| structural studies of the nudix hydrolase dr1025 from deinococcus radiodurans and its ligand complexes. | we have determined the crystal structure, at 1.4a, of the nudix hydrolase dr1025 from the extremely radiation resistant bacterium deinococcus radiodurans. the protein forms an intertwined homodimer by exchanging n-terminal segments between chains. we have identified additional conserved elements of the nudix fold, including the metal-binding motif, a kinked beta-strand characterized by a proline two positions upstream of the nudix consensus sequence, and participation of the n-terminal extension ... | 2004 | 15123424 |
| distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the deinococcus-thermus phylum. | the deinococcus-thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16s rrna trees. no unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. in this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the deinococcus-thermus phylum but are not found in any other group of b ... | 2004 | 15126471 |
| characterization of a nudix hydrolase from deinococcus radiodurans with a marked specificity for (deoxy)ribonucleoside 5'-diphosphates. | nudix hydrolases form a protein family whose function is to hydrolyse intracellular nucleotides and so regulate their levels and eliminate potentially toxic derivatives. the genome of the radioresistant bacterium deinococcus radiodurans encodes 25 nudix hydrolases, an unexpectedly large number. these may contribute to radioresistance by removing mutagenic oxidised and otherwise damaged nucleotides. characterisation of these hydrolases is necessary to understand the reason for their presence. her ... | 2004 | 15147580 |
| crystal structure of the deinococcus radiodurans single-stranded dna-binding protein suggests a mechanism for coping with dna damage. | single-stranded dna (ssdna)-binding (ssb) proteins are uniformly required to bind and protect single-stranded intermediates in dna metabolic pathways. all bacterial and eukaryotic ssb proteins studied to date oligomerize to assemble four copies of a conserved domain, called an oligonucleotide/oligosaccharide-binding (ob) fold, that cooperate in nonspecific ssdna binding. the vast majority of bacterial ssb family members function as homotetramers, with each monomer contributing a single ob fold. ... | 2004 | 15159541 |
| solution structure of hypothetical nudix hydrolase dr0079 from extremely radiation-resistant deinococcus radiodurans bacterium. | using nuclear magnetic resonance (nmr) based methods, including residual dipolar coupling restraints, we have determined the solution structure of the hypothetical deinococcus radiodurans nudix protein dr0079 (171 residues, mw = 19.3 kda). the protein contains eight beta-strands and three alpha-helices organized into three subdomains: an n-terminal beta-sheet (1-34), a central nudix core (35-140), and a c-terminal helix-turn-helix (141-171). the nudix core and the c-terminal helix-turn-helix for ... | 2004 | 15162484 |
| quantifying intrachromosomal gc heterogeneity in prokaryotic genomes. | the sequencing of prokaryotic genomes covering a wide taxonomic range has sparked renewed interest in intrachromosomal compositional (gc) heterogeneity, largely in view of lateral transfers. we present here a brief overview of some methods for visualizing and quantifying gc variation in prokaryotes. we used these methods to examine heterogeneity levels in sequenced prokaryotes, for a range of scales or stringencies. some species are consistently homogeneous, whereas others are markedly heterogen ... | 2004 | 15177687 |
| signature sequences in diverse proteins provide evidence for the late divergence of the order aquificales. | the aquificales species are presently believed to be the earliest branching lineage within bacteria. however, the branching order of this group in different phylogenetic trees is highly variable and not resolved. in the present work, the phylogenetic placement of aquificales was examined by means of a cladistic approach based on the shared presence or absence of definite signature sequences (consisting of conserved inserts or deletions) in many highly conserved and important proteins, e.g. rna p ... | 2004 | 15179606 |
| sequence-based approach to finding functional lipases from microbial genome databases. | a sequence-based approach was used to retrieve functional lipases from microbial genome databases. many novel genes assigned as putative lipases were tested using the criteria of the typical lipase sequence rule, based on a consensus sequence of a catalytic triad (ser, asp, his) and oxyanion hole sequence (hg). to obtain the lipase genes satisfying the sequence rule, pcr cloning was performed, while the lipase activities were tested using a tributyrin/tricaprylin plate and p-nitrophenyl caproate ... | 2004 | 15183884 |
| [identification of the horizontal gene transfer based on phylogenetic data]. | we suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. the search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. numeric values are introduced to measure the discrepancy between the trees. this approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. this resulted in a list of the candidate genes ... | 2003 | 12942641 |
| using dna microarray data to understand the ionizing radiation resistance of deinococcus radiodurans. | in a recent paper, liu et al. documented the changes in gene expression as stationary phase deinococcus radiodurans cultures recover from acute exposure to gamma radiation. given that the biochemical details of the response of d. radiodurans to ionizing radiation are poorly understood, this work represents an important first step towards achieving an understanding of the ionizing radiation resistance in this species. | 2003 | 12948669 |
| geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state. | 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), (137)cs, and (99)tc. investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultiva ... | 2004 | 15240306 |
| protein recycling is a major component of post-irradiation recovery in deinococcus radiodurans strain r1. | exposure to 6kgy dose of (60)co gamma-rays resulted in immediate growth arrest, followed by complete recovery of deinococcus radiodurans strain r1 cells. selective degradation and resynthesis of several predicted highly expressed proteins (including major chaperones, key tca cycle enzymes, and few stress proteins) and several hypothetical proteins marked the lag period, preceding resumption of growth. a major exercise in protein recycling appears to be an integral component of post-irradiation r ... | 2004 | 15249204 |
| proteome analyses using accurate mass and elution time peptide tags with capillary lc time-of-flight mass spectrometry. | we describe the application of capillary liquid chromatography (lc) time-of-flight (tof) mass spectrometric instrumentation for the rapid characterization of microbial proteomes. previously (lipton et al., proc. natl. acad. sci. u.s.a. 2002, 99, 11049) the peptides from a series of growth conditions of deinococcus radiodurans have been characterized using capillary lc ms/ms and accurate mass measurements which are captured as an accurate mass and time (amt) tag database. using this amt tag datab ... | 2003 | 12954166 |
| [specificity of bacterial response to variation of isotopic composition of water]. | culture growth of bacteria with different membrane lipid composition was studied in liquid media with different isotope content of water. the concentration of deuterium in water was varied from 0.01 to 90%. it was shown that large concentrations of deuterium cause the inhibition of all cultures except deinococcus radiodurans, the most stable living cell. two cultures, methylobacterium organophilum and hyphomonas jannaschiana, showed a pronounced activation at a deuterium concentration of 0.01%. ... | 2003 | 14515487 |
| a dna pairing-enhanced conformation of bacterial reca proteins. | the reca proteins of escherichia coli (ec) and deinococcus radiodurans (dr) both promote a dna strand exchange reaction involving two duplex dnas. the four-strand exchange reaction promoted by the drreca protein is similar to that promoted by ecreca, except that key parts of the reaction are inhibited by ec single-stranded dna-binding protein (ssb). in the absence of ssb, the initiation of strand exchange is greatly enhanced by dsdna-ssdna junctions at the ends of dna gaps. this same trend is se ... | 2003 | 14530291 |
| definition of bases in 23s rrna essential for ribosomal subunit association. | the ribosome is a two-subunit molecular machine, sporting a working cycle that involves coordinated movements of the subunits. recent structural studies of the 70s ribosome describe a rather large number of intersubunit contacts, some of which are dynamic during translocation. we set out to determine which intersubunit contacts are functionally indispensable for the association of ribosome subunits by using a modification interference approach. modification of the n-1 position of a715, a1912, or ... | 2004 | 15037769 |
| dna toroids: framework for dna repair in deinococcus radiodurans and in germinating bacterial spores. | | 2004 | 15342565 |
| gelbank: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes. | gelbank is a publicly available database of two-dimensional gel electrophoresis (2de) gel patterns of proteomes from organisms with known genome information (available at http://gelbank.anl.gov and ftp://bioinformatics.anl.gov/gelbank/). currently it includes 131 completed, mostly microbial proteomes available from the national center for biotechnology information. a web interface allows the upload of 2d gel patterns and their annotation for registered users. the images are organized by species, ... | 2004 | 14681486 |
| preserving genome integrity: the ddra protein of deinococcus radiodurans r1. | the bacterium deinococcus radiodurans can withstand extraordinary levels of ionizing radiation, reflecting an equally extraordinary capacity for dna repair. the hypothetical gene product dr0423 has been implicated in the recovery of this organism from dna damage, indicating that this protein is a novel component of the d. radiodurans dna repair system. dr0423 is a homologue of the eukaryotic rad52 protein. following exposure to ionizing radiation, dr0423 expression is induced relative to an untr ... | 2004 | 15361932 |
| macrolide resistance from the ribosome perspective. | macrolides are important antibiotics used in treatment of respiratory tract infections in humans. although some of these compounds have been in use for 50 years, it has not been until the last few years that their mechanism of action and the nature of ribosomal-based resistance could be more fully understood. with the advent of robust crystals of ribosomal 50s subunits, and structural resolution of macrolides and ketolides complexed to either haloarcula marismortui or deinococcus radiodurans 50s ... | 2004 | 15379729 |
| oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in suiyo seamount. | a novel thermophilic, microaerophilic, sulfur-reducing bacterium designated strain st55bt was isolated from a sulfide chimney in the hydrothermal field of suiyo seamount (izu-bonin arc, western pacific). cells of the isolate were rod-shaped and tended to form a chain-link circular structure (a rotund body) at exponential phase under good growth conditions. the isolate was a chemoheterotroph requiring yeast extract for growth. although strain st55bt used oxygen as an electron acceptor, it could n ... | 2004 | 15388711 |
| ultrasensitive proteomics using high-efficiency on-line micro-spe-nanolc-nanoesi ms and ms/ms. | ultrasensitive nanoscale proteomics approaches for characterizing proteins from complex proteomic samples of <50 ng of total mass are described. protein identifications from 0.5 pg of whole proteome extracts were enabled by ultrahigh sensitivity (<75 zmol for individual proteins) achieved using high-efficiency (peak capacities of approximately 10(3)) 15-microm-i.d. capillary liquid chromatography separations (i.e., using nanolc, approximately 20 nl/min mobile-phase flow rate at the optimal linea ... | 2004 | 14697044 |
| multiple uracil-dna glycosylase activities in deinococcus radiodurans. | the extremely radiation resistant bacterium, deinococcus radiodurans, contains a spectrum of genes that encode for multiple activities that repair dna damage. we have cloned and expressed the product of three predicted uracil-dna glycosylases to determine their biochemical function. dr0689 is a homologue of the escherichia coli uracil-dna glycosylase, the product of the ung gene; this activity is able to remove uracil from a u : g and u : a base pair in double-stranded dna and uracil from single ... | 2004 | 14706350 |
| analysis of deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. | during the first hour after a sublethal dose of ionizing radiation, 72 genes were upregulated threefold or higher in d. radiodurans r1. thirty-three of these loci were also among a set of 73 genes expressed in r1 cultures recovering from desiccation. the five transcripts most highly induced in response to each stress are the same and encode proteins of unknown function. the genes (ddra, ddrb, ddrc, ddrd, and ppra) corresponding to these transcripts were deleted, both alone and in all possible tw ... | 2004 | 15454524 |
| ppra: a novel protein from deinococcus radiodurans that stimulates dna ligation. | the extraordinary radiation resistance of deinococcus radiodurans results from the efficient capacity of the bacterium to repair dna double-strand breaks. by analysing the dna damage repair-deficient mutant, kh311, a unique radiation-inducible gene (designated ppra) responsible for loss of radiation resistance was identified. investigations in vitro showed that the gene product of ppra (ppra) preferentially bound to double-stranded dna carrying strand breaks, inhibited escherichia coli exonuclea ... | 2004 | 15458422 |
| a novel structure of dna repair protein reco from deinococcus radiodurans. | recovery of arrested replication requires coordinated action of dna repair, replication, and recombination machineries. bacterial reco protein is a member of recf recombination repair pathway important for replication recovery. reco possesses two distinct activities in vitro, closely resembling those of eukaryotic protein rad52: dna annealing and reca-mediated dna recombination. here we present the crystal structure of the reco protein from the extremely radiation resistant bacteria deinococcus ... | 2004 | 15458636 |
| accumulation of mn(ii) in deinococcus radiodurans facilitates gamma-radiation resistance. | deinococcus radiodurans is extremely resistant to ionizing radiation. how this bacterium can grow under chronic gamma radiation [50 grays (gy) per hour] or recover from acute doses greater than 10 kgy is unknown. we show that d. radiodurans accumulates very high intracellular manganese and low iron levels compared with radiation-sensitive bacteria and that resistance exhibits a concentration-dependent response to manganous chloride [mn(ii)]. among the most radiation-resistant bacterial groups re ... | 2004 | 15459345 |
| the structure of the organic hydroperoxide resistance protein from deinococcus radiodurans. do conformational changes facilitate recycling of the redox disulfide? | the three-dimensional structure of the organic hydroperoxide resistance protein (ohrp) from deinococcus radiodurans as determined using single crystal xray diffraction techniques is reported. comparison of the structure with that obtained for ohrp from pseudomonas aeruginosa reveals that the polypeptide chain of ohrps can adopt two significantly different conformations ("in" and "out") in the region of the active site disulfide moiety. it is postulated that the closed configuration is consistent ... | 2004 | 15054099 |
| dna helicase activity of the recd protein from deinococcus radiodurans. | the bacterium deinococcus radiodurans is extremely resistant to high levels of dna-damaging agents, including gamma rays and ultraviolet light that can lead to double-stranded dna breaks. surprisingly, the organism does not appear to have a recbcd enzyme, an enzyme that is critical for double-strand break repair in many other bacteria. the d. radiodurans genome does encode a protein whose closest characterized homologues are recd subunits of recbcd enzymes in other bacteria. we have purified thi ... | 2004 | 15466873 |
| asymmetrically acting lycopene beta-cyclases (crtlm) from non-photosynthetic bacteria. | carotenoids have important functions in photosynthesis, nutrition, and protection against oxidative damage. some natural carotenoids are asymmetrical molecules that are difficult to produce chemically. biological production of carotenoids using specific enzymes is a potential alternative to extraction from natural sources. here we report the isolation of lycopene beta-cyclases that selectively cyclize only one end of lycopene or neurosporene. the crtlm genes encoding the asymmetrically acting ly ... | 2004 | 14740205 |
| an automated high performance capillary liquid chromatography-fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics. | we describe a fully automated high performance liquid chromatography 9.4 tesla fourier transform ion resonance cyclotron (fticr) mass spectrometer system designed for proteomics research. a synergistic suite of ion introduction and manipulation technologies were developed and integrated as a high-performance front-end to a commercial bruker daltonics fticr instrument. the developments incorporated included a dual-esi-emitter ion source; a dual-channel electrodynamic ion funnel; tandem quadrupole ... | 2004 | 14766289 |
| histone-like protein hu from deinococcus radiodurans binds preferentially to four-way dna junctions. | the histone-like protein hu from escherichia coli is involved in dna compaction and in processes such as dna repair and recombination. its participation in these events is reflected in its ability to bend dna and in its preferred binding to dna junctions and dna with single-strand breaks. deinococcus radiodurans is unique in its ability to reconstitute its genome from double strand breaks incurred after exposure to ionizing radiation. using electrophoretic mobility shift assays (emsa), we show t ... | 2004 | 15019777 |
| gene prediction using the self-organizing map: automatic generation of multiple gene models. | many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. it is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. | 2004 | 15070404 |
| cold sensitivity of thermophilic and mesophilic rna polymerases. | rna polymerase from mesophilic deinococcus radiodurans displays the same cold sensitivity of promoter opening as rna polymerase from the closely related thermophilic thermus aquaticus. this suggests that, contrary to the accepted view, cold sensitivity of promoter opening by thermophilic rna polymerases may not be a consequence of their thermostability. | 2004 | 15516599 |
| an unusual tryptophanyl trna synthetase interacts with nitric oxide synthase in deinococcus radiodurans. | in mammals, nitric oxide synthases (noss) produce nitric oxide for signaling and defense functions; in streptomyces, nos proteins nitrate a tryptophanyl moiety in synthesis of a phytotoxin. we have discovered that the nos protein from the radiation-resistant bacterium deinococcus radiodurans (deinos) associates with an unusual tryptophanyl trna synthetase (trprs). d. radiodurans contains genes for two trprss: the first has approximately 40% sequence identity to typical trprss, whereas the second ... | 2004 | 15520379 |
| a genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. | the timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. however, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. we assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species ... | 2004 | 15535883 |
| ring-shaped architecture of recr: implications for its role in homologous recombinational dna repair. | recr, together with recf and reco, facilitates reca loading in the recf pathway of homologous recombinational dna repair in procaryotes. the human rad52 protein is a functional counterpart of recfor. we present here the crystal structure of recr from deinococcus radiodurans (dr recr). a monomer of dr recr has a two-domain structure: the n-terminal domain with a helix-hairpin-helix (hhh) motif and the c-terminal domain with a cys4 zinc-finger motif, a toprim domain and a walker b motif. four such ... | 2004 | 15116069 |
| heat shock and cold shock in deinococcus radiodurans. | on the basis of acquired thermotolerance and cryotolerance, the optimal heat shock and cold shock temperatures have been determined for deinococcus radiodurans. a heat shock at 42 degrees c maximized survival at the lethal temperature of 52 degrees c and a cold shock at 20 degrees c maximized survival after repeated freeze-thawing. enhanced survival from heat shock was found to be strongly dependent on growth stage, with its greatest effect shortly after phase. increased synthesis of a total of ... | 2004 | 15211028 |
| vectors for regulated gene expression in the radioresistant bacterium deinococcus radiodurans. | deinococcus radiodurans possesses an exceptional capacity to withstand the lethal and mutagenic effects of most form of dna damage and has received considerable interest for use in both fundamental and applied research. here we describe vectors that allow regulated expression of deinococcal genes for functional analysis. the vectors contain the iptg-regulated spac system (pspac promoter and laci repressor gene), originally designed for bacillus subtilis, that we have adapted to be functional in ... | 2004 | 15225873 |
| diversity and abundance of bacteria and archaea in the bor khlueng hot spring in thailand. | the prokaryotic diversity in the bor khlueng hot spring in ratchaburi province, thailand was investigated by a culture-independent molecular approach. this hydrothermal pool is located in the central part of thailand and contains sulfide-rich mineral water that is believed to relieve muscle ache and pain. the water flow year-round with temperature ranging between 50-57 degrees c. community dna was extracted directly from sediment samples by coring to depth of approximately 20-30 cm. small-subuni ... | 2004 | 15558824 |
| the antioxidative effect of the bacteria dienococcus radiophilus against ldl lipid peroxidation. | lipid peroxidation is an important process in the development of atherosclerosis. thus agents with antioxidant properties may play an important role in the inhibition of atherosclerosis. | 2005 | 15278372 |
| deinoccocus radiodurans: getting a better fix on dna repair. | | 2003 | 12953078 |
| structural basis for catalytic racemization and substrate specificity of an n-acylamino acid racemase homologue from deinococcus radiodurans. | n-acylamino acid racemase (naaar) catalyzes the racemization of n-acylamino acids and can be used in concert with an aminoacylase to produce enantiopure alpha-amino acids, a process that has potential industrial applications. here we have cloned and characterized an naaar homologue from a radiation-resistant ancient bacterium, deinococcus radiodurans. the expressed naaar racemized various substrates at an optimal temperature of 60 degrees c and had km values of 24.8 mm and 12.3 mm for n-acetyl-d ... | 2004 | 15313614 |
| mechanism of thermotolerance induction by split-dose hyperthermia in deinococcus radiodurans dna repair deficient mutants. | we examined the phenomenon of thermotolerance induction in the radioresistant prokaryote, deinococcus radiodurans, which was initially exposed to 30 min at 52 degrees c followed by various intervals up to 6 h at 30 degrees c in tgy medium and then re-exposed to 52 degrees c for various periods, i.e., split-dose hyperthermia. this thermotolerance induction was analyzed in dna repair deficient mutants (strain 302, 251, uvs25, rec30 and kh840) and the wild-type strain mr1. the strain uvs25 is a dou ... | 2003 | 14533003 |
| expression of deinococcus radiodurans ppri enhances the radioresistance of escherichia coli. | ppri, a newly identified gene switch responsible for extreme radioresistance of deinococcus radiodurans, plays a central regulatory role in multiple dna damage repair and protection pathways in response to radiation stress [biochem. biophy. res. commun. 306 (2003) 354]. to evaluate whether ppri also functions in the radioresistance in other organisms, d. radiodurans ppri protein (deira-ppri) was expressed in escherichia coli. the complemented e. coli strain showed an increase of approximately 1. ... | 2003 | 14642569 |
| x-ray crystallography study on ribosome recycling: the mechanism of binding and action of rrf on the 50s ribosomal subunit. | this study presents the crystal structure of domain i of the escherichia coli ribosome recycling factor (rrf) bound to the deinococcus radiodurans 50s subunit. the orientation of rrf is consistent with the position determined on a 70s-rrf complex by cryoelectron microscopy (cryo-em). alignment, however, requires a rotation of 7 degrees and a shift of the cryo-em rrf by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. at 3.3 a resolution, rrf is se ... | 2004 | 15616575 |
| molecular phylogenetic diversity of bacteria associated with the leachate of a closed municipal solid waste landfill. | a 16s rdna-based molecular study was performed to determine the nature of the bacterial constituents of the leachate from a closed municipal solid waste landfill. total community dna was extracted and bacterial 16s rrna genes were subsequently amplified and cloned. recombinant rdna clones in the library were randomly selected, and they were sequenced for a single run and then grouped. a total of 76 sequence types representing 138 randomly selected nonchimeric clones were identified. full-length ... | 2005 | 15621451 |
| actinide and metal toxicity to prospective bioremediation bacteria. | bacteria may be beneficial for alleviating actinide contaminant migration through processes such as bioaccumulation or metal reduction. however, sites with radioactive contamination often contain multiple additional contaminants, including metals and organic chelators. bacteria-based bioremediation requires that the microorganism functions in the presence of the target contaminant, as well as other contaminants. here, we evaluate the toxicity of actinides, metals and chelators to two different b ... | 2005 | 15643939 |
| rep code: defining bacterial identity in extragenic space. | through the analysis of 57 bacterial genomes we have detected repetitive extragenic palindromic dna sequences (reps) in 11 species. for a sequence to be considered as rep, the following criteria should be met: (i) it should be extragenic, (ii) palindromic, (iii) of a length between 21 and 65 bases and (iv) should constitute more than 0.5% of the total extragenic space. species-specific reps have been found in human pathogens such as escherichia coli, salmonella enterica, neisseria meningitidis, ... | 2005 | 15658989 |
| nanoscale proteomics. | efforts to develop a liquid chromatography (lc)/mass spectrometry (ms) technology for ultra-sensitive proteomics studies (i.e., nanoscale proteomics) are described. the approach combines high-efficiency nanoscale lc (separation peak capacity of approximately 10(3); 15-microm-i.d. packed capillaries with flow rates of 20 nl min(-1), the optimal separation linear velocity) with advanced ms, including high-sensitivity and high-resolution fourier transform ion cyclotron resonance ms, to perform both ... | 2004 | 14647945 |
| lexa analog (dra0074) is a regulatory protein that is irrelevant to reca induction. | the protein dra0074 is suggested to be another lexa in deinococcus radiodurans, having similar motifs and reca-mediated cleavage activity to d. radiodurans lexa (dra0344). however, its function has not been studied. we disrupted the gene dra0074 and measured its effect on reca induction using fusion translation, immunoblot, and proteomic analysis. results showed that the product of gene dra0074 is not involved in reca induction, but is a regulator of other metabolisms in d. radiodurans. | 2004 | 15671489 |
| cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the ggdef protein domain. | proteins containing ggdef domains are encoded in the majority of sequenced bacterial genomes. in several species, these proteins have been implicated in biosynthesis of exopolysaccharides, formation of biofilms, establishment of a sessile lifestyle, surface motility, and regulation of gene expression. however, biochemical activities of only a few ggdef domain proteins have been tested. these proteins were shown to be involved in either synthesis or hydrolysis of cyclic-bis(3'-->5') dimeric gmp ( ... | 2005 | 15716451 |
| characterization and distribution of is8301 in the radioresistant bacterium deinococcus radiodurans. | the insertion sequence element is8301 isolated from the radiation resistant bacterium deinococcus radiodurans strain kd8301 was characterized. is8301 is comprised of 1,736-bp, lacks terminal inverted repeats and does not duplicate target dna upon its insertion. the amino acid sequence homology of two open reading frames encoded in is8301 indicates that this insertion sequence element belongs to the is200/is605 group. there were seven loci completely identical with the is8301 sequence in the publ ... | 2003 | 14676423 |
| hspr is a global negative regulator of heat shock gene expression in deinococcus radiodurans. | the hspr protein functions as a negative regulator of chaperone and protease gene expression in a diversity of bacteria. here we have identified, cloned and deleted the deinococcus radiodurans hspr homologue, dr0934. delta hspr mutants exhibit moderate growth defects when shifted to mild heat shock temperatures, but are severely impaired for survival at 48 degrees c. using quantitative reverse transcription polymerase chain reaction and global transcriptional analysis, we have identified 14 gene ... | 2005 | 15720562 |
| structure and activity of an aminoacyl-trna synthetase that charges trna with nitro-tryptophan. | the most divergent of two tryptophanyl trna synthetases (trprs ii) found in deinococcus radiodurans interacts with a nitric oxide synthase protein that produces 4-nitro-tryptophan (4-nrp). trprs ii efficiently charges transfer rna(trp) with 4-nrp and 5-hydroxy-tryptophan (5-hrp). the crystal structures of trprs ii bound to tryptophan and 5-hrp reveal residue substitutions that accommodate modified indoles. a class of auxiliary bacterial trprss conserve this capacity to charge trna with nonstanda ... | 2005 | 15723076 |
| developing a genetic system in deinococcus radiodurans for analyzing mutations. | we have applied a genetic system for analyzing mutations in escherichia coli to deinococcus radiodurans, an extremeophile with an astonishingly high resistance to uv- and ionizing-radiation-induced mutagenesis. taking advantage of the conservation of the beta-subunit of rna polymerase among most prokaryotes, we derived again in d. radiodurans the rpob/rif(r) system that we developed in e. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. we seq ... | 2004 | 15020457 |
| a copper(i) protein possibly involved in the assembly of cua center of bacterial cytochrome c oxidase. | sco1 and cox17 are accessory proteins required for the correct assembly of eukaryotic cytochrome c oxidase. at variance with sco1, cox17 orthologs are found only in eukaryotes. we browsed bacterial genomes to search proteins functionally equivalent to cox17, and we identified a class of proteins of unknown function displaying a conserved gene neighborhood to bacterial sco1 genes, all sharing a potential metal binding motif h(m)x10mx21hxm. two members of this group, dr1885 from deinococcus radiod ... | 2005 | 15753304 |
| deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in west bengal, india. | an arsenic- and radiation-resistant bacterium, strain wt/1a(t), was isolated from water from an arsenic-contaminated aquifer located in the chakdah district of west bengal, india. the bacterium stains gram-negative and is rod-shaped, non-motile, non-sporulating and red-pigmented. cell-wall peptidoglycan contains ornithine as the diamino acid, mk-8 is the major menaquinone, c(15 : 1) and c(16 : 1) are the major fatty acids and the dna g+c content of the organism is 65.8 mol%. based on these pheno ... | 2004 | 15023960 |
| recx is involved in antioxidant mechanisms of the radioresistant bacterium deinococcus radiodurans. | deinococcus radiodurans shows remarkable resistance to reactive oxygen species (ros), generated by irradiation. disruption of recx (dr1310) in d. radiodurans using targeted mutagenesis method enhanced its ros scavenging activity, and recx overexpression in this bacterium repressed its antioxidant activity significantly. further analyses on catalase and superoxide dismutase, two important antioxidant proteins in cells, showed that recx could repress the induction of antioxidant enzymes, revealing ... | 2005 | 15766776 |
| the biliverdin chromophore binds covalently to a conserved cysteine residue in the n-terminus of agrobacterium phytochrome agp1. | phytochromes are widely distributed biliprotein photoreceptors. typically, the chromophore becomes covalently linked to the protein during an autocatalytic lyase reaction. plant and cyanobacterial phytochromes incorporate bilins with a ring a ethylidene side chain, whereas other bacterial phytochromes utilize biliverdin as chromophore, which has a vinyl ring a side chain. for agrobacterium phytochrome agp1, site-directed mutagenesis provided evidence that biliverdin is bound to cysteine 20. this ... | 2004 | 15035636 |
| single-stranded dna-binding protein of deinococcus radiodurans: a biophysical characterization. | the highly conserved bacterial single-stranded dna-binding (ssb) proteins play an important role in dna replication, repair and recombination and are essential for the survival of the cell. they are functional as tetramers, in which four ob(oligonucleotide/oligosaccharide binding)-folds act as dna-binding domains. the protomer of the ssb protein from the extremely radiation-resistant organism deinococcus radiodurans (drassb) has twice the size of the other bacterial ssb proteins and contains two ... | 2005 | 15781492 |
| cysteinyl-trna(cys) formation in methanocaldococcus jannaschii: the mechanism is still unknown. | most organisms form cys-trna(cys), an essential component for protein synthesis, through the action of cysteinyl-trna synthetase (cysrs). however, the genomes of methanocaldococcus jannaschii, methanothermobacter thermautotrophicus, and methanopyrus kandleri do not contain a recognizable cyss gene encoding cysrs. it was reported that m. jannaschii prolyl-trna synthetase (c. stathopoulos, t. li, r. longman, u. c. vothknecht, h. d. becker, m. ibba, and d. söll, science 287:479-482, 2000; r. s. lip ... | 2004 | 14679218 |
| a ring-like nucleoid is not necessary for radioresistance in the deinococcaceae. | transmission electron microscopy images of deinococcus radiodurans r1 suggest that the nucleoid of this species exists as a "ring-like" body, and have led to speculation that this structure contributes to the radioresistance of the species. since extreme radioresistance is characteristic of six other species of deinococcus, we have attempted to correlate nucleoid morphology and radioresistance by determining whether the genomic dna of each of these species exhibit similar structures. | 2005 | 15799787 |
| crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily. | agmatine is the product of arginine decarboxylation and can be hydrolyzed by agmatinase to putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and spermine. besides being an intermediate in polyamine metabolism, recent findings indicate that agmatine may play important regulatory roles in mammals. agmatinase is a binuclear manganese metalloenzyme and belongs to the ureohydrolase superfamily that includes arginase, formiminoglutamase, and proclavaminate amidinohydrolase. ... | 2004 | 15355972 |
| how radiation kills cells: survival of deinococcus radiodurans and shewanella oneidensis under oxidative stress. | we have recently shown that deinococcus radiodurans and other radiation resistant bacteria accumulate exceptionally high intracellular manganese and low iron levels. in comparison, the dissimilatory metal-reducing bacterium shewanella oneidensis accumulates fe but not mn and is extremely sensitive to radiation. we have proposed that for fe-rich, mn-poor cells killed at radiation doses which cause very little dna damage, cell death might be induced by the release of fe(ii) from proteins during ir ... | 2005 | 15808748 |
| electrochemical nanofabrication using crystalline protein masks. | we have developed a simple and robust method to fabricate nanoarrays of metals and metal oxides over macroscopic substrates using the crystalline surface layer (s-layer) protein of deinococcus radiodurans as an electrodeposition mask. substrates are coated by adsorption of the s-layer from a detergent-stabilized aqueous protein extract, producing insulating masks with 2-3 nm diameter solvent-accessible openings to the deposition substrate. the coating process can be controlled to achieve complet ... | 2005 | 15826095 |
| crystallization and preliminary x-ray crystallographic analysis of a putative agmatinase from deinococcus radiodurans. | agmatine, which results from the decarboxylation of arginine by arginine decarboxylase, is a metabolic intermediate in the biosynthesis of putresine and higher polyamines. the enzyme agmatinase catalyses the hydrolysis of agmatine to putresine and urea. recent studies indicate that agmatinase plays important roles in mammals. human mitochondrial agmatinase shows a considerable level of sequence similarity to bacterial agmatinases, including a putative agmatinase from deinococcus radiodurans. the ... | 2004 | 15388942 |
| global transcriptional and proteomic analysis of the sig1 heat shock regulon of deinococcus radiodurans. | the sig1 gene, predicted to encode an extracytoplasmic function-type heat shock sigma factor of deinococcus radiodurans, has been shown to play a central role in the positive regulation of the heat shock operons groesl and dnakj. to determine if sig1 is required for the regulation of additional heat shock genes, we monitored the global transcriptional and proteomic profiles of a d. radiodurans r1 sig1 mutant and wild-type cells in response to elevated temperature stress. thirty-one gene products ... | 2005 | 15866918 |
| fluorescence in situ hybridisation coupled to ultra small immunogold detection to identify prokaryotic cells using transmission and scanning electron microscopy. | we describe a method based on fluorescence in situ hybridisation (fish) that allows the identification of individual cells by electron microscopy. we hybridised universal and specific fluorescein-labelled oligonucleotide probes to the ribosomal rna of prokaryotic microorganisms in heterogeneous cell mixtures. we then used antibodies against fluorescein coupled to sub-nanometer gold particles to label the hybridised probes in the ribosome. after increasing the diameter of the metal particles by s ... | 2005 | 15893390 |
| hucr, a novel uric acid-responsive member of the marr family of transcriptional regulators from deinococcus radiodurans. | the marr family of transcriptional regulators comprises a subset of winged helix dna-binding proteins and includes numerous members that function in environmental surveillance of aromatic compounds. we describe the characterization of hucr, a novel marr homolog from deinococcus radiodurans that demonstrates phenolic sensing capabilities. hucr binds as a homodimer to a single site within its promoter/operator region with kd = 0.29 +/- 0.02 nm. the hucr binding site contains a pseudopalindromic se ... | 2004 | 15448166 |
| regioselective nitration of tryptophan by a complex between bacterial nitric-oxide synthase and tryptophanyl-trna synthetase. | bacterial nitric-oxide synthase proteins (noss) from certain streptomyces strains have been shown to participate in biosynthetic nitration of tryptophanyl moieties in vivo (kers, j. a., wach, m. j., krasnoff, s. b., cameron, k. d., widom, j., bukhaid, r. a., gibson, d. m., and crane, b. r., and loria, r. (2004) nature 429, 79-82). we report that the complex between deinococcus radiodurans nos (deinos) and an unusual tryptophanyl-trna synthetase (trprs ii) catalyzes the regioselective nitration o ... | 2004 | 15466862 |
| heptameric (l12)6/l10 rather than canonical pentameric complexes are found by tandem ms of intact ribosomes from thermophilic bacteria. | ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. these properties pose considerable challenges for modern-day structural biology. despite these obstacles, high-resolution x-ray structures of the 30s and 50s subunits have revealed the rna architecture and its interactions with proteins for ribosomes from thermus thermophilus, deinococcus radiodurans, and haloarcula ma ... | 2005 | 15923259 |
| automatic selection of representative proteins for bacterial phylogeny. | although there are now about 200 complete bacterial genomes in genbank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence. | 2005 | 15927057 |
| truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of trueperaceae fam. nov. | two isolates, belonging to a new species of a novel genus of the phylum "deinococcus/thermus ", were recovered from hot spring runoffs on the island of são miguel in the azores. strains rq-24(t) and tu-8 are the first cultured representatives of a distinct phylogenetic lineage within this phylum. these strains form orange/red colonies, spherical-shaped cells, have an optimum growth temperature of about 50 degrees c, an optimum ph for growth between about 7.5 and 9.5, and do not grow at ph below ... | 2005 | 15927420 |
| capillary sieving electrophoresis-micellar electrokinetic chromatography fully automated two-dimensional capillary electrophoresis analysis of deinococcus radiodurans protein homogenate. | we report the one- and two-dimensional (1-d and 2-d) capillary electrophoresis separation of deinococcus radiodurans protein homogenate. proteins are labeled with the fluorogenic reagent 3-(2-furoyl)quinoline-2-carboxaldehyde (fq), which reacts with lysine residues and creates a highly fluorescent product. detection is by laser-induced fluorescence. 1-d capillary sieving electrophoresis (cse) produces over 150,000 plates and micellar electrokinetic capillary chromatography (mekc) produces over 9 ... | 2004 | 15472976 |
| structural basis of 5-nitroimidazole antibiotic resistance: the crystal structure of nima from deinococcus radiodurans. | 5-nitroimidazole-based antibiotics are compounds extensively used for treating infections in humans and animals caused by several important pathogens. they are administered as prodrugs, and their activation depends upon an anaerobic 1-electron reduction of the nitro group by a reduction pathway in the cells. bacterial resistance toward these drugs is thought to be caused by decreased drug uptake and/or an altered reduction efficiency. one class of resistant strains, identified in bacteroides, ha ... | 2004 | 15492014 |
| a rational approach for discovering and validating cancer markers in very small samples using mass spectrometry and elisa microarrays. | identifying useful markers of cancer can be problematic due to limited amounts of sample. some samples such as nipple aspirate fluid (naf) or early-stage tumors are inherently small. other samples such as serum are collected in larger volumes but archives of these samples are very valuable and only small amounts of each sample may be available for a single study. also, given the diverse nature of cancer and the inherent variability in individual protein levels, it seems likely that the best appr ... | 2004 | 15502246 |
| mismatch repair ensures fidelity of replication and recombination in the radioresistant organism deinococcus radiodurans. | we have characterized the mismatch repair system (mmr) of the highly radiation-resistant type strain of deinococcus radiodurans, atcc 13939. we show that the mmr system is functional in this organism, where it participates in ensuring the fidelity of dna replication and recombination. the system relies on the activity of two key proteins, muts1 and mutl, which constitute a conserved core involved in mismatch recognition. inactivation of muts1 or mutl resulted in a seven-fold increase in the freq ... | 2004 | 15503140 |
| novel beta-carotene ketolases from non-photosynthetic bacteria for canthaxanthin synthesis. | we reported previously that the rhodococcus erythropolis strain an12 synthesizes the monocyclic carotenoids 4-keto gamma-carotene and gamma-carotene. we also identified a novel lycopene beta-monocyclase in this strain. here we report the identification of the rest of the carotenoid synthesis genes in an12. two of these showed apparent homology to putative phytoene dehydrogenases. analysis of rhodococcus knockout mutants suggested that one of them ( crti) encodes a phytoene dehydrogenase, whereas ... | 2004 | 15538629 |
| crystal structure of reca from deinococcus radiodurans: insights into the structural basis of extreme radioresistance. | the resistance of deinococcus radiodurans (dr) to extreme doses of ionizing radiation depends on its highly efficient capacity to repair dsdna breaks. dr reca, the key protein in the repair of dsdna breaks by homologous recombination, promotes dna strand-exchange by an unprecedented inverse pathway, in which the presynaptic filament is formed on dsdna instead of ssdna. in order to gain insight into the remarkable repair capacity of dr and the novel mechanistic features of its reca protein, we ha ... | 2004 | 15544805 |
| inhibition of peptide bond formation by pleuromutilins: the structure of the 50s ribosomal subunit from deinococcus radiodurans in complex with tiamulin. | 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 pleur ... | 2004 | 15554968 |
| structural determination of the polar glycoglycerolipids from thermophilic bacteria meiothermus taiwanensis. | the polar glycolipids were isolated from the thermophilic bacteria meiothermus taiwanensis atcc baa-400 by ethanol extraction and purified by sephadex lh-20 and silica gel column chromatography. the fatty acid composition of o-acyl groups in the glycolipids was obtained by gas chromatography mass spectroscopy analysis on their methyl esters derived from methanolysis and was made mainly of c(15:0) (34.0%) and c(17:0) (42.3%) fatty acids, with the majority as branched fatty acids (over 80%). remov ... | 2004 | 15560795 |
| pyrroloquinoline-quinone: a reactive oxygen species scavenger in bacteria. | transgenic escherichia coli expressing pyrroloquinoline-quinone (pqq) synthase gene from deinococcus radiodurans showed superior survival during rose bengal induced oxidative stress. such cells showed significantly low levels of protein carbonylation as compared to non-transgenic control. in vitro, pqq reacted with reactive oxygen species with rate constants comparable to other well known antioxidants, producing non-reactive molecular products. pqq also protected plasmid dna and proteins from th ... | 2004 | 15581610 |
| a comparative categorization of gene flux in diverse microbial species. | microbial genomes harbor genomic islands (gis), genes presumably acquired via horizontal gene transfer (hgt). we compared gis of hyperthermophilic, thermophilic, mesophilic, and pathogenic/nonpathogenic species and of small and large genomes. the cog database was used to characterize gene-encoded functions. putative donors were determined to quantify gene flux between superkingdoms. in hyperthermophiles, more than 10% of the genes were on average acquired across the superkingdom border. for ther ... | 2005 | 16026964 |
| proteomic analysis of deinococcus radiodurans recovering from gamma-irradiation. | in order to reveal the mechanisms of the extreme radioresistance and dna repair in deinococcus radiodurans, we examined proteome changes in a wild-type strain following gamma-irradiation using two-dimensional polyacrylamide gel electrophoresis and silver-staining. the expression levels of 26 protein spots showed significant changes under radiation stress. of these spots, 21 were identified with peptide mass fingerprinting using matrix-assisted laser desorption/ionization-time of flight mass spec ... | 2005 | 15593145 |
| structure of mycobacterium smegmatis single-stranded dna-binding protein and a comparative study involving homologus ssbs: biological implications of structural plasticity and variability in quaternary association. | the structure of mycobacterium smegmatis single-stranded dna-binding protein (ssb) has been determined using three data sets collected from related crystals. the structure is similar to that of its homologue from mycobacterium tuberculosis, indicating that the clamp arrangement that stabilizes the dimer and the ellipsoidal shape of the tetramer are characteristic features of mycobacterial ssbs. the central ob fold is conserved in mycobacterial ssbs as well as those from escherichia coli, deinoco ... | 2005 | 16041080 |
| deinococcus frigens sp. nov., deinococcus saxicola sp. nov., and deinococcus marmoris sp. nov., low temperature and draught-tolerating, uv-resistant bacteria from continental antarctica. | 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, t ... | 2004 | 15612620 |
| an rna ligase from deinococcus radiodurans. | although dna repair pathways have been the focus of much attention, there is an emerging appreciation that distinct pathways exist to maintain or manipulate rna structure in response to breakage events. here we identify an rna ligase (drarnl) from the radiation-resistant bacterium deinococcus radiodurans. drarnl seals 3'-oh/5'-po4 rna nicks in either a duplex rna or an rna: dna hybrid, but it cannot seal 3'-oh/5'-po4 dna nicks. the specificity of drarnl arises from a requirement for rna on the 3 ... | 2004 | 15333634 |
| involvement of an x family dna polymerase in double-stranded break repair in the radioresistant organism deinococcus radiodurans. | dna polymerases of the x family have been implicated in a variety of dna repair processes in eukaryotes. here we show that deinococcus radiodurans, a highly radioresistant bacterium able to mend hundreds of radiation-induced double-stranded dna breaks, expresses a dna polymerase belonging to the x family. this novel bacterial polymerase, named polx(dr), was identified as the product of the deinococcal dr0467 gene. the purified polx(dr) protein possesses a dna polymerase activity that is stimulat ... | 2004 | 15341650 |
| crystallization and preliminary x-ray characterization of the atypical glutaminyl-trna synthetase from deinococcus radiodurans. | the glutaminyl-trna synthetase (glnrs) from the radiation-resistant bacterium deinococcus radiodurans differs from known glnrss and other trna synthetases by the presence of an additional c-terminal domain resembling the c-terminal region of the gatb subunit of trna-dependent amidotransferase (adt). this atypical synthetase was overexpressed in escherichia coli, purified and crystallized in the presence of peg 3350. orthorhombic crystals were obtained that belong to space group p2(1)2(1)2(1) and ... | 2004 | 15614972 |
| number, position, and significance of the pseudouridines in the large subunit ribosomal rna of haloarcula marismortui and deinococcus radiodurans. | the number and position of the pseudouridines of haloarcula marismortui and deinococcus radiodurans large subunit rna have been determined by a combination of total nucleoside analysis by hplc-mass spectrometry and pseudouridine sequencing by the reverse transcriptase method and by lc/ms/ms. three pseudouridines were found in h. marismortui, located at positions 1956, 1958, and 2621 corresponding to escherichia coli positions 1915, 1917, and 2586, respectively. the three pseudouridines are all i ... | 2005 | 15659360 |
| crystal structure and dna-binding analysis of reco from deinococcus radiodurans. | the recfor pathway has been shown to be essential for dna repair through the process of homologous recombination in bacteria and, recently, to be important in the recovery of stalled replication forks following uv irradiation. reco, along with recr, recf, recq and recj, is a principal actor in this fundamental dna repair pathway. here we present the three-dimensional structure of a member of the reco family. the crystal structure of deinococcus radiodurans reco (drreco) reveals possible binding ... | 2005 | 15719017 |
| characterisation of a novel amylosucrase from deinococcus radiodurans. | the blast search for amylosucrases has yielded several gene sequences of putative amylosucrases, however, with various questionable annotations. the putative encoded proteins share 32-48% identity with neisseria polysaccharea amylosucrase (as) and contain several amino acid residues proposed to be involved in as specificity. first, the b-domains of the putative proteins and as are highly similar. in addition, they also reveal additional residues between putative beta-strand 7 and alpha-helix 7 w ... | 2005 | 15733849 |
| differential dna binding and protection by dimeric and dodecameric forms of the ferritin homolog dps from deinococcus radiodurans. | bacterial iron storage proteins such as ferritin serve as intracellular iron reserves. members of the dna protection during starvation (dps) family of proteins are structurally related to ferritins, and their function is to protect the genome from iron-induced free radical damage. some members of the dps family bind dna and are thought to do so only as fully assembled dodecamers. we present the cloning and characterization of a dps homolog encoded by the radiation-resistant eubacterium deinococc ... | 2005 | 15755446 |
| aspartyl-trna synthetase requires a conserved proline in the anticodon-binding loop for trna(asn) recognition in vivo. | most prokaryotes require asp-trna(asn) for the synthesis of asn-trna(asn). this misacylated trna species is synthesized by a non-discriminating aspartyl-trna synthetase (asprs) that acylates both trna(asp) and trna(asn) with aspartate. in contrast, a discriminating asprs forms only asp-trna(asp). here we show that a conserved proline (position 77) in the l1 loop of the non-discriminating deinococcus radiodurans asprs2 is required for trna(asn) recognition in vivo. escherichia coli trpa34 was tra ... | 2005 | 15781458 |
| crystal structure of maltooligosyltrehalose trehalohydrolase from deinococcus radiodurans in complex with disaccharides. | trehalose (alpha-d-glucopyranosyl-1,1-alpha-d-glucopyranose) is a non-reducing diglucoside found in various organisms that serves as a carbohydrate reserve and as an agent that protects against a variety of physical and chemical stresses. deinococcus radiodurans possesses an alternative biosynthesis pathway for the synthesis of trehalose from maltooligosaccharides. this reaction is mediated by two enzymes: maltooligosyltrehalose synthase (mtsase) and maltooligosyltrehalose trehalohydrolase (mtha ... | 2005 | 15784255 |
| [cloning and expression of superoxide dismutase gene from deinococcus radiodurans in e. coli]. | to construct expressing recombinant of mn-sod of deinococcus radiodurans and express the target protein in e. coli bl21(de3). | 2005 | 15807266 |
| radiation response mechanisms of the extremely radioresistant bacterium deinococcus radiodurans. | effect of microgravity on recovery of bacterial cells from radiation damage was examined in iml-2, s/mm-4 and s/mm-9 experiments using the extremely radioresistant bacterium deinococcus radiodurans. the cells were irradiated with gamma rays before the space flight and incubated on board the space shuttle. the survival of the wild type cells incubated in space increased compared with the ground controls, suggesting that the recovery of this bacterium from radiation damage was enhanced under the s ... | 2004 | 15858357 |
| characterization of pathways dependent on the uvse, uvra1, or uvra2 gene product for uv resistance in deinococcus radiodurans. | the genome of a radiation-resistant bacterium, deinococcus radiodurans, contains one uvse gene and two uvra genes, uvra1 and uvra2. using a series of mutants lacking these genes, we determined the biological significance of these components to uv resistance. the uv damage endonuclease (uvse)-dependent excision repair (uver) pathway and uvra1-dependent pathway show some redundancy in their function to counteract the lethal effects of uv. loss of these pathways does not cause increased sensitivity ... | 2005 | 15901692 |
| dual negative regulatory mechanisms of recx on reca functions in radiation resistance, dna recombination and consequent genome instability in deinococcus radiodurans. | reca protein plays a central role in homologous recombination and dna repair. recx, a gene directly downstream in escherichia coli and some other bacterial species, down regulates it. however, the precise mechanism of regulation of reca by recx is not known. in order to study the function of recx in the highly radioresistant bacterium deinococcus radiodurans, null and overexpression strains were constructed. our data demonstrates that recx represses radiation resistance, dna recombination and co ... | 2005 | 15907774 |