospect as microbial fertilizer.

Microbacter margulisiae gen. nov., sp. nov., a novel propionigenic bacterium isolated from sediments of an acid rock drainage pond

NARCIS (Netherlands)

Sanchez Andrea, I.; Luis Sanz, J.; Stams, A.J.M.

2014-01-01

A novel anaerobic propionigenic bacterium, strain ADRIT, was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4-0.6 x 1-1.7 µm), non-motile and non-spore forming rods. Cells possessed a Gram-negative cell wall structure and were vancomycin

Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment.

Science.gov (United States)

Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M P

2015-04-02

Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. Copyright © 2015 Pereira et al.

Characterization of a novel chitinase from a moderately halophilic bacterium, Virgibacillus marismortui strain M3-23

OpenAIRE

Essghaier, Badiaa; Hedi, Abdeljabbar; Bajji, Mohammed; Jijakli, Haissam; Boudabous, Abdellatif; Sadfi-Zouaoui, Najla

2012-01-01

A new chitinase produced by the moderately halophilic bacterium Virgibacillus marismortui strain M3- 23 was identified and characterized. Distinguishable characteristics of high activity and stability at different pH, temperatures and salinity of M3-23 chitinase are reported. Analysis of the catalytic domain sequence from the enzyme highlighted its relationship to glycosyl hydrolase family 18. Comparison of the deduced chitinase sequence from strain M3-23 to known chitinases from Bacillus spe...

Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

KAUST Repository

Haroon, Mohamed

2016-02-11

A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

KAUST Repository

Haroon, Mohamed; Thompson, Luke R.; Stingl, Ulrich

2016-01-01

A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

Virus-Bacterium Interactions in Water and Sediment of West African Inland Aquatic Systems

Science.gov (United States)

Bettarel, Yvan; Bouvy, Marc; Dumont, Claire; Sime-Ngando, Télesphore

2006-01-01

The ecology of virioplankton in tropical aquatic ecosystems is poorly documented, and in particular, there are no references concerning African continental waters in the literature. In this study, we examined virus-bacterium interactions in the pelagic and benthic zones of seven contrasting shallow inland waters in Senegal, including one hypersaline lake. SYBR Gold-stained samples revealed that in the surface layers of the sites, the numbers of viruses were in the same range as the numbers of viruses reported previously for productive temperate systems. Despite high bacterial production rates, the percentages of visibly infected cells (as determined by transmission electron microscopy) were similar to the lowest percentages (range, 0.3 to 1.1%; mean, 0.5%) found previously at pelagic freshwater or marine sites, presumably because of the local environmental and climatic conditions. Since the percentages of lysogenic bacteria were consistently less than 8% for pelagic and benthic samples, lysogeny did not appear to be a dominant strategy for virus propagation at these sites. In the benthic samples, viruses were highly concentrated, but paradoxically, no bacteria were visibly infected. This suggests that sediment provides good conditions for virus preservation but ironically is an unfavorable environment for proliferation. In addition, given the comparable size distributions of viruses in the water and sediment samples, our results support the paradigm that aquatic viruses are ubiquitous and may have moved between the two compartments of the shallow systems examined. Overall, this study provides additional information about the relevance of viruses in tropical areas and indicates that the intensity of virus-bacterium interactions in benthic habitats may lower than the intensity in the adjacent bodies of water. PMID:16885276

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk

OpenAIRE

Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Fran?oise; Loux, Valentin; Vidal, Marie; Passot, St?phanie; B?al, Catherine; Layec, S?verine; Fonseca, Fernanda

2016-01-01

Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes.

Mutagenesis and reparation processes in the methylotrophic bacterium Pseudomonas methanolica after UV irradiation

International Nuclear Information System (INIS)

Naumov, G.N.; Bokhan, I.K.; Multykh, I.G.

1986-01-01

High resistance of cells of methylotrophic bacterium Pseudomonas methanolica to bactericidal and mutagenous effects of ultraviolet irradiation is shown as well as activity of reparation processes after UV irradiation. The presence of low photoreactivating activity in P. methanolica is shown as well. Observed recovery in innutritious medium and decrease of irradiated cells survival rates under effect of reparation inhibitors (coffeine and acriflavine) testify to activity of excision reparation and, perhaps, recombination branch of postreplicative reparation. No manifestation of inducible reparation system is discovered. It is concluded that increased resistance of P. methanolica cells to bactericidal and mutagenous effects of short-wave ultraviolet radiation is related to activity of exact reparation systems

Going from Microbial Ecology to Genome Data and Back: Studies on a Haloalkaliphilic Bacterium Isolated from Soap Lake, Washington State

Directory of Open Access Journals (Sweden)

Melanie R. Mormile

2014-11-01

Full Text Available Soap Lake is a meromictic, alkaline (~pH 9.8 and saline (~14 to 140 g liter-1 lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years and the extremely high sulfide level (~140 mM in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. H. hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment.

A soluble fatty acyl-acyl carrier protein synthetase from the bioluminescent bacterium Vibrio harveyi.

Science.gov (United States)

Byers, D M; Holmes, C G

1990-01-01

An enzyme catalyzing the ligation of long chain fatty acids to bacterial acyl carrier protein (ACP) has been detected and partially characterized in cell extracts of the bioluminescent bacterium Vibrio harveyi. Acyl-ACP synthetase activity (optimal pH 7.5-8.0) required millimolar concentrations of ATP and Mg2+ and was slightly activated by Ca2+, but was inhibited at high ionic strength and by Triton X-100. ACP from either Escherichia coli (apparent Km = 20 microM) or V. harveyi was used as a substrate. Of the [14C]fatty acids tested as substrates (8-18 carbons), a preference for fatty acids less than or equal to 14 carbons in length was observed. Vibrio harveyi acyl-ACP synthetase appears to be a soluble hydrophilic enzyme on the basis of subcellular fractionation and Triton X-114 phase partition assay. The enzyme was not coinduced with luciferase activity or light emission in vivo during the late exponential growth phase in liquid culture. Acyl-ACP synthetase activity was also detected in extracts from the luminescent bacterium Vibrio fischeri, but not Photobacterium phosphoreum. The cytosolic nature and enzymatic properties of V. harveyi acyl-ACP synthetase indicate that it may have a different physiological role than the membrane-bound activity of E. coli, which has been implicated in phosphatidylethanolamine turnover. Acyl-ACP synthetase activity in V. harveyi could be involved in the intracellular activation and elongation of exogenous fatty acids that occurs in this species or in the reactivation of free myristic acid generated by luciferase.

Bacterial host and reporter gene optimization for genetically encoded whole cell biosensors.

Science.gov (United States)

Brutesco, Catherine; Prévéral, Sandra; Escoffier, Camille; Descamps, Elodie C T; Prudent, Elsa; Cayron, Julien; Dumas, Louis; Ricquebourg, Manon; Adryanczyk-Perrier, Géraldine; de Groot, Arjan; Garcia, Daniel; Rodrigue, Agnès; Pignol, David; Ginet, Nicolas

2017-01-01

Whole-cell biosensors based on reporter genes allow detection of toxic metals in water with high selectivity and sensitivity under laboratory conditions; nevertheless, their transfer to a commercial inline water analyzer requires specific adaptation and optimization to field conditions as well as economical considerations. We focused here on both the influence of the bacterial host and the choice of the reporter gene by following the responses of global toxicity biosensors based on constitutive bacterial promoters as well as arsenite biosensors based on the arsenite-inducible P ars promoter. We observed important variations of the bioluminescence emission levels in five different Escherichia coli strains harboring two different lux-based biosensors, suggesting that the best host strain has to be empirically selected for each new biosensor under construction. We also investigated the bioluminescence reporter gene system transferred into Deinococcus deserti, an environmental, desiccation- and radiation-tolerant bacterium that would reduce the manufacturing costs of bacterial biosensors for commercial water analyzers and open the field of biodetection in radioactive environments. We thus successfully obtained a cell survival biosensor and a metal biosensor able to detect a concentration as low as 100 nM of arsenite in D. deserti. We demonstrated that the arsenite biosensor resisted desiccation and remained functional after 7 days stored in air-dried D. deserti cells. We also report here the use of a new near-infrared (NIR) fluorescent reporter candidate, a bacteriophytochrome from the magnetotactic bacterium Magnetospirillum magneticum AMB-1, which showed a NIR fluorescent signal that remained optimal despite increasing sample turbidity, while in similar conditions, a drastic loss of the lux-based biosensors signal was observed.

Expression of a Clostridium perfringens genome-encoded putative N-acetylmuramoyl-L-alanine amidase as a potential antimicrobial to control the bacterium

Science.gov (United States)

Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium that plays a substantial role in non-foodborne human, animal and avian diseases as well as human foodborne disease. Previously discovered C. perfringens bacteriophage lytic enzyme amino acid sequences were utilized to iden...

First report of a lipopeptide biosurfactant from thermophilic bacterium Aneurinibacillus thermoaerophilus MK01 newly isolated from municipal landfill site.

Science.gov (United States)

Sharafi, Hakimeh; Abdoli, Mahya; Hajfarajollah, Hamidreza; Samie, Nima; Alidoust, Leila; Abbasi, Habib; Fooladi, Jamshid; Zahiri, Hossein Shahbani; Noghabi, Kambiz Akbari

2014-07-01

A biosurfactant-producing thermophile was isolated from the Kahrizak landfill of Tehran and identified as a bacterium belonging to the genus Aneurinibacillus. A thermostable lipopeptide-type biosurfactant was purified from the culture medium of this bacterium and showed stability in the temperature range of 20-90 °C and pH range of 5-10. The produced biosurfactant could reduce the surface tension of water from 72 to 43 mN/m with a CMC of 1.21 mg/mL. The strain growing at a temperature of 45 °C produces a substantial amount of 5 g/L of biosurfactant in the medium supplemented with sunflower oil as the sole carbon source. Response surface methodology was employed to optimize the biosurfactant production using sunflower oil, sodium nitrate, and yeast extract as variables. The optimization resulted in 6.75 g/L biosurfactant production, i.e., 35% improved as compared to the unoptimized condition. Thin-layer chromatography, FTIR spectroscopy, 1H-NMR spectroscopy, and biochemical composition analysis confirmed the lipopeptide structure of the biosurfactant.

ORF Alignment: NC_001264 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available einococcus radiodurans (strain ... R1) ... Length = 233 ... Query: 7 ... TVEQAVRVLEYFDADHT...EWTLSDLARALALPTSTLHEQLSTLTASGLLRRTGRGRYQLGW 66 ... TVEQAVRVLEYFDADHTEWTLSDLARALALPT...STLHEQLSTLTASGLLRRTGRGRYQLGW Sbjct: 1 ... TVEQAVRVLEYFDADHTEWTLSDLARALALPTSTLHEQLSTLTASGLLRRTGRGRYQLGW 60 ... Que

BOG: R-package for Bacterium and virus analysis of Orthologous Groups

Directory of Open Access Journals (Sweden)

Jincheol Park

2015-01-01

Full Text Available BOG (Bacterium and virus analysis of Orthologous Groups is a package for identifying groups of differentially regulated genes in the light of gene functions for various virus and bacteria genomes. It is designed to identify Clusters of Orthologous Groups (COGs that are enriched among genes that have gone through significant changes under different conditions. This would contribute to the detection of pathogens, an important scientific research area of relevance in uncovering bioterrorism, among others. Particular statistical analyses include hypergeometric, Mann–Whitney rank sum, and gene set enrichment. Results from the analyses are organized and presented in tabular and graphical forms for ease of understanding and dissemination of results. BOG is implemented as an R-package, which is available from CRAN or can be downloaded from http://www.stat.osu.edu/~statgen/SOFTWARE/BOG/.

Cell Morphological Change and Caspase-3 Protein Expression on Epithelial Cells under Stimulation of Oral Bacterium Streptococcus sanguinis

Directory of Open Access Journals (Sweden)

Suryani Hutomo

2015-07-01

Full Text Available Oral commensal bacterium Streptococcus sanguinis may find in periodontal lesions, deep seated infection, and infective endocarditis that are usually dominated by anaerobes. This bacterium caused cell death on some cells but host responses to this species remained unclear. Objective: This study was aimed to detect cell morphologica change and role of caspase-3 in cell death mechanism induced by S. sanguinis. Methods: HeLa cells as representative model for oral epithelial cells were exposed to 107 cells/ml bacteria for 48 h. Morphological change was observed microscopically after hematoxyline-eosin staining. Expression of active caspase-3 was examined by immunocytochemical analysis after cell stimulation for 36 and 48 h with wild type supragingival S. sanguinis. Doxorubicin (0.5625 μg/ml was used as positive control for caspase-3 activation. Results: The results showed cell shrinkage of bacterial-treated cells; and active caspase-3 molecules were detected after 36 and 48 hours cell stimulation. Conclusion: This study would suggest cell shrinkage and caspase-3-dependent apoptotic cell death induced by S. sanguinis.DOI: 10.14693/jdi.v22i1.375

Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment

DEFF Research Database (Denmark)

Finster, Kai; Liesack, Werner; Thamdrup, Bo

1998-01-01

A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidized marine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite. Elemental sulfur was disproportionated to hydrogen sulfide and sulfate. Growth was ...

First Insights into the Genome Sequence of Clostridium thermopalmarium DSM 5974, a Butyrate-Producing Bacterium Isolated from Palm Wine.

Science.gov (United States)

Poehlein, Anja; Hettwer, Eva; Mohnike, Lennart; Daniel, Rolf

2018-04-26

Clostridium thermopalmarium is a moderate thermophilic, rod-shaped, and endospore-forming bacterium, which was isolated from palm wine in Senegal. Butyrate is produced from a broad variety of sugar substrates. Here, we present the draft genome sequence of C. thermopalmarium DSM 5974 (2.822 Mb) containing 2,665 predicted protein-encoding genes. Copyright © 2018 Poehlein et al.

Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant Growth-Promoting Bacterium Isolated from Rice Rhizosphere

Science.gov (United States)

Wang, Yinghuan; Greenfield, Paul; Jin, Decai

2014-01-01

Bacillus amyloliquefaciens strain EBL11 is a bacterium that can promote plant growth by inhibiting the growth of fungi on plant surfaces and providing nutrients as a nonchemical biofertilizer. The estimated genome of this strain is 4.05 Mb in size and harbors 3,683 coding genes (CDSs). PMID:25059875

Thermophilic anaerobic degradation of butyrate by a butyrate-utilizing bacterium in coculture and triculture with methanogenic bacteria.

Science.gov (United States)

Ahring, B K; Westermann, P

1987-02-01

We studied syntrophic butyrate degradation in thermophilic mixed cultures containing a butyrate-degrading bacterium isolated in coculture with Methanobacterium thermoautotrophicum or in triculture with M. thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic bacterium. Butyrate was beta-oxidized to acetate with protons as the electron acceptors. Acetate was used concurrently with its production in the triculture. We found a higher butyrate degradation rate in the triculture, in which both hydrogen and acetate were utilized, than in the coculture, in which acetate accumulated. Yeast extract, rumen fluid, and clarified digestor fluid stimulated butyrate degradation, while the effect of Trypticase was less pronounced. Penicillin G, d-cycloserine, and vancomycin caused complete inhibition of butyrate utilization by the cultures. No growth or degradation of butyrate occurred when 2-bromoethanesulfonic acid or chloroform, specific inhibitors of methanogenic bacteria, was added to the cultures and common electron acceptors such as sulfate, nitrate, and fumarate were not used with butyrate as the electron donor. Addition of hydrogen or oxygen to the gas phase immediately stopped growth and butyrate degradation by the cultures. Butyrate was, however, metabolized at approximately the same rate when hydrogen was removed from the cultures and was metabolized at a reduced rate in the cultures previously exposed to hydrogen.

Yersinia ruckeri sp. nov., the redmouth (RM) bacterium

Science.gov (United States)

Ewing, W.H.; Ross, A.J.; Brenner, Don J.; Fanning, G. R.

1978-01-01

Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

Plant growth-promoting bacterium Acinetobacter calcoaceticus P23 increases the chlorophyll content of the monocot Lemna minor (duckweed) and the dicot Lactuca sativa (lettuce).

Science.gov (United States)

Suzuki, Wakako; Sugawara, Masayuki; Miwa, Kyoko; Morikawa, Masaaki

2014-07-01

Acinetobacter calcoaceticus P23 is a plant growth-promoting bacterium that was isolated from the surface of duckweed (Lemna aoukikusa). The bacterium was observed to colonize on the plant surfaces and increase the chlorophyll content of not only the monocotyledon Lemna minor but also the dicotyledon Lactuca sativa in a hydroponic culture. This effect on the Lactuca sativa was significant in nutrient-poor (×1/100 dilution of H2 medium) and not nutrient-rich (×1 or ×1/10 dilutions of H2 medium) conditions. Strain P23 has the potential to play a part in the future development of fertilizers and energy-saving hydroponic agricultural technologies. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

The Perfect Match: Simultaneous Strawberry Pollination and Bio-Sampling of the Plant Pathogenic Bacterium Erwinia pyrifoliae by Honey Bees Apis mellifera

NARCIS (Netherlands)

Steen, van der Sjef; Bergsma-Vlami, M.; Wenneker, M.

2018-01-01

In this study we show that honey bee colonies placed in a greenhouse for pollination of strawberry can simultaneously be used to indicate the presence of the plant pathogenic bacterium Erwinia pyrifoliae. This was demonstrated by using two methods of qualitative sacrificial and non-sacrificial bio

“Nigerium massiliense” gen. nov., sp. nov., a new bacterium isolated from the gut from a patient with acute malnutrition

Directory of Open Access Journals (Sweden)

Sory Ibrahima Traore

2016-09-01

Full Text Available We propose the main characteristics of a new bacterium named “Nigerium massiliense” strain SIT5 (CSURP1302 that was isolated from the stool of a 2-year-old Nigerian child suffering from kwashiorkor, a form of severe acute malnutrition. Keywords: Culturomics, Taxonomy, Genomics, Taxono-genomics, “Nigerium massiliense”

Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.

Science.gov (United States)

Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine; Fonseca, Fernanda

2016-03-03

Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. Copyright © 2016 Meneghel et al.

Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

Science.gov (United States)

Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

2010-01-01

Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

Borders of life: lessons from Microbiology of deep-sea hydrothermal vents

Science.gov (United States)

Prieur, D.

deep-sea vents, hydrothermal fluids remain liquid at temperatures above 100°C (boiling water temperature under atmospheric pressure). If strictly barophilic thermophiles or hyperthermophiles have not been reported yet (the deepest vents known are 3500 m in depth), barophilic Bacteria and Archaea have been reported that grow much more faster when exposed to in situ (pressurized) conditions. Morover, they grow preferentially at pressures above those existing at captures depth, that may indicate that their natural habitat is situated below the sea floor. Recently, several studies reported that hyperthermophiles and particularly deep-sea organisms may resist to elevated doses of gamma ionizing radiations, as strong as 20 kGy, similarly to the famous radioresistant bacterium Deinococcus radiodurans. From these reports, it can be concluded that exploration of Earth is not already finished: novel biotopes, novel organisms with novel metabolic and physiologic properties are waiting for their discovery. Also, severe physio-chemical conditions allow for florishing living forms that use efficiently chemical energy sources. If these data do not allow to claim that life arose at deep-sea hydrothermal vents, they clearly extend physio-chemical and spatial borders of life and stimulate to further exploration of Earth and the solar system.

Effects of Calcium Ions on the Thermostability and Spectroscopic Properties of the LH1-RC Complex from a New Thermophilic Purple Bacterium Allochromatium tepidum.

Science.gov (United States)

Kimura, Yukihiro; Lyu, Shuwen; Okoshi, Akira; Okazaki, Koudai; Nakamura, Natsuki; Ohashi, Akira; Ohno, Takashi; Kobayashi, Manami; Imanishi, Michie; Takaichi, Shinichi; Madigan, Michael T; Wang-Otomo, Zheng-Yu

2017-05-18

The light harvesting-reaction center (LH1-RC) complex from a new thermophilic purple sulfur bacterium Allochromatium (Alc.) tepidum was isolated and characterized by spectroscopic and thermodynamic analyses. The purified Alc. tepidum LH1-RC complex showed a high thermostability comparable to that of another thermophilic purple sulfur bacterium Thermochromatium tepidum, and spectroscopic characteristics similar to those of a mesophilic bacterium Alc. vinosum. Approximately 4-5 Ca 2+ per LH1-RC were detected by inductively coupled plasma atomic emission spectroscopy and isothermal titration calorimetry. Upon removal of Ca 2+ , the denaturing temperature of the Alc. tepidum LH1-RC complex dropped accompanied by a blue-shift of the LH1 Q y absorption band. The effect of Ca 2+ was also observed in the resonance Raman shift of the C3-acetyl νC═O band of bacteriochlorophyll-a, indicating changes in the hydrogen-bonding interactions between the pigment and LH1 polypeptides. Thermodynamic parameters for the Ca 2+ -binding to the Alc. tepidum LH1-RC complex indicated that this reaction is predominantly driven by the largely favorable electrostatic interactions that counteract the unfavorable negative entropy change. Our data support a hypothesis that Alc. tepidum may be a transitional organism between mesophilic and thermophilic purple bacteria and that Ca 2+ is one of the major keys to the thermostability of LH1-RC complexes in purple bacteria.

Reduction of chalcogen oxyanions and generation of nanoprecipitates by the photosynthetic bacterium Rhodobacter capsulatus

Energy Technology Data Exchange (ETDEWEB)

Borghese, Roberto, E-mail: roberto.borghese@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Baccolini, Chiara; Francia, Francesco [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Sabatino, Piera [Department of Chemistry G. Ciamician, University of Bologna (Italy); Turner, Raymond J. [Department of Biological Sciences, University of Calgary, Calgary, Alberta (Canada); Zannoni, Davide, E-mail: davide.zannoni@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy)

2014-03-01

Graphical abstract: - Highlights: • R. capsulatus cells produce extracellular chalcogens nanoprecipitates when lawsone is present. • Lawsone acts as a redox mediator from reducing equivalents to tellurite and selenite. • Nanoprecipitates production depends on carbon source and requires metabolically active cells. • Te{sup 0} and Se{sup 0} nanoprecipitates are identified by X-ray diffraction (XRD) spectroscopy. - Abstract: The facultative photosynthetic bacterium Rhodobacter capsulatus is characterized in its interaction with the toxic oxyanions tellurite (Te{sup IV}) and selenite (Se{sup IV}) by a highly variable level of resistance that is dependent on the growth mode making this bacterium an ideal organism for the study of the microbial interaction with chalcogens. As we have reported in the past, while the oxyanion tellurite is taken up by R. capsulatus cells via acetate permease and it is reduced to Te{sup 0} in the cytoplasm in the form of splinter-like black intracellular deposits no clear mechanism was described for Se{sup 0} precipitation. Here, we present the first report on the biotransformation of tellurium and selenium oxyanions into extracellular Te{sup 0} and Se{sup 0}nanoprecipitates (NPs) by anaerobic photosynthetically growing cultures of R. capsulatus as a function of exogenously added redox-mediator lawsone, i.e. 2-hydroxy-1,4-naphthoquinone. The NPs formation was dependent on the carbon source used for the bacterial growth and the rate of chalcogen reduction was constant at different lawsone concentrations, in line with a catalytic role for the redox mediator. X-ray diffraction (XRD) analysis demonstrated the Te{sup 0} and Se{sup 0} nature of the nanoparticles.

Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology.

Science.gov (United States)

Kindzierski, Viktoria; Raschke, Silvia; Knabe, Nicole; Siedler, Frank; Scheffer, Beatrix; Pflüger-Grau, Katharina; Pfeiffer, Friedhelm; Oesterhelt, Dieter; Marin-Sanguino, Alberto; Kunte, Hans-Jörg

2017-01-01

Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem. However, as more of these reconstructions become available, it becomes clear that processes predicted by genome annotation may not reflect the processes that are active in vivo. As a case in point, E. coli is unable to grow aerobically on citrate in spite of having all the necessary genes to do it. It has also been shown that the realization of this genetic potential into an actual capability to metabolize citrate is an extremely unlikely event under normal evolutionary conditions. Moreover, many marine bacteria seem to have the same pathways to metabolize glucose but each species uses a different one. In this work, a metabolic network inferred from genomic annotation of the halophilic bacterium Halomonas elongata and proteomic profiling experiments are used as a starting point to motivate targeted experiments in order to find out some of the defining features of the osmoregulatory strategies of this bacterium. This new information is then used to refine the network in order to describe the actual capabilities of H. elongata, rather than its genetic potential.