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Cultivable bacteria from ancient algal mats from the McMurdo Dry Valleys, Antarctica.The McMurdo Dry Valleys in Antarctica are a favorable location for preservation of dormant microbes due to their persistent cold and dry climate. In this study, we examined cultivable bacteria in a series of algal mat samples ranging from 8 to 26539 years old. Cultivable bacteria were found in all samples except one (12303 years old), but abundance and diversity of cultivable bacteria decreased with increasing sample age. Only members of the Actinobacteria, Bacteroidetes, and Firmicutes were fou ...201222065250
Recombinant D. radiodurans cells for bioremediation of heavy metals from acidic/neutral aqueous wastes.The stability and superior metal bioremediation ability of genetically engineered Deinococcus radiodurans cells, expressing a non-specific acid phosphatase, PhoN in high radiation environment has already been established. The lyophilized recombinant DrPhoN cells retained PhoN activity and uranium precipitation ability. Such cells also displayed an extended shelf life of 6 mo during storage at room temperature and showed surface associated precipitation of uranium as well as other metals like cad ...201222179144
physiology of resistant deinococcus geothermalis bacterium aerobically cultivated in low manganese medium.this dynamic proteome study describes the physiology of growth and survival of deinococcus geothermalis, in conditions simulating paper machine waters being aerobic, warm, and low in carbon and manganese. industrial environment of this species differ from its natural habitats, geothermal springs and deep ocean subsurfaces, by being highly exposed to oxygen. quantitative proteome analysis using two-dimensional gel electrophoresis and bioinformatic tools showed expression change for 165 proteins f ...201222228732
detoxification of toxins by bacillithiol in staphylococcus aureus.bacillithiol (bsh), an α-anomeric glycoside of l-cysteinyl-d-glucosaminyl-l-malate, is a major low molecular weight thiol found in bacteria such as bacillus sp., staphylococcus aureus, and deinococcus radiodurans. like other low molecular weight thiols such as glutathione and mycothiol, bsh is likely to be involved in protection against environmental toxins including thiol reactive antibiotics. we report here a bsh dependent detoxification mechanism in s. aureus. when s. aureus newman strain wa ...201222262099
high-pressure tolerance in halobacterium salinarum nrc-1 and other non-piezophilic prokaryotes.in this study, we examined the high-pressure survival of a range of prokaryotes not found in high-pressure environments to determine the effects of adaptations to osmotic and oxidative stresses on piezo-resistance. the pressure survivals of halobacterium salinarum nrc-1, deinococcus radiodurans r1, and chromohalobacter salexigens were compared to that of escherichia coli mg1655. c. salexigens, which uses the compatible solute ectoine as an osmolyte, was as piezo-sensitive as e. coli mg1655, sugg ...201222212652
deinococcus humi sp. nov., isolated from soil.a gram-staining-positive, strictly aerobic, spherical-shaped, non-motile red-pigmented bacterial strain mk03t, was isolated from a soil sample. a polyphasic approach was applied to study the taxonomic position of strain mk03t. phylogenetic analysis based on 16s rrna gene sequences showed that strain mk03t belonged to the clade formed by members of the genus deinococcus in the family deinococcaceae. the g+c content of the genomic dna was 64.5 mol %. strain mk03t showed highest 16s rrna gene seque ...201222228662
transcriptional regulation of central carbon and energy metabolism in bacteria by redox responsive repressor rex.redox-sensing repressor rex was previously implicated in the control of anaerobic respiration in response to the cellular nadh/nad(+) levels in gram-positive bacteria. we utilized the comparative genomics approach to infer candidate rex-binding dna motifs and assess the rex regulon content in 119 genomes from 11 taxonomic groups. both dna-binding and nad-sensing domains are broadly conserved in rex orthologs identified in the phyla firmicutes, thermotogales, actinobacteria, chloroflexi, deinococ ...201122210771
death by protein damage in irradiated cells.a founding concept of radiobiology that deals with x-rays, γ-rays and ultraviolet light is that radiation indiscriminately damages cellular macromolecules. mounting experimental evidence does not fit into this theoretical framework. whereas dna lesion-yields in cells exposed to a given dose and type of radiation appear to be fixed, protein lesion-yields are highly variable. extremely radiation resistant bacteria such as deinococcus radiodurans have evolved extraordinarily efficient antioxidant c ...201122112864
the structure and enzymatic properties of a novel rnase ii family enzyme from deinococcus radiodurans.exoribonucleases are vital in nearly all aspects of rna metabolism, including rna maturation, end-turnover, and degradation. rnase ii and rnase r are paralogous members of the rnr superfamily of nonspecific, 3'→5', processive exoribonucleases. in escherichia coli, rnase ii plays a primary role in mrna decay and has a preference for unstructured rna. rnase r, in contrast, is capable of digesting structured rna and plays a role in the degradation of both mrna and stable rna. deinococcus radioduran ...201122133431
Chemical contrast in soft x-ray ptychography.The unique strengths of x-ray microscopy are high penetration depth and near-edge resonances that provide chemical information. We use ptychography, a coherent diffractive imaging technique that disposes of the requirement for isolated specimens, and demonstrate resonant imaging by exploiting resonances near the oxygen K edge to differentiate between two oxygen-containing materials. To highlight a biological system where resonant ptychography might be used for chemical mapping of unsliced cells, ...201122181778
characterization of deinococcus sahariens sp. nov., a radiation-resistant bacterium isolated from a saharan hot spring.an ultraviolet-radiation-resistant, gram-positive, orange-pigmented, thermophilic and strictly aerobic cocci was isolated from saharan water hot spring in tunisia. the newly isolated bacterium, designated han-23(t), was identified based on polyphasic taxonomy including genotypic, phenotypic and chemotaxonomic characterization. phylogenetic analysis based on 16s rrna gene sequences placed this strain within deinococcus genus. however, strain han-23(t) is different from recognized species of the g ...201122012026
On the stoichiometry of Deinococcus radiodurans Dps-1 binding to duplex DNA.DNA protection during starvation (Dps) proteins, dodecameric assemblies of four-helix bundle subunits, contribute to protection against reactive oxygen species. Deinococcus radiodurans, which is characterized by resistance to DNA damaging agents, encodes two Dps homologs, of which Dps-1 binds DNA with high affinity. DNA binding requires N-terminal extensions preceding the four-helix bundle core. Composed of six Dps-1 dimers, each capable of DNA binding by N-terminal extensions interacting in con ...201122114047
utilization of glycosyltransferases for the synthesis of a densely packed hyperbranched polysaccharide brush coating as artificial glycocalyx.densely packed polysaccharide brushes consisting of α-d-glucose residues were grafted from modified silicon substrates. potato phosphorylase was herein used to grow linear polysaccharide chains from silicon tethered maltoheptaose oligosaccharides using glucose-1-phosphate as donor substrate. the combined use of potato phosphorylase and deinococcusgeothermalis branching enzyme resulted in a hyperbranched brush coating as the latter one redistributes short oligosaccharides from the α(1-4)-linked p ...201121888377
Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health.To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known.201121912695
the role of bacillus anthracis recd2 helicase in dna mismatch repair.dna mismatch repair (mmr) systems can be classified as either muth-dependent or muth-independent. in bacteria, extensive studies have been conducted with the muth-dependent mmr in escherichia coli and its close relatives. the picture of muth-independent mmr in other bacteria is less clear, as mmr components other than muts and mutl have not been identified in the majority of bacteria. bacillus anthracis is one of the muth-less gram(+) bacteria in the phylum of firmicutes. we used papillation as ...201121940221
the structural basis of the response regulator drrra from deinococcus radiodurans.drrra, a vital and recently discovered gene product of deinococcus radiodurans, is a member of the ompr/phob family of response regulators that couple with the cognate histidine kinase (hk) to form a typical two component system (tcs). it is known that the drrra is responsible for the transcriptional levels of numerous genes mostly relating to the stress response and dna repair. in this paper, the crystal structures of the effector domain and full-length protein of drrra with resolutions of 1.6 ...201122227191
Pigment-based whole-cell biosensor system for cadmium detection using genetically engineered Deinococcus radiodurans.In this study, a colorimetric whole-cell biosensor for cadmium (Cd) was designed using a genetically engineered red pigment producing bacterium, Deinococcus radiodurans. Based on the previous microarray data, putative promoter regions of highly Cd-inducible genes (DR_0070, DR_0659, DR_0745, and DR_2626) were screened and used for construction of lacZ reporter gene cassettes. The resultant reporter cassettes were introduced into D. radiodurans R1 to evaluate promoter activity and specificity. Amo ...201121928095
marr homologs with urate-binding signature.bacteria that associate with living hosts require intricate mechanisms to detect and respond to host defenses. part of the early host defense against invading bacteria is the production of reactive oxygen species, and xanthine oxidase is one of the main producers of such agents. the end-product of the enzymatic activity of xanthine oxidase, urate, was previously shown to be the natural ligand for deinococcus radiodurans-encoded hucr and it was shown to attenuate dna binding by agrobacterium tume ...201121207455
uncultured bacterial diversity in tropical maize (zea mays l.) rhizosphere.structure of maize (zea mays l.) rhizosphere bacteria was evaluated to explore the feasibility of identifying novel rhizosphere bacteria using culture-independent method based on direct amplification and analysis of 16s rrna gene (rrna) sequences and especially to obtain a better understanding of bacterial community structure and diversity from maize. a total of 274 sequences were analyzed and assigned 48.00% proteobacteria, 10.30% actinobacteria, 9.90% bacteroidetes, 6.60% verrucomicrobia, 4.80 ...201121259285
laboratory-evolved mutants of an exogenous global regulator, irre from deinococcus radiodurans, enhance stress tolerances of escherichia coli.the tolerance of cells toward different stresses is very important for industrial strains of microbes, but difficult to improve by the manipulation of single genes. traditional methods for enhancing cellular tolerances are inefficient and time-consuming. recently, approaches employing global transcriptional or translational engineering methods have been increasingly explored. we found that an exogenous global regulator, irre from an extremely radiation-resistant bacterium, deinococcus radioduran ...201121267412
epigenetic changes of dna repair genes in cancer.'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 ...201121278452
crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.the structures of the large ribosomal subunit of deinococcus radiodurans (d50s) in complex with the antibiotic lankamycin (3.2 å) and a double antibiotic complex of lankamycin and lankacidin c (3.45 å) have been determined, in continuation of previous crystallographic studies on lankacidin-d50s complex. these two drugs have been previously reported to inhibit ribosomal function with mild synergistic effect. lankamycin, a member of the macrolide family, binds in a similar manner to erythromycin. ...201121282615
gene cloning and protein expression of ?-glutamyltranspeptidases from thermus thermophilus and deinococcus radiodurans: comparison of molecular and structural properties with mesophilic counterparts.?-glutamyltranspeptidase (?-gt) is an ubiquitous enzyme that catalyzes the hydrolysis of ?-glutamyl bonds in glutathione and glutamine and the transfer of the released ?-glutamyl group to amino acids or short peptides. ?-gts from extremophiles, bacteria adapted to live in hostile environments, were selected as model systems to study the molecular underpinnings of their adaptation to extreme conditions and to find out special properties of potential biotechnological interest. here, we report the ...201121298394
composition of the bacterial biota in slime developed in two machines at a canadian paper mill.during the process of papermaking by pulp and paper plants, a thick and viscous deposits, termed slime, is quickly formed around the paper machines, which can affect the papermaking process. in this study, we explored the composition of the bacterial biota in slime that developed on shower pipes from 2 machines at a canadian paper mill. firstly, the composition was assessed for 12 months by dna profiling with polymerase chain reaction coupled with denaturing gradient gel electrophoresis. except ...201121326351
on the antibacterial activity of roots of capparis spinosa l.a decoction of capparis spinosa l. roots, widely used in the traditional folk medicine of southern italy, was prepared and submitted to antibacterial activity tests, which showed an interesting bacteriostatic activity on the growth of deinococcus radiophilus. heterocyclic compounds were also recovered from the chloroformic extract of the roots.201121328135
deinococcus reticulitermitis sp. nov., isolated from a termite gut.bacterial strain tm-1t was isolated from the gut of a wood-feeding termite, reticulitermes chinensis snyder. cells of the strain tm-1t were gram-negative, spherical (1.0-2.0 µm in diameter), non-motile, non-sporulating with red-pigmented color. strain tm-1t was found to be resistant to uv radiation, showing 34 % survival after exposure to uv light at a dose of 100 j m-2. growth occurred at 20-40°c (optimum, 30°c) and ph 6.0-10.0 (optimum, ph 6.0-7.0), and in the presence of 0-1% (w/v) nacl (opti ...201121335505
an expanded collection and refined consensus model of glms ribozymes.self-cleaving glms ribozymes selectively bind glucosamine-6-phosphate (glcn6p) and use this metabolite as a cofactor to promote self-cleavage by internal phosphoester transfer. representatives of the glms ribozyme class are found in gram-positive bacteria where they reside in the 5' untranslated regions (utrs) of glms messenger rnas that code for the essential enzyme l-glutamine:d-fructose-6-phosphate aminotransferase. by using comparative sequence analyses, we have expanded the number of glms r ...201121367971
oxidative stress resistance in deinococcus radiodurans.deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive dna damage efficiently and accurately. it is extremely resistant to many dna-damaging agents, including ionizing radiation and uv radiation (100 to 295 nm), desiccation, and mitomycin c, which induce oxidative damage not only to dna but also to all cellular macromolecules via the production of reactive oxygen species. the extreme resilience of d. radiodurans to oxidative stress is imparted synergistically ...201121372322
genome-wide transcriptome and proteome analysis of escherichia coli expressing irre, a global regulator of deinococcus radiodurans.gram-negative bacterium escherichia coli and the gram-positive deinococcus radiodurans fundamentally differ in their cell structures and gene regulations. we have previously reported that irre, a deinococcus genus-specific global regulator, confers significantly enhanced tolerance to various abiotic stresses. to better understand the global effects of irre on the regulatory networks, we carried out combined transcriptome and proteome analysis of e. coli expressing the irre protein. our analysis ...201121380435
molecular characterization of activated sludge from a seawater-processing wastewater treatment plant.the prokaryotic community composition of activated sludge from a seawater-processing wastewater treatment plant (almeria, spain) was investigated by using the rrna approach, combining different molecular techniques such as denaturing gradient gel electrophoresis (dgge), clone libraries and in situ hybridization (fish and card-fish). most of the sequences retrieved in the dgge and the clone libraries were similar to uncultured members of different phyla. the most abundant sequence recovered from ...201121414181
marr homologs with urate-binding signature.bacteria that associate with living hosts require intricate mechanisms to detect and respond to host defenses. part of the early host defense against invading bacteria is the production of reactive oxygen species, and xanthine oxidase is one of the main producers of such agents. the end-product of the enzymatic activity of xanthine oxidase, urate, was previously shown to be the natural ligand for deinococcus radiodurans-encoded hucr and it was shown to attenuate dna binding by agrobacterium tume ...201121432936
the flexibility of uv-inducible mutation in deinococcus ficus as evidenced by the existence of the imub-dnae2 gene cassette and generation of superior feather degrading bacteria.the lexa-imub-dnae2 gene cassette contributing to the tls (translesion synthesis) polymerase activity and can easily cause mutation after dna damage in many bacteria. but it was previously thought that tls polymerase activity was unlikely to exist in the radio-resistant genus deinococcus. in our preliminary studies, the lexa-imub-dnae2 gene cassette was found in a newly isolated feather-degrading deinococcus ficus. here we have attempted to determine the imub gene sequence from another deinococc ...201121459566
effects of polarization in the presence and absence of biocides on biofilms in a simulated paper machine water.the antifouling potential of electric polarization combined and not combined with biocides was studied in nonsaline warm water with high organic content. deinococcus geothermalis is a bacterium known for forming colored biofilms in paper machines and for its persistence against cleaning and chemical treatments. when d. geothermalis biofilms grown for 24 h in simulated paper machine water were exposed to cathodic or cathodically weighted pulsed polarization at least 60% (p < 0.05) of the biofilms ...201121461746
design of deinococcus radiodurans thioredoxin reductase with altered thioredoxin specificity using computational alanine mutagenesis.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 th ...201121465613
complete genome sequence of truepera radiovictrix type strain (rq-24).truepera radiovictrix albuquerque et al. 2005 is the type species of the genus truepera within the phylum "deinococcus/thermus". t. radiovictrix is of special interest not only because of its isolated phylogenetic location in the order deinococcales, but also because of its ability to grow under multiple extreme conditions in alkaline, moderately saline, and high temperature habitats. of particular interest is the fact that, t. radiovictrix is also remarkably resistant to ionizing radiation, a f ...201121475591
culturable bacterial diversity at the princess elisabeth station (utsteinen, sør rondane mountains, east antarctica) harbours many new taxa.we studied the culturable heterotrophic bacterial diversity present at the site of the new princess elisabeth station at utsteinen (dronning maud land, east antarctica) before construction. about 800 isolates were picked from two terrestrial microbial mat samples after incubation on several growth media at different temperatures. they were grouped using rep-pcr fingerprinting and partial 16s rrna gene sequencing. phylogenetic analysis of the complete 16s rrna gene sequences of 93 representatives ...201121501941
phylogeny and molecular signatures for the phylum thermotogae and its subgroups.thermotogae species are currently identified mainly on the basis of their unique toga and distinct branching in the rrna and other phylogenetic trees. no biochemical or molecular markers are known that clearly distinguish the species from this phylum from all other bacteria. the taxonomic/evolutionary relationships within this phylum, which consists of a single family, are also unclear. we report detailed phylogenetic analyses on thermotogae species based on concatenated sequences for many ribos ...201121503713
mechanism of reco recruitment to dna by single-stranded dna binding protein.reco is a recombination mediator protein (rmp) important for homologous recombination, replication repair and dna annealing in bacteria. in all pathways, the single-stranded (ss) dna binding protein, ssb, plays an inhibitory role by protecting ssdna from annealing and recombinase binding. conversely, ssb may stimulate each reaction through direct interaction with reco. we present a crystal structure of escherichia coli reco bound to the conserved ssb c-terminus (ssb-ct). ssb-ct binds the hydroph ...201121504984
characterization of dra0282 from deinococcus radiodurans for its role in bacterial resistance to dna damage.dra0282 a hypothetical protein, was found in a pool of nucleotide binding proteins in deinococcus radiodurans cells recovering from gamma radiation stress. this pool exhibited an unusual inhibition of nuclease activity by atp. n-terminal of dra0282 showed similarity with human ku80 homologues, while c terminal showed no similarities with known proteins. the recombinant protein required mn2+ for its interaction with dna and protected dsdna from exonuclease iii degradation. the binding of the prot ...201121511764
making heads or tails of the hu-proteins in the planctomycete gemmata obscuriglobus.gemmata obscuriglobus has a highly condensed nucleoid which is implicated in its resistance to radiation. however, the mechanisms by which such compaction is achieved, or the proteins responsible involved are still unknown. here we have examined the genome of g.obscuriglobus for presence of proteins homologous to those that have been associated with nucleoid condensation. we found two different proteins homologous to the bacterial nucleoid-associated protein hu, one with an n-terminal and one wi ...201121511768
reca proteins from deinococcus geothermalis and deinococcus murrayi - cloning, purification and biochemical characterisation.abstract:201121513512
genome-wide response of deinococcus radiodurans on cadmium toxicity.deinococcus radiodurans is extremely resistant to various genotoxic conditions and chemicals. in this study, we characterized the effect of a sublethal concentration (100 microm) of cadmium (cd) on d. radiodurans using a whole-genome dna microarray. time-course global gene expression profiling showed that 1,505 genes out of 3,116 total orfs were differentially expressed more than 2-fold in response to cd treatment for at least one timepoint. the majority of the upregulated genes are related to i ...201121532329
characterization of the role of dr0171 in transcriptional response to radiation in the extremely radioresistant bacterium deinococcus radiodurans.the extremely radioresistant bacterium deinococcus radiodurans encodes a number of function-unknown genes, and some of them involve in the radioresistance. the radiation-inducible gene dr0171 has a reca-like expression pattern in the postirradiation recovery and was also supposed to encode a transcriptional regulator to contribute to the radioresistance. here, we found that the egfp-tagged dr0171 proteins gathered in the nucleoid regions after radiation. further, we constructed a null mutant of ...201121567175
exploring biological effects of low level radiation from the other side of background. 201121595063
presequence-dependent folding ensures mrpl32 processing by the m-aaa protease in mitochondria.m-aaa proteases exert dual functions in the mitochondrial inner membrane: they mediate the processing of specific regulatory proteins and ensure protein quality control degrading misfolded polypeptides to peptides. loss of these activities leads to neuronal cell death in several neurodegenerative disorders. however, it is unclear how the m-aaa protease chooses between specific processing and complete degradation. a central and conserved function of the m-aaa protease is the processing of the rib ...201121610694
phon-expressing, lyophilized, recombinant deinococcus radiodurans cells for uranium bioprecipitation.employment of genetically engineered radiation resistant organisms to recover radionuclides/heavy metals from radioactive wastes is an attractive proposition. cells of recombinant deinococcus radiodurans strain expressing, a non-specific acid phosphatase encoding phon gene, were lyophilized. lyophilized recombinant deinococcus cells retained viability and phon activity and could efficiently precipitate uranium from aqueous solutions for up to six months of storage at room temperature. batch proc ...201121616102
survival of thermophilic and hyperthermophilic microorganisms after exposure to uv-c, ionizing radiation and desiccation.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 sur ...201121638055
genomic analysis reveals versatile organisms for quorum quenching enzymes: acyl-homoserine lactone-acylase and -lactonase.microbial virulence and their resistance to multiple drugs have obliged researchers to look for novel drug targets. virulence of pathogenic microbes is regulated by signal molecules such as acylated homoserine lactone (ahl) produced during a cell density dependent phenomenon of quorum sensing (qs). in contrast, certain microbes produce ahl-lactonases and -acylases to degrade qs signals, also termed as quorum quenching. mining sequenced genome databases has revealed organisms possessing conserved ...201121660112
community variability of bacteria in alpine snow (mont blanc) containing saharan dust deposition and their snow colonisation potential.microorganisms uplifted during dust storms survive long-range transport in the atmosphere and could colonize high-altitude snow. bacterial communities in alpine snow on a mont blanc glacier, associated with four depositions of saharan dust during the period 2006-2009, were studied using 16s rrna gene sequencing and flow cytometry. also, sand from the tunisian sahara, saharan dust collected in grenoble and mont blanc snow containing no saharan dust (one sample of each) were analyzed. the bacteria ...201121666389
global effect of an rna polymerase ß-subunit mutation on gene expression in the radiation-resistant bacterium deinococcus radiodurans.the ß-subunit of rna polymerase, which is involved in rifampin binding, is highly conserved among prokaryotes, and rif(r) mutants detected in many bacteria are the result of amino acid changes. spontaneous rifampin resistance mutations resulting in amino acid replacement (l420r) and deletion (1258-66 9 bp deletion) have been previously isolated in the rpob gene of deinococcus radiodurans. in this study, a ß-subunit mutation in d. radiodurans resulted in a unique effect on growth rate. we used dn ...201121809039
bacterial communities in the gut of the freshwater copepod eudiaptomus gracilis.eudiaptomus gracilis is the most abundant member of the zooplankton, plays a key role in the food web of lake balaton (hungary). in the present study the composition of bacterial communities of this copepod was investigated based on cultivation and molecular cloning. the cultivated bacterial strains from the gut homogenate samples of eudiaptomus gracilis belonged to four different clades: firmicutes, actinobacteria, bacteriodetes and proteobacteria. clone library showed high species diversity, f ...201121780147
deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant.a gram-staining-positive, strictly aerobic, spherical-shaped, non-motile red-pigmented bacterial strain designated mj27t, was isolated from a sludge sample of the daejeon sewage disposal plant in south korea. a polyphasic approach was applied to study the taxonomic position of strain mj27t. strain mj27t showed highest 16s rrna gene sequence similarity with deinococcus grandis dsm 3963t (98.8%), deinococcus caeni ho-08t (97.5%) and deinococcus aquaticus pb314t (96.6%.), whereas, sequence similari ...201121764979
leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes.abstract: background: shine-dalgarno (sd) signal has long been viewed as the dominant translation initiation signal in prokaryotes. recently, leaderless genes, which lack 5'-untranslated regions (5'-utr) on their mrnas, have been shown abundant in archaea. however, current large-scale in silico analyses on initiation mechanisms in bacteria are mainly based on the sd-led initiation way, other than the leaderless one. the study of leaderless genes in bacteria remains open, which causes uncertain u ...201121749696
complete genome sequence of deinococcus maricopensis type strain (lb-34).deinococcus maricopensis (rainey and da costa 2005) is a member of the genus deinococcus, which is comprised of 44 validly named species and is located within the deeply branching bacterial phylum deinococcus-thermus. strain lb-34(t) was isolated from a soil sample from the sonoran desert in arizona. various species of the genus deinococcus are characterized by extreme radiation resistance, with d. maricopensis being resistant in excess of 10 kgy. even though the genomes of three deinococcus spe ...201121677853
characterization of rads/radr two-component system role in radiation resistance of deinococcus radiodurans.deinococcus radiodurans shows extraordinary tolerance to dna damage and exhibits differential gene expression and protein recycling, in spite of it lacking the typical sos response as characterized in other bacteria. a putative response regulator, the product of drb0091 (radr) gene, was identified from the pool of radiation-induced proteins. the radr is annotated upstream to drb0090 encoding a putative sensor histidine kinase (rads) on the megaplasmid. deletion of these genes individually as wel ...201121737498
emerging roles for the ro 60-kda autoantigen in noncoding rna metabolism.all cells contain an enormous variety of ribonucleoprotein (rnp) complexes that function in diverse processes. although the mechanisms by which many of these rnps contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. a member of this latter category, the ro 60-kda protein and its associated noncoding y rnas, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases s ...201121823229
origin of diderm (gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes.the prokaryotic organisms can be divided into two main groups depending upon whether their cell envelopes contain one membrane (monoderms) or two membranes (diderms). it is important to understand how these and other variations that are observed in the cell envelopes of prokaryotic organisms have originated. in 2009, james lake proposed that cells with two membranes (primarily gram-negative bacteria) originated from an ancient endosymbiotic event involving an actinobacteria and a clostridia (lak ...201121717204
atp-dependent fructose uptake system in deinococcus radiodurans.the bacterial phosphoenolpyruvate (pep)-dependent group translocation system (pts) requires the presence of both membrane-bound and cytoplasmic components to phosphorylate and translocate sugar. deinococcus radiodurans has a functional frua gene coding for the membrane-bound components of the fructose-specific pts. however, frub gene coding for the fructose-specific cytosolic components of pts is a pseudogene. yet, this bacterium metabolized fructose readily. in vitro studies showed that both ce ...201121822900
identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in e. coli 23s rrna.complete characterization of a biomolecule's chemical structure is crucial in the full understanding of the relations between their structure and function. the dominating components in ribosomes are ribosomal rnas (rrnas), and the entire rrna-but a single modified nucleoside at position 2501 in 23s rrna-has previously been characterized in the bacterium escherichia coli. despite a first report nearly 20-áyears ago, the chemical nature of the modification at position 2501 has remained elusive, an ...201121723290
structural and functional insights into dr2231 protein, the mazg-like nucleoside triphosphate pyrophosphohydrolase from deinococcus radiodurans.deinococcus radiodurans is among the very few bacterial species extremely resistant to ionizing radiation, uv light, oxidizing agents, and cycles of prolonged desiccation. the proteome of d. radiodurans reflects the evolutionary pressure exerted by chronic exposure to (nonradioactive) forms of dna and protein damage. a clear example of this adaptation is the overrepresentation of protein families involved in the removal of non-canonical nucleoside triphosphates (ntps) whose incorporation into na ...201121733847
high-temperature cultivation and 5' mrna optimization are key factors for the efficient overexpression of thermostable deinococcus geothermalis purine nucleoside phosphorylase in escherichia coli.overexpression of genes from thermophiles in escherichia coli is an attractive approach towards the large-scale production of thermostable biocatalysts. however, various factors can challenge efficient heterologous protein expression--one example is the formation of stable 5' mrna secondary structures that can impede an efficient translation initiation. in this work, we describe the expression optimization of purine nucleoside phosphorylase from the thermophilic microbe deinococcus geothermalis ...201121871934
sequence of the hyperplastic genome of the naturally competent thermus scotoductus sa-01.many strains of thermus have been isolated from hot environments around the world. thermus scotoductus sa-01 was isolated from fissure water collected 3.2 km below surface in a south african gold mine. the isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. the genomes from two different thermus thermophilus strains have been com ...201122115438
investigating deinococcus radiodurans reca protein filament formation on double-stranded dna by a real-time single-molecule approach.with the aid of an efficient, precise, and almost error-free dna repair system, deinococcus radiodurans can survive hundreds of double-strand breaks inflicted by high doses of irradiation or desiccation. reca of d. radiodurans (drreca) plays a central role both in the early phase of repair by an extended synthesis-dependent strand annealing process and in the later more general homologous recombination phase. both roles likely require drreca filament formation on duplex dna. we have developed si ...201121853996
survival of deinococcus radiodurans against laboratory-simulated solar wind charged particles.in this experimental study, cells of the radiation-resistant bacterium deinococcus radiodurans were exposed to several different sources of radiation chosen to replicate the charged particles found in the solar wind. naked cells or cells mixed with dust grains (basalt or sandstone) differing in elemental composition were exposed to electrons, protons, and ions to determine the probability of cell survival after irradiation. doses necessary to reduce the viability of cell population to 10% (ld(10 ...201122059692
Biosynthesis of (+)-catechin glycosides using recombinant amylosucrase from Deinococcus geothermalis DSM 11300.Amylosucrase (ASase, EC 2.4.1.4) is a glucosyltransferase that hydrolyzes sucrose into glucose and fructose and produces amylose-like glucan polymers from the released glucose. (+)-Catechin is a plant polyphenolic metabolite having skin-whitening and antioxidant activities. In this study, the ASase gene from Deinococcus geothermalis (dgas) was expressed in Escherichia coli, while the recombinant DGAS enzyme was purified using a glutathione S-transferase fusion system. The (+)-catechin glycoside ...201122112416
the deinococcal ddrb protein is involved in an early step of dna double strand break repair and in plasmid transformation through its single-strand annealing activity.the deinococcus radiodurans bacterium exhibits an extreme resistance to ionizing radiation. here, we investigated the in vivo role of ddrb, a radiation-induced deinococcus specific protein that was previously shown to exhibit some in vitro properties akin to those of ssb protein from escherichia coli but also to promote annealing of single stranded dna. first we report that the deletion of the c-terminal motif of the ddrb protein, which is similar to the ssb c-terminal motif involved in recruitm ...201121968057
dna binding is essential for ppri function in response to radiation damage in deinococcus radiodurans.the extremely radioresistant bacterium deinococcus radiodurans possesses a rapid and efficient but poorly known dna damage response mechanism that mobilizes one-third of its genome to survive lethal radiation damage. deinococcal ppri serves as a general switch to regulate the expression of dozens of proteins from different pathways after radiation, including the dna repair proteins reca, ppra and ssb. however, the underlying mechanism is poorly understood. in this study, we analyzed the dynamic ...201122051194
structural investigation of the thermostability and product specificity of amylosucrase from the bacterium deinococcus geothermalis.amylosucrases are sucrose-utilizing α-transglucosidases that naturally catalyze the synthesis of α-glucans, linked exclusively through α-1,4 linkages. side-products and in particular sucrose isomers such as turanose and trehalulose are also produced by these enzymes. here, we report the first structural and biophysical characterization of the most thermostable amylosucrase identified so far, the amylosucrase from deinoccocus geothermalis (dgas). the 3d-structure revealed a homodimeric quaterna ...201122210773
analysis of the bacterial diversity in the fecal material of the endangered yangtze finless porpoise, neophocaena phocaenoides asiaeorientalis.the aim of this study was to determine the bacteria present in the fecal material of the endangered yangtze finless porpoise, neophocaena phocaenoides asiaeorientalis. fecal samples were collected from 12 yangtze finless porpoises living in the wild at poyang lake, located in jiangxi province, china. to determine the bacterial diversity, a 16s rrna gene clone library using the bacterial pcr primers fd1 and rp2, was prepared. a total of 138 near-full-length sequences were analyzed and 39 operatio ...201122201021
gamma radiation-induced proteome of deinococcus radiodurans primarily targets dna repair and oxidative stress alleviation.the extraordinary radioresistance of deinococcus radiodurans primarily originates from its efficient dna repair ability. the kinetics of proteomic changes induced by a 6-kgy dose of gamma irradiation was mapped during the post-irradiation growth arrest phase by two-dimensional protein electrophoresis coupled with mass spectrometry. the results revealed that at least 37 proteins displayed either enhanced or de novo expression in the first 1 h of post-irradiation recovery. all of the radiation-res ...201121989019
comparative survival analysis of deinococcus radiodurans and the haloarchaea natrialba magadii and haloferax volcanii exposed to vacuum ultraviolet irradiation.abstract the haloarchaea natrialba magadii and haloferax volcanii, as well as the radiation-resistant bacterium deinococcus radiodurans, were exposed to vacuum uv (vuv) radiation at the brazilian synchrotron light laboratory. cell monolayers (containing 10(5) to 10(6) cells per sample) were prepared over polycarbonate filters and irradiated under high vacuum (10(-5) pa) with polychromatic synchrotron radiation. n. magadii was remarkably resistant to high vacuum with a survival fraction of (3.7 ...201122165956
bacterial community associated with the intestinal tract of p. monodon in commercial farms.the potentially important roles of intestinal bacteria on immune response, disease resistance, and nutrition for the black tiger shrimp penaeus monodon have been increasingly investigated. however, so far, little is known about the intestinal bacterial community of the shrimp in the commercial aquaculture settings. in this study, the intestinal bacterial communities of juvenile p. monodon (70 individuals) from eight commercial farms in thailand were examined using 16s rdna pcr-dgge, and seven 16 ...201121915632
deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a finnish paper mill.a rod-shaped, non-spore-forming, non-motile, aerobic, oxidase and catalase-positive and radiation-resistant bacterium (designated strain k4.1(t)) was isolated from biofilm collected from a finnish paper mill. the bacterium grew as pale pink colonies on oligotrophic medium at 12 to 50 °c (optimum 37 to 45 °c) and at ph 6 to 10.3. the dna g+c content of the strain was 66.8 l%. according to 16s rrna gene sequence analysis, strain k4.1(t) was distantly related to the genus deinococcus, sharing highe ...201120382794
inference of the phylogenetic position of the phylum deferribacteres from gene order comparison.the phylogenetic placement of the phylum deferribacteres was investigated on the basis of gene order comparisons of completely sequenced bacterial genomes. two completely sequenced deferribacteres species share five sets of gene arrangements with a group of phyla, proteobacteria, aquificae, planctomycetes, spirochaetes, bacteroidetes, chlorobi, acidobacteria, verrucomicrobia, elusimicrobia and nitrospirae, while the other group of phyla, synergistetes, firmicutes, actinobacteria, thermotogae, ch ...201120706870
peroxide stress elicits adaptive changes in bacterial metal ion homeostasis.exposure to hydrogen peroxide (h(2)o(2)) and other reactive oxygen species is a universal feature of life in an aerobic environment. bacteria express enzymes to detoxify h(2)o(2) and to repair the resulting damage, and their synthesis is typically regulated by redox-sensing transcription factors. the best characterized bacterial peroxide-sensors are escherichia coli oxyr and bacillus subtilis perr. analysis of their regulons has revealed that, in addition to inducible detoxification enzymes, ada ...201120977351
characterization of deinococcus radiophilus thioredoxin reductase active with both nadh and nadph.thioredoxin reductase (trxr, ec 1.6.4.5) of deinococcus radiophilus was purified by steps of sonication, ammonium sulfate fractionation, 2'5' adp sepharose 4b affinity chromatography, and sephadex g-100 gel filtration. the purified trxr, which was active with both nadph and nadh, gave a 368 u/mg protein of specific activity with 478-fold purification and 18% recovery from the cell-free extract. an isoelectric point of the purified enzymes was ca. 4.5. the molecular weights of the purified trxr e ...201021046342
characterization of a glycoside hydrolase family 42 β-galactosidase from deinococcus geothermalis.a putative recombinant β-galactosidase from deinococcus geothermalis was purified as a single 79 kda band of 42 u activity/mg using his-trap affinity chromatography. the molecular mass of the native enzyme was a 158 kda dimer. the catalytic residues e151 and e325 of β-galactosidase from d. geothermalis were conserved in all aligned gh family 42 β-galactosidases, indicating that this enzyme is also a gh family 42 β-galactosidase. maximal activity of the enzyme was at ph 6.5 and 60°c. it has a uni ...201021053047
effects of mn and fe levels on bacillus subtilis spore resistance and effects of mn2+, other divalent cations, orthophosphate, and dipicolinic acid on protein resistance to ionizing radiation.spores of bacillus subtilis strains with (wild type) or without (α(-)β(-)) most dna-binding α/β-type small, acid-soluble proteins (sasp) were prepared in medium with additional mncl(2) concentrations of 0.3 μm to 1 mm. these haploid spores had mn levels that varied up to 180-fold and mn/fe ratios that varied up to 300-fold. however, the resistance of these spores to desiccation, wet heat, dry heat, and in particular ionizing radiation was unaffected by their level of mn or their mn/fe ratio; thi ...201021057011
the importance of peptide detectability for protein identification, quantification, and experiment design in ms/ms proteomics.peptide detectability is defined as the probability that a peptide is identified in an lc-ms/ms experiment and has been useful in providing solutions to protein inference and label-free quantification. previously, predictors for peptide detectability trained on standard or complex samples were proposed. although the models trained on complex samples may benefit from the large training data sets, it is unclear to what extent they are affected by the unequal abundances of identified proteins. to a ...201021067214
modeling the interactions of the nucleotide excision repair uvra(2) dimer with dna.the uvra protein initiates the dna damage recognition process by the bacterial nucleotide excision repair (ner) system. recently, crystallographic structures of holo-uvra(2) dimers from two different microorganisms have been released (protein data bank entries 2r6f , 2vf7 , and 2vf8 ). however, the details of the dna binding by uvra(2) and other peculiarities involved in the damage recognition process remain unknown. we have undertaken a molecular modeling approach to appraise the possible modes ...201021090726
an empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences.global protein identification through current proteomics methods typically depends on the availability of sequenced genomes. in spite of increasingly high throughput sequencing technologies, this information is not available for every microorganism and rarely available for entire microbial communities. nevertheless, the protein-level homology that exists between related bacteria makes it possible to extract biological information from the proteome of an organism or microbial community by using t ...201021103051
bacterial adhesion inhibition of the quaternary ammonium functionalized silica nanoparticles.quaternary ammonium compounds have been considered as excellent antibacterial agents due to their effective biocidal activity, long term durability and environmentally friendly performance. in this work, 3-(trimethoxysilyl)-propyldimethyloctadecylammonium chloride as a quaternary ammonium silane was applied for the surface modification of silica nanoparticles. the quaternary ammonium silane provided silica surface with hydrophobicity and antibacterial properties. in addition, the glass surface w ...201021115282
potential of cathodoluminescence microscopy and spectroscopy for the detection of prokaryotic cells on minerals.detecting mineral-hosted ecosystems to assess the extent and functioning of the biosphere from the surface to deep earth requires appropriate techniques that provide, beyond the morphological criteria, indubitable clues of the presence of prokaryotic cells. here, we evaluate the capability of cathodoluminescence microscopy and spectroscopy, implemented on a scanning electron microscope, to identify prokaryotes on mineral surfaces. for this purpose, we used, as a first step, a simple model of eit ...201021118024
purification, crystallization and preliminary x-ray diffraction analysis of dna damage response a protein from deinococcus radiodurans.dna damage response a protein (ddra) from deinococcus radiodurans has been suggested to be involved in dna-repair processes through binding to 3'-ends of single-stranded dna, thereby protecting the ends from nuclease digestion. in this study, a recombinant c-terminally truncated form of d. radiodurans ddra (ddra157) comprising the first 157 residues of ddra was expressed in escherichia coli, purified and crystallized. single crystals of ddra157 were obtained by the hanging-drop method at 293 k. ...201021139208
molecular recognition determinants for type iv secretion of diverse families of conjugative relaxases.in preparation for transfer conjugative type iv secretion systems (t4ss) produce a nucleoprotein adduct containing a relaxase enzyme covalently linked to the 5' end of single-stranded plasmid dna. the bound relaxase is expected to present features necessary for selective recognition by the type iv coupling protein (t4cp), which controls substrate entry to the envelope spanning secretion machinery. we prove that the incf plasmid r1 relaxase trai is translocated to the recipient cells. using a cre ...201021143323
bacterial killing by dry metallic copper surfaces.metallic copper surfaces rapidly and efficiently kill bacteria. cells exposed to copper surfaces accumulated large amounts of copper ions, and this copper uptake was faster from dry copper than from moist copper. cells suffered extensive membrane damage within minutes of exposure to dry copper. further, cells removed from copper showed loss of cell integrity. acute contact with metallic copper surfaces did not result in increased mutation rates or dna lesions. these findings are important first ...201021148701
insight into the strong antioxidant activity of deinoxanthin, a unique carotenoid in deinococcus radiodurans.deinoxanthin (dx) is a unique carotenoid synthesized by deinococcus radiodurans, one of the most radioresistant organisms known. in comparison with other carotenoids, dx was proven to exhibit significantly stronger reactive oxygen species (ros)-scavenging activity, which plays an important role in the radioresistance of d. radiodurans. in this work, to gain deeper insights into the strong antioxidant activity of dx, the parameters characterizing ros-scavenging potential were calculated by means ...201021151452
identification and evaluation of the role of the manganese efflux protein in deinococcus radiodurans.deinococcus radiodurans accumulates high levels of manganese ions, and this is believed to be correlated with the radiation resistance ability of this microorganism. however, the maintenance of manganese ion homeostasis in d. radiodurans remains to be investigated.201021156049
effect of relative humidity on deinococcus radiodurans' resistance to prolonged desiccation, heat, ionizing, germicidal, and environmentally relevant uv radiation.to test the effect of humidity on the radiation resistance of deinococcus radiodurans, air-dried cells were irradiated with germicidal 254 nm uv, and simulated environmental uv or γ-radiation and survival was compared to cells in suspension. it was observed that desiccated cells exhibited higher levels of resistance than cells in suspension toward uv or γ-radiation as well as after 85°c heat shock. it was also shown that low relative humidity improves survival during long-term storage of desicca ...201021161207
biofilm-forming bacteria with varying tolerance to peracetic acid from a paper machine.biofilms cause runnability problems in paper machines and are therefore controlled with biocides. peracetic acid is usually effective in preventing bulky biofilms. this study investigated the microbiological status of a paper machine where low concentrations (≤15 ppm active ingredient) of peracetic acid had been used for several years. the paper machine contained a low amount of biofilms. biofilm-forming bacteria from this environment were isolated and characterized by 16s rrna gene sequencing, ...201021161323
on the accuracy and limits of peptide fragmentation spectrum prediction.we estimated the reproducibility of tandem mass spectra for the widely used collision-induced dissociation (cid) of peptide ions. using the pearson correlation coefficient as a measure of spectral similarity, we found that the within-experiment reproducibility of fragment ion intensities is very high (about 0.85). however, across different experiments and instrument types/setups, the correlation decreases by more than 15% (to about 0.70). we further investigated the accuracy of current predictor ...201021175207
comparison of the genomes of deinococcal species using oligonucleotide microarrays.the bacterium deinococcus radiodurans is one of the most resistant organisms to ionizing radiation and other dnadamaging agents. although, at present, 30 deinococcus species have been identified, the whole-genome sequences of most species remain unknown, with the exception of d. radiodurans (drd), d. geothermalis, and d. deserti. in this study, comparative genomic hybridization (cgh) microarray analysis of three deinococcus species, d. radiopugnans (drp), d. proteolyticus (dpl), and d. radiophil ...201021193818
unstructured hydrophilic sequences in prokaryotic proteomes correlate with dehydration tolerance and host association.water loss or desiccation is among the most life-threatening stresses. it leads to dna double-strand breakage, protein aggregation, cell shrinkage, and low water activity precluding all biological functions. yet, in all kingdoms of life, rare organisms are resistant to desiccation through prevention or reversibility of such damage. here, we explore possible hallmarks of prokaryotic desiccation tolerance in their proteomes. the content of unstructured, low complexity (lc) regions was analyzed in ...201020709076
bacillithiol, a new player in bacterial redox homeostasis.abstract bacillithiol (bsh), the α-anomeric glycoside of l-cysteinyl-d-glucosamine with l-malic acid, plays a dominant role in the cytosolic thiol redox chemistry of the low guanine and cytosine (gc) gram-positive bacteria (phylum firmicutes). bsh is functionally analogous to glutathione (gsh) but differs sufficiently in chemical structure that cells have evolved a distinct set of enzymes that use bsh as cofactor. bsh was discovered in bacillus subtilis as a mixed disulfide with the redox-sensin ...201020712413
proteomic analysis of membrane proteins from a radioresistant and moderate thermophilic bacterium deinococcus geothermalis.deinococcus geothermalis is a radioresistant and moderate thermophilic bacterium. little was known about the membrane or membrane associated proteins of this bacterium. this study established the membrane subproteome profile of d. geothermalis, using 1-d page and lc-ms/ms analysis following triton x-114 detergent extraction. a total of 552 proteins from the membrane preparations were identified from two independent trials. in the total identified proteins, 117 were membrane subproteomic proteins ...201020714501
investigation of the highly active manganese superoxide dismutase from saccharomyces cerevisiae.manganese superoxide dismutase (mnsod) from different species differs in its efficiency in removing high concentrations of superoxide (o(2)(-)), due to different levels of product inhibition. human mnsod exhibits a substantially higher level of product inhibition than the mnsods from bacteria. in order to investigate the mechanism of product inhibition and whether it is a feature common to eukaryotic mnsods, we purified mnsod from saccharomyces cerevisiae (scmnsod). it was a tetramer with 0.6 eq ...201020726524
an extreme thermophile, thermus thermophilus, is a polyploid bacterium.an extremely thermophilic bacterium, thermus thermophilus hb8, is one of the model organisms for systems biology. its genome consists of a chromosome (1.85 mb), a megaplasmid (0.26 mb) designated ptt27, and a plasmid (9.3 kb) designated ptt8, and the complete sequence is available. we show here that t. thermophilus is a polyploid organism, harboring multiple genomic copies in a cell. in the case of the hb8 strain, the copy number of the chromosome was estimated to be four or five, and the copy n ...201020729360
urate-responsive marr homologs from burkholderia.the genus burkholderia includes a large number of species, some of which are serious human pathogens. a genomic locus is conserved that consists of a gene encoding a member of the multiple antibiotic resistance regulator (marr) family of transcriptional regulators and a divergently oriented gene encoding a major facilitator transport protein (mftp), a predicted membrane efflux pump. homology modeling shows that the marr homolog conserves the location of four conserved amino acid residues previou ...201020730247
binding of the dimeric deinococcus radiodurans single-stranded dna binding protein to single-stranded dna.deinococcus radiodurans single-stranded (ss) dna binding protein (drssb) originates from a radiation-resistant bacterium and participates in dna recombination, replication, and repair. although it functions as a homodimer, it contains four dna binding domains (ob-folds) and thus is structurally similar to the escherichia coli ssb (ecossb) homotetramer. we examined the equilibrium binding of drssb to ssdna for comparison with that of ecossb. we find that the occluded site size of drssb on poly(dt ...201020795631
dra0336, another oxyr homolog, involved in the antioxidation mechanisms in deinococcus radiodurans.a novel oxyr (dr0615) with one conserved cysteine that senses hydrogen peroxide in deinococcus radiodurans had been identified in our previous work. comparative genomics revealed that d. radiodurans possesses another oxyr homolog, oxyr(2) (dra0336). in this study, we constructed the deletion mutant of oxyr(2) and the double mutant of both the oxyr homologs to investigate the role of oxyr in response to oxidative stress in d. radiodurans. deletion of oxyr(2) resulted in an obviously increased sen ...201020799089
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