| a crevice adjoining the ribosome tunnel: hints for cotranslational folding. | rna protection experiments and the crystal structure of a complex of the large ribosomal subunit from the eubacterium deinococcus radiodurans with rapamycin, a polyketide compound resembling macrolides and ketolides, showed that rapamycin binds to a crevice located at the boundaries of the nascent protein exit tunnel, near its entrance. at this location rapamycin cannot occlude the ribosome exit tunnel, consistent with its failure to act as a ribosomal antibiotic drug. in accord with recent bioc ... | 2005 | 15943964 |
| global whole-cell fticr mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium deinococcus radiodurans. | the results of previous studies indicated that d. radiodurans mounts a regulated protective response to heat shock, and that expression of more than 130 genes, including classical chaperones such as the groesl and dnakj operons and proteases such as clpb are induced in response to elevated temperature. in addition, previous qualitative whole-cell mass spectrometric studies conducted under heat shock conditions indicated global changes in the d. radiodurans proteome. to enable the discovery of no ... | 2005 | 15952717 |
| negative cooperativity of uric acid binding to the transcriptional regulator hucr from deinococcus radiodurans. | members of the marr family of winged helix transcriptional regulators have been shown to regulate multidrug and oxidative stress response, pathogenesis, and catabolism of aromatic compounds. many respond to anionic lipophilic compounds in their capacity to bind dna, and the co-crystal structure of marr bound to salicylate revealed two ligand-binding pockets, sal-a and sal-b. the marr homolog, hucr, from deinococcus radiodurans has been shown to repress expression of a predicted uricase, and dna- ... | 2005 | 15967460 |
| the utility of accurate mass and lc elution time information in the analysis of complex proteomes. | the combination of mass and normalized elution time (net) of a peptide identified by liquid chromatography-mass spectrometry (lc-ms) measurements can serve as a unique signature for that peptide. however, the specificity of an lc-ms measurement depends upon the complexity of the proteome (i.e., the number of possible peptides) and the accuracy of the lc-ms measurements. in this work, theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity w ... | 2005 | 15979333 |
| [characterization of the changes in protease of deinococcus radiodurans following irradiation]. | the activity of protease from deinococcus radiodurans r1 (drr1) recovered from uv light and gamma-ray irradiation were characterized by sds-page zymography or fitc-labeled casein as substrate. it was demonstrated that proteases with large molecular weight were abundantly and constitutively expressed in drr1, which consistent with the hypothesis that proteases were among the phx (predicted highly expressed) proteins in drr1. a broad range of gelatinolytic protease with molecular mass more than 14 ... | 2005 | 15989273 |
| structures of tryptophanyl-trna synthetase ii from deinococcus radiodurans bound to atp and tryptophan. insight into subunit cooperativity and domain motions linked to catalysis. | an auxiliary tryptophanyl trna synthetase (drtrprs ii) that interacts with nitric-oxide synthase in the radiation-resistant bacterium deinococcus radiodurans charges trna with tryptophan and 4-nitrotryptophan, a specific nitration product of nitric-oxide synthase. crystal structures of drtrprs ii, empty of ligands or bound to either trp or atp, reveal that drtrprs ii has an overall structure similar to standard bacterial trprss but undergoes smaller amplitude motions of the helical trna anti-cod ... | 2005 | 15998643 |
| alteration in location of a conserved gtpase-associated center of the ribosome induced by mutagenesis influences the structure of peptidyltransferase center and activity of elongation factor g. | translocation catalyzed by elongation factor g occurs after the peptidyltransferase reaction on the large ribosomal subunit. deacylated trna in the p-site stimulates multiple turnover gtpase activity of ef-g. we suggest that the allosteric signal from the peptidyltransferase center that activates ef-g may involve the alteration in the conformation of elongation factor binding center of the ribosome. the latter consists of the moveable gtpase-associated center and the sarcin-ricin loop that keeps ... | 2005 | 16014631 |
| 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 |
| structure of the uracil-dna n-glycosylase (ung) from deinococcus radiodurans. | uracil-dna glycosylases are dna-repair enzymes that catalyse the removal of promutagenic uracil from single- and double-stranded dna, thereby initiating the base-excision repair (ber) pathway. uracil in dna can occur by mis-incorporation of dump in place of dtmp during dna synthesis or by deamination of cytosine, resulting in u-a or u-g mispairs. the radiation-resistant bacterium deinococcus radiodurans has an elevated number of uracil-dna glycosylases compared with most other organisms. the cry ... | 2005 | 16041069 |
| 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 radiodurans strain r1 contains n6-methyladenine in its genome. | methylation of dna is known to be involved in dna repair mechanisms in bacteria. deinococcus radiodurans strain r1 on exposure to high radiation undergoes significant dna damage, which is repaired without mutations. however, the presence of modified nucleotides has not been reported in its genome. we report here the detection of n6-methyladenine in the genome of d. radiodurans strain r1 using immunochemical techniques. this n6-methyladenine is not a part of gatc restriction-modification system. ... | 2005 | 16084831 |
| structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action. | trigger factor (tf), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. here, we present the 3.5-a crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium deinococcus radiodurans with the n-terminal domain of tf (tfa) from the same organism. for anchoring, tfa exploits a small ribosomal surface area in the ... | 2005 | 16091460 |
| [analysis of bacterial composition of the pink mat from spectacles hot spring in tengchong by culture-independent approach]. | the bacterial composition of the pink mat was studied by culture-independent approach. 23 complete 16s rdna sequences were obtained. according to the sequences alignment and analysis of comparability, the bacteria of the pink mat was consisted of proteobacteria, firmicutes, bacteroidetes, actinobacter, deinococcus-thermus, aquificals. and compared with bacterial composition of the mats from octopus spring in yellowstone park and haegindi and fluidir spring, olkelduhals, grensdalur spring in icel ... | 2004 | 16110968 |
| identification of a novel trifunctional homoisocitrate dehydrogenase and modulation of the broad substrate specificity through site-directed mutagenesis. | a gene encoding homoisocitrate dehydrogenase (hicdh) of deinococcus radiodurans was cloned, sequenced, and overexpressed in escherichia coli. the amino acid sequence was 63% identical to hicdh from thermus thermophilus (tth-hicdh). similar to tth-hicdh, purified, recombinant dra-hicdh was a tetramer, required k+ and mn2+ for activity, and used nad+ as a coenzyme. however, unlike tth-hicdh, which has a 20-fold preference for isocitrate over homoisocitrate, dra-hicdh preferred homoisocitrate to is ... | 2005 | 16139794 |
| extensive diversity of ionizing-radiation-resistant bacteria recovered from sonoran desert soil and description of nine new species of the genus deinococcus obtained from a single soil sample. | the ionizing-radiation-resistant fractions of two soil bacterial communities were investigated by exposing an arid soil from the sonoran desert and a nonarid soil from a louisiana forest to various doses of ionizing radiation using a (60)co source. the numbers of surviving bacteria decreased as the dose of gamma radiation to which the soils were exposed increased. bacterial isolates surviving doses of 30 kgy were recovered from the sonoran desert soil, while no isolates were recovered from the n ... | 2005 | 16151108 |
| dichotomy of major bacterial phyla inferred from gene arrangement comparisons. | a computer search for gene arrangements that are present in gram-positive bacteria but are absent from proteobacteria and vice versa was carried out. four such arrangements were detected, based on which major bacterial phyla were divided into two groups; thermotoga, deinococcus-thermus, chloroflexi (green non-sulfur bacteria), and fusobacteria, represent gram-positive bacterial gene arrangements, while aquifex, spirochetes, planctomycetes, chlorobi (green sulfur bacteria), bacteroides show prote ... | 2006 | 16159660 |
| antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation. | antibiotics target ribosomes at distinct locations within functionally relevant sites. they exert their inhibitory action by diverse modes, including competing with substrate binding, interfering with ribosomal dynamics, minimizing ribosomal mobility, facilitating miscoding, hampering the progression of the mrna chain, and blocking the nascent protein exit tunnel. although the ribosomes are highly conserved organelles, they possess subtle sequence and/or conformational variations. these enable d ... | 2005 | 16180279 |
| the radiation responsive promoter of the deinococcus radiodurans ppra gene. | in a previous study, we identified a novel radiation-inducible protein ppra that plays a critical role in the radiation resistance of deinococcus radiodurans [narumi, i., satoh, k., cui, s., funayama, t., kitayama, s., watanabe, h., 2004. ppra: a novel protein from deinococcus radiodurans that stimulates dna ligation. mol. microbiol. 54, 278-285.]. despite the interest in mechanisms underlying radiation responses in d. radiodurans, little is known about the radiation responsive promoter for radi ... | 2005 | 16203111 |
| comparison of probability and likelihood models for peptide identification from tandem mass spectrometry data. | we evaluate statistical models used in two-hypothesis tests for identifying peptides from tandem mass spectrometry data. the null hypothesis h(0), that a peptide matches a spectrum by chance, requires information on the probability of by-chance matches between peptide fragments and peaks in the spectrum. likewise, the alternate hypothesis h(a), that the spectrum is due to a particular peptide, requires probabilities that the peptide fragments would indeed be observed if it was the causative agen ... | 2005 | 16212422 |
| the crystal structure of mismatch-specific uracil-dna glycosylase (mug) from deinococcus radiodurans reveals a novel catalytic residue and broad substrate specificity. | deinococcus radiodurans is extremely resistant to the effects of ionizing radiation. the source of the radiation resistance is not known, but an expansion of specific protein families related to stress response and damage control has been observed. dna repair enzymes are among the expanded protein families in d. radiodurans, and genes encoding five different uracil-dna glycosylases are identified in the genome. here we report the three-dimensional structure of the mismatch-specific uracil-dna gl ... | 2006 | 16223719 |
| evolutionary relationships among photosynthetic bacteria. | to understand the evolution of photosynthetic bacteria it is necessary to understand how the main groups within bacteria have evolved from a common ancestor, a critical issue that has not been resolved in the past. recent analysis of shared conserved inserts or deletions (indels) in protein sequences has provided a powerful means to resolve this long-standing problem in microbiology. based on a set of 25 indels in highly conserved and widely distributed proteins, all main groups within bacteria ... | 2003 | 16228576 |
| comparative genomics of thermus thermophilus and deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. | thermus thermophilus and deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. t. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas d. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria. | 2005 | 16242020 |
| deinococcus radiodurans - the consummate survivor. | relatively little is known about the biochemical basis of the capacity of deinococcus radiodurans to endure the genetic insult that results from exposure to ionizing radiation and can include hundreds of dna double-strand breaks. however, recent reports indicate that this species compensates for extensive dna damage through adaptations that allow cells to avoid the potentially detrimental effects of dna strand breaks. it seems that d. radiodurans uses mechanisms that limit dna degradation and th ... | 2005 | 16261171 |
| the binding mode of the trigger factor on the ribosome: implications for protein folding and srp interaction. | this study presents the x-ray structure of the n-terminal binding domain of the d. radiodurans trigger factor (tf) in complex with the d. radiodurans large ribosomal subunit. at 3.35 a, a complete description of the interactions with ribosomal proteins l23, l29, and 23s rrna are disclosed, many of which differ from those found previously for a heterologous bacterial-archaeal tf-ribosome complex. the beta hairpin loop of eubacterial l24, which is shorter in archaeal ribosomes, contacts the tf and ... | 2005 | 16271892 |
| [comparative genomics of genes contributed to dna repair in the radiation-resistant deinococcus radiodurans]. | | 2003 | 16276882 |
| [isolation and characterization of a novel radiation-resistant rod-shaped bacterium]. | a novel radiation-resistant bacterium was isolated from soil of lake bank in beijing. the bacterium produced orange-pigmented colonies and formed rod-shaped cells that stained gram negative alike the deinobacter grandis previously described by japan's scientist. it was found with electron microscopy that the isolate is of 0.6 microm - 1.6 microm size and has a 30-40 nm thickness of cell wall, being slightly larger and thicker than the deinobacter grandis. there was a difference in the concentrat ... | 2003 | 16279194 |
| deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the sahara desert. | two gamma- and uv-radiation-tolerant, gram-negative, rod-shaped bacterial strains, vcd115t and vcd117, were isolated from a mixture of sand samples collected in the sahara desert in morocco and tunisia, after exposure of the sand to 15 kgy gamma radiation. phylogenetic analysis based on 16s rrna gene sequences and dna-dna hybridizations showed that vcd115t and vcd117 are members of a novel species belonging to the genus deinococcus, with deinococcus grandis as its closest relative. the dna g+c c ... | 2005 | 16280508 |
| characterization of heterologous hemoglobin and flavohemoglobin promoter regulation in escherichia coli. | bacterial hemoglobins and flavohemoglobins have been used to improve cell growth and productivity in biotechnological applications. the expression of globin genes can be induced by reducing the oxygen supply or applying external stressors, which provide a simple and inexpensive mechanism for induction of heterologous protein production. it is in the interest of the biotechnological industry to seek new promoters, which are non-patented, cheap and simple to induce. therefore, new globin gene prom ... | 2006 | 16290305 |
| fine structure of the deinococcus radiodurans nucleoid revealed by cryoelectron microscopy of vitreous sections. | transmission electron microscopy revealed that the nucleoid of the extremely radioresistant bacteria deinococcus radiodurans may adopt an unusual ring shape. this led to the hypothesis that the tight toroidal package of the d. radiodurans genome might contribute to radioresistance by preventing diffusion of ends of double-stranded dna breaks. the molecular arrangement of dna in the nucleoid, which must be determined to test this hypothesis, is not discernible by conventional methods of electron ... | 2005 | 16291678 |
| a light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. | phytochromes are red/far-red light photoreceptors that direct photosensory responses across the bacterial, fungal and plant kingdoms. these include photosynthetic potential and pigmentation in bacteria as well as chloroplast development and photomorphogenesis in plants. phytochromes consist of an amino-terminal region that covalently binds a single bilin chromophore, followed by a carboxy-terminal dimerization domain that often transmits the light signal through a histidine kinase relay. here we ... | 2005 | 16292304 |
| sensitivity to polychromatic uv-radiation of strains of deinococcus radiodurans differing in their dna repair capacity. | to characterize the ultraviolet (uv) sensitivity and establish the uv-induced dna damage profile of cells of four deinococcus radiodurans strains. the investigated strains differ in their radiation susceptibility, leading to a classification into a uv-sensitive (uvs78 and 1r1a) and a uv-resistant class (wild type strain r1 and 262). | 2005 | 16298941 |
| isolation and characterization of thermus bacteriophages. | one-hundred-fifteen bacteriophage strains were isolated from alkaline hot springs in iceland, new zealand, russia (kamchatka), and the u.s.a. the phages belonged to the myoviridae, siphoviridae, tectiviridae, and inoviridae families. over 50% of isolates were isometric or filamentous. one type of siphovirus had giant tails of over 800 nm in length. phages were further characterized by host range, genome size, dna restriction endonuclease digestion patterns, and temperature and ph sensitivity. my ... | 2006 | 16308675 |
| analysis of interaction between dna and deinococcus radiodurans ppra protein by atomic force microscopy. | a dna repair-promoting protein, ppra, was isolated from a radiation resistant bacterium, deinococcus radiodurans [i. narumi, k. sato, s. cui, t. funayama, s. kitayama, h. watanabe, ppra: a novel protein from deinococcus radiodurans that stimulates dna ligation, mol. microbiol. 54 (2004) 278-285]. despite several studies, however, the function of ppra is not still clear. we used atomic force microscopy (afm) to elucidate the role of this protein in the dna repair pathway. in the present study, in ... | 2006 | 16309981 |
| crystal structures of the tryptophan repressor binding protein wrba and complexes with flavin mononucleotide. | the tryptophan repressor binding protein wrba binds to the tryptophan repressor protein trpr. although the biological role of wrba remains unclear, it has been proposed to function in enhancing the stability of trpr-dna complexes. sequence database analysis has identified wrba as a founding member of a flavodoxin-like family of proteins. here we present crystal structures of wrba from deinococcus radiodurans and pseudomonas aeruginosa and their complexes with flavin mononucleotide. the protomer ... | 2005 | 16322580 |
| hydrocarbon contamination changes the bacterial diversity of soil from around scott base, antarctica. | a combination of culture-independent and culturing methods was used to determine the impacts of hydrocarbon contamination on the diversity of bacterial communities in coastal soil from ross island, antarctica. while numbers of culturable aerobic heterotrophic microbes were 1-2 orders of magnitude higher in the hydrocarbon-contaminated soil than control soil, the populations were less diverse. members of the divisions fibrobacter/acidobacterium, cytophaga/flavobacterium/bacteroides, deinococcus/t ... | 2004 | 16329936 |
| species-specific antibiotic-ribosome interactions: implications for drug development. | in the cell, the protein synthetic machinery is a highly complex apparatus that offers many potential sites for functional interference and therefore represents a major target for antibiotics. the recent plethora of crystal structures of ribosomal subunits in complex with various antibiotics has provided unparalleled insight into their mode of interaction and inhibition. however, differences in the conformation, orientation and position of some of these drugs bound to ribosomal subunits of deino ... | 2005 | 16336118 |
| mutagenesis via is transposition in deinococcus radiodurans. | analysis of the complete genome indicates that insertion sequences (iss) are abundant in the radio-resistant bacterium deinococcus radiodurans. by developing a forward mutagenesis assay to detect any inactivation events in d. radiodurans, we found that in the presence of an active mismatch repair system 75% of the mutations to trimethoprim-resistance (tmp(r)) resulted from an is insertion into the thya coding region. analysis of their distribution among the spontaneous tmp(r) mutants indicated t ... | 2006 | 16359337 |
| limited concentration of reca delays dna double-strand break repair in deinococcus radiodurans r1. | to evaluate the importance of reca in dna double-strand break (dsb) repair, we examined the effect of low and high reca concentrations such as 2500 and 100 000 molecules per cell expressed from the inducible pspac promoter in deinococcus radiodurans in absence or in presence of iptg respectively. we showed that at low concentration, reca has a negligible effect on cell survival after gamma-irradiation when bacteria were immediately plated on tgy agar whereas it significantly decreased the surviv ... | 2006 | 16359339 |
| destruction of deinococcus geothermalis biofilm by photocatalytic ald and sol-gel tio2 surfaces. | the aim of the present work was to explore possibilities of photocatalytic tio2 coating for reducing biofilms on non-living surfaces. the model organism, deinococcus geothermalis, known to initiate growth of durable, colored biofilms on machine surfaces in the paper industry, was allowed to form biofilms on stainless steel, glass and tio2 film coated glass or titanium. field emission electron microscopy revealed that the cells in the biofilm formed at 45 degrees c under vigorous shaking were con ... | 2006 | 16362272 |
| crystal structure of a bacterial type ib dna topoisomerase reveals a preassembled active site in the absence of dna. | type ib dna topoisomerases are found in all eukarya, two families of eukaryotic viruses (poxviruses and mimivirus), and many genera of bacteria. they alter dna topology by cleaving and resealing one strand of duplex dna via a covalent dna-(3-phosphotyrosyl)-enzyme intermediate. bacterial type ib enzymes were discovered recently and are described as poxvirus-like with respect to their small size, primary structures, and bipartite domain organization. here we report the 1.75-a crystal structure of ... | 2006 | 16368685 |
| identification and characterization of a novel bacterial sulfite oxidase with no heme binding domain from deinococcus radiodurans. | an open reading frame (draso) encoding a putative sulfite oxidase (so) was identified in the sequence of chromosome ii of deinococcus radiodurans; the predicted gene product showed significant amino acid sequence homology to several bacterial and eukaryotic sos, such as the biochemically and structurally characterized enzyme from arabidopsis thaliana. cloning of the deinococcus so gene was performed by pcr amplification from the bacterial genomic dna, and heterologous gene expression of a histid ... | 2006 | 16385059 |
| the aspartate transcarbamoylase-dihydroorotase complex in deinococcus radiophilus has an active dihydroorotase. | aspartate transcarbamoylase (atcase) and dihydroorotase (dhoase) catalyse the first two steps unique to pyrimidine synthesis. in many bacteria they form non-covalently bonded complexes. there are two types of dhoase, type i and type ii which share a common ancestry. type i is the more ancient form and is present in the complexes. in recently evolved bacteria the dhoase is defective and its function has been replaced by a type ii dhoase which is separate from the complex. deinococcus radiophilus ... | 2006 | 16395552 |
| method for detecting dna strand breaks in mammalian cells using the deinococcus radiodurans ppra protein. | in a previous study, we identified the novel protein ppra that plays a critical role in the radiation resistance of deinococcus radiodurans. in this study, we focussed on the ability of ppra protein to recognize and bind to double-stranded dna carrying strand breaks, and attempted to visualize radiation-induced dna strand breaks in mammalian cultured cells by employing ppra protein using an immunofluorescence technique. increased ppra protein binding to cho-k1 nuclei immediately following irradi ... | 2006 | 16406432 |
| molecular analysis of the bacterial microbiota in the human stomach. | the microbiota of the human stomach and the influence of helicobacter pylori colonization on its composition remain largely unknown. we characterized bacterial diversity within the human gastric mucosa by using a small subunit 16s rdna clone library approach and analyzed 1,833 sequences generated by broad-range bacterial pcr from 23 gastric endoscopic biopsy samples. a diverse community of 128 phylotypes was identified, featuring diversity at this site greater than previously described. the majo ... | 2006 | 16407106 |
| bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of n-acetylated intermediates in prokaryotes. | the n-acetylation of l-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical n-acetylglutamate synthase (nags, gene arga) first characterized in escherichia coli and pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (oat, gene argj) present in bacteria, a ... | 2006 | 16409639 |
| is radiation damage dependent on the dose rate used during macromolecular crystallography data collection? | this paper focuses on the radiation-damage effects when applying the same total x-ray dose to protein crystals at different dose rates. these experiments have been performed on both a selenomethionated protein and on bovine trypsin using dose rates that span nearly two orders of magnitude. the results show no clear dose-rate effect on the global indicators of radiation damage, but a small measurable dose-rate effect could be found when studying specific radiation damage. it is hypothesized that ... | 2006 | 16421442 |
| distribution of f- and a/v-type atpases in thermus scotoductus and other closely related species. | the presence of an a/v-type atpase in different thermus species and in the deeper branching species meiothermus ruber and deinococcus radiodurans suggests that the presence of the archaeal-type atpase is a primitive character of the deinococci that was acquired through horizontal gene transfer (hgt). however, the presence of a bacterial type f-atpases was reported in two newly identified thermus species (thermus scotoductus dsm 8553 and thermus filiformis dsm 4687). two different scenarios can e ... | 2006 | 16423651 |
| transcriptome analysis applied to survival of shewanella oneidensis mr-1 exposed to ionizing radiation. | the ionizing radiation (ir) dose that yields 20% survival (d20) of shewanella oneidensis mr-1 is lower by factors of 20 and 200 than those for escherichia coli and deinococcus radiodurans, respectively. transcriptome analysis was used to identify the genes of mr-1 responding to 40 gy (d20). we observed the induction of 170 genes and repression of 87 genes in mr-1 during a 1-h recovery period after irradiation. the genomic response of mr-1 to ir is very similar to its response to uv radiation (25 ... | 2006 | 16428429 |
| an exonuclease i-sensitive dna repair pathway in deinococcus radiodurans: a major determinant of radiation resistance. | deinococcus radiodurans r1 recovering from acute dose of gamma radiation shows a biphasic mechanism of dna double-strand break repair. the possible involvement of microsequence homology-dependent, or non-homologous end joining type mechanisms during initial period followed by reca-dependent homologous recombination pathways has been suggested for the reconstruction of complete genomes in this microbe. we have exploited the known roles of exonuclease i in dna recombination to elucidate the nature ... | 2006 | 16430702 |
| analysis of codon usage pattern in the radioresistant bacterium deinococcus radiodurans. | the main factors shaping codon usage bias in the deinococcus radiodurans genome were reported. correspondence analysis (coa) was carried out to analyze synonymous codon usage bias. the results showed that the main trend was strongly correlated with gene expression level assessed by the "codon adaptation index" (cai) values, a result that was confirmed by the distribution of genes along the first axis. the results of correlation analysis, variance analysis and neutrality plot indicated that gene ... | 2006 | 16431014 |
| deinococcus mumbaiensis sp. nov., a radiation-resistant pleomorphic bacterium isolated from mumbai, india. | a radiation-resistant, gram-negative and pleomorphic bacterium (con-1) was isolated from a contaminated tryptone glucose yeast extract agar plate in the laboratory. it was red pigmented, nonmotile, nonsporulating, and aerobic, and contained mk-8 as respiratory quinone. the cell wall of this bacterium contained ornithine. the major fatty acids were c16:0, c16:1, c17:0, c18:1 and iso c18:0. the dna of con-1 had a g+c content of 70 mol%. phylogenetic analysis based on 16s rrna gene sequences showed ... | 2006 | 16445756 |
| bacterial community changes with n'-n' dimethylforamide (dmf) additives during polycyclic aromatic hydrocarbons (pah) biodegardation. | this study examined the changes in the bacterial community during biodegradation of polycyclic aromatic hydrocarbon (pah) substrate when n'-n' dimethylformamide (dmf) was added. the microbial populations that biodegrade the pah substrate were assessed by fluorescence in-situ hybridization (fish) and changed from 49.45% archaea and 49.15% bacteria to 42.00% archaea and 51.78% bacteria when the pah was supplemented with dmf. nine microorganisms were classified as gram-negative alpha-, beta- and ga ... | 2006 | 16457170 |
| normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. | central tendency, linear regression, locally weighted regression, and quantile techniques were investigated for normalization of peptide abundance measurements obtained from high-throughput liquid chromatography-fourier transform ion cyclotron resonance mass spectrometry (lc-fticr ms). arbitrary abundances of peptides were obtained from three sample sets, including a standard protein sample, two deinococcus radiodurans samples taken from different growth phases, and two mouse striatum samples fr ... | 2006 | 16457593 |
| the deinococcus radiodurans-encoded hu protein has two dna-binding domains. | deinococcus radiodurans can reconstitute its genome from double-strand breaks, most likely due to unusually efficient dna repair and recombination. factors that may contribute to such processes include the histone-like protein hu. the d. radiodurans-encoded hu (drhu), which binds preferentially to dna recombination intermediates, contains a 47-amino acid extension preceding the fold characteristic of hu proteins. here we use electrophoretic mobility shift assays and dna footprinting to show that ... | 2006 | 16460019 |
| the desert of tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. | the phylogenetic diversity of prokaryotic communities exposed to arid conditions in the hot desert of tataouine (south tunisia) was estimated with a combination of a culture and - molecular-based analysis. thirty-one isolates, representative of each dominant morphotypes, were affiliated to actinobacteria, firmicutes, proteobacteria and the cfb group while none related to archaea. analysis of 16s rrna gene libraries revealed the presence of species related to bacteria and archaea. sequences relat ... | 2006 | 16478457 |
| characterization of a mn-dependent fructose-1,6-bisphosphate aldolase in deinococcus radiodurans. | the key enzyme of the glycolytic pathway of deinococcus radiodurans, fructose-1,6-bisphosphate aldolase, could be induced independently by glucose and mn. the enzyme exhibited the characteristics of the metal-dependent class ii aldolases. unlike most class ii aldolases, the deinococcal aldolase preferred mn, not zn, as a cofactor. the fbaa gene encoding the deinococcal aldolase was cloned and the protein overproduced in various escherichia coli expression hosts. however, the overexpressed deinoc ... | 2006 | 16502329 |
| hg(ii) sequestration and protection by the merr metal-binding domain (mbd). | merr, the metalloregulator of the bacterial mercury resistance (mer) operon, binds hg(ii) with high affinity. to study the mechanism of metal-induced activation, a small protein was previously engineered embodying in a single polypeptide the metal-binding domain (mbd) ordinarily formed between two monomers of merr. here the physiological and biochemical properties of mbd expressed on the cell surface or in the cytosol were examined, to better understand the environments in which specific metal b ... | 2006 | 16514151 |
| molecular microbial diversity of a soil sample and detection of ammonia oxidizers from cape evans, mcmurdo dry valley, antarctica. | the aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, cape evans, mcmurdo, antarctica by an ssu rdna gene library approach. our study by sequencing of clones from ssu rdna gene library approach revealed high diversity in the soil sample from antarctica. more than 50% of clones showed homology to cytophaga-flavobacterium-bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, thermus-deinococcus and high gc ... | 2007 | 16517136 |
| three hrdc domains differentially modulate deinococcus radiodurans recq dna helicase biochemical activity. | recq helicases are key genome maintenance enzymes that function in dna replication, recombination, and repair. in contrast to nearly every other identified recq family member, the recq helicase from the radioresistant bacterium deinococcus radiodurans encodes three "helicase and rnase d c-terminal" (hrdc) domains at its c terminus. hrdc domains have been implicated in structure-specific nucleic acid binding with roles in targeting recq proteins to particular dna structures; however, only recq pr ... | 2006 | 16531400 |
| a computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions. | phytochromes are photoreceptors, discovered in plants, that control a wide variety of developmental processes. they have also been found in bacteria and fungi, but for many species their biological role remains obscure. this work concentrates on the phytochrome system of agrobacterium tumefaciens, a non-photosynthetic soil bacterium with two phytochromes. to identify proteins that might share common functions with phytochromes, a co-distribution analysis was performed on the basis of protein seq ... | 2006 | 16539742 |
| internal promoter characterization and expression of the deinococcus radiodurans ppri-folp gene cluster. | ppri is a general gene switch responsible for the extraordinary radioresistance of deinococcus radiodurans. from ncbi dna sequence analysis, it was predicted that the translation start codon of the downstream folp (dr0168) gene overlaps the ppri (dr0167) stop codon, suggesting that these genes may form an operon. in this study, we show that a mutant containing an inserted sequence in folp does not grow unless folate is added to the medium, but is not affected in extreme radioresistance, whereas ... | 2006 | 16553853 |
| dna polymerase x from deinococcus radiodurans possesses a structure-modulated 3'-->5' exonuclease activity involved in radioresistance. | recently a family x dna polymerase (polxdr) was identified in the radioresistant bacterium deinococcus radiodurans. knockout cells show a delay in double-strand break repair (dsbr) and an increased sensitivity to gamma-irradiation. here we show that polxdr possesses 3'-->5' exonuclease activity that stops cutting close to a loop. polxdr consists of a dna polymerase x domain (polxc) and a polymerase and histidinol phosphatase (php) domain. deletion of the php domain abolishes only the structure-m ... | 2006 | 16556228 |
| development of a defined medium supporting rapid growth for deinococcus radiodurans and analysis of metabolic capacities. | a morpholinepropanesulfonic acid (mops)-buffered rich defined medium (rdm) was optimized to support a reproducible 2.6-h doubling time at 35 degrees c for deinococcus radiodurans r1 and used to gain insight into vitamin and carbon metabolism. d. radiodurans was shown to require biotin and niacin for growth in this medium. a glutamine-serine simple defined medium (sdm) was developed that supported a 4-h doubling time, and this medium was used to probe sulfur and methionine metabolism. vitamin b(1 ... | 2006 | 16575566 |
| structure of the manganese superoxide dismutase from deinococcus radiodurans in two crystal forms. | the structure of the manganese superoxide dismutase (mn-sod; dr1279) from deinococcus radiodurans has been determined in two different crystal forms. both crystal forms are monoclinic with space group p2(1). form i has unit-cell parameters a = 44.28, b = 83.21, c = 59.52 angstroms, beta = 110.18 degrees and contains a homodimer in the asymmetric unit, with structure refinement (r = 16.8%, r(free) = 23.6%) carried out using data to d(min) = 2.2 angstroms. form ii has unit-cell parameters a = 43.5 ... | 2006 | 16582477 |
| bionanofabrication of metallic and semiconductor nanoparticle arrays using s-layer protein lattices with different lateral spacings and geometries. | two-dimensional (2-d) surface layer (s-layer) protein lattices isolated from the gram-positive bacterium deinococcus radiodurans and the acidothermophilic archaeon sulfolobus acidocaldarius were investigated and compared for their ability to biotemplate the formation of self-assembled, ordered arrays of inorganic nanoparticles (nps). the nps employed for these studies included citrate-capped gold nps and various species of cdse/zns core/shell quantum dots (qds). the qd nanocrystals were function ... | 2006 | 16584254 |
| deinococcus ficus sp. nov., isolated from the rhizosphere of ficus religiosa l. | a pale-pink strain (cc-fr2-10t) from the rhizosphere of the sacred tree ficus religiosa l. in taiwan was investigated by using a polyphasic taxonomic approach. the cells were gram-positive, rod-shaped and non-spore-forming. phylogenetic analyses using the 16s rrna gene sequence of the isolate indicated that the organism belongs to the genus deinococcus, the highest sequence similarities being found with deinococcus grandis (96.1 %), deinococcus radiodurans (94.3 %), deinococcus radiopugnans (93. ... | 2006 | 16585695 |
| ppra: a protein implicated in radioresistance of deinococcus radiodurans stimulates catalase activity in escherichia coli. | ppra: a pleiotropic protein promoting dna repair, role in radiation resistance of deinococcus radiodurans was demonstrated. in this study, the effect of radiation and oxidative stress on transgenic escherichia coli expressing ppra has been studied. the ppra gene from d. radiodurans kr1 was cloned and expressed in e. coli. transgenic e. coli cells expressing ppra showed twofold to threefold higher tolerance to hydrogen peroxide as compared to control. the 2.8-fold in vivo stimulation of catalase ... | 2006 | 16586106 |
| functional analysis of helicase and three tandem hrdc domains of recq in deinococcus radiodurans. | recq is a highly conserved helicase necessary for maintaining genome stability in all organisms. genome comparison showed that a homologue of recq in deinococcus radiodurans designated as dr1289 is a member of recq family with unusual domain arrangement: a helicase domain, an recq c-terminal domain, and surprisingly three hrdc domain repeats, whose function, however, remains obscure currently. using an insertion deletion, we discovered that the drrecq mutation causes an increase in gamma radiati ... | 2006 | 16615167 |
| structural insights into enzyme-substrate interaction and characterization of enzymatic intermediates of organic hydroperoxide resistance protein from xylella fastidiosa. | organic hydroperoxide resistance proteins (ohr) belong to a family of proteins that possess thiol-dependent peroxidase activity endowed by reactive cysteine residues able to reduce peroxides. the crystal structure of ohr from xylella fastidiosa in complex with polyethylene glycol, providing insights into enzyme-substrate interactions is described herein. in addition, crystallographic studies, molecular modeling and biochemical assays also indicated that peroxides derived from long chain fatty ac ... | 2006 | 16631787 |
| microbial survival rates of escherichia coli and deinococcus radiodurans under low temperature, low pressure, and uv-irradiation conditions, and their relevance to possible martian life. | viability rates were determined for microbial populations of escherichia coli and deinococcus radiodurans under the environmental stresses of low temperature (-35 degrees c), low-pressure conditions (83.3 kpa), and ultraviolet (uv) irradiation (37 w/m(2)). during the stress tests the organisms were suspended in saltwater soil and freshwater soil media, at variable burial depths, and in seawater. microbial populations of both organisms were most susceptible to dehydration stress associated with l ... | 2006 | 16689650 |
| characterization of monofunctional catalase kata from radioresistant bacterium deinococcus radiodurans. | catalase plays a key role in protecting cells against toxic reactive oxygen species. here we report on the cloning, purification and characterization of a catalase (kata, dr1998) from the extremely radioresistant bacterium deinococcus radiodurans. the size of purified d. radiodurans kata monomer was 65 kda while gel filtration revealed that the size of the enzyme was 240 kda, suggesting that kata formed a homotetramer in solution. purified kata displayed a final specific activity of 68,800 u/mg ... | 2006 | 16716939 |
| an alternating sheared aa pair and elements of stability for a single sheared purine-purine pair flanked by sheared ga pairs in rna. | a previous nmr structure of the duplex 5'ggu gga ggcu/pccg aag ccg5' revealed an unusually stable rna internal loop with three consecutive sheared ga pairs. here, we report nmr studies of two duplexes, 5'ggu gga ggcu/pcca aag ccg5' (replacing the ug pair with a ua closing pair) and 5'ggu gaa ggcu/pccg aag ccg5' (replacing the middle ga pair with an aa pair). an unusually stable loop with three consecutive sheared ga pairs forms in the duplex 5'ggu gga ggcu/pcca aag ccg5'. the structure contrasts ... | 2006 | 16734425 |
| [construction of the recq double mutants and analysis of adversity in deinococcus radiodurans]. | as a subfamily member of sf1 superfamily, the reco helicases are highly conserved in evolution and are required for maintaining genome stability in all organisms. loss of reco helicase function leads to a breakdown in the maintenance of genome integrity, in particular hyper-recombination. named after the recq gene of escherichia coli, lower eukaryotic species generally only contain a single recq family representative; for example, sgsl in the budding yeast, saccharomyces cerevisiae, and rqhl in ... | 2006 | 16736577 |
| [construction and functional analysis of the crtl gene disruptant in deinococcus radiodurans]. | with the method of polymerase chain reaction and homologous genetic recombination in vivo, the key gene encoding bacterial-type phytoene desaturase (crtl) which controls the carotenoids biosynthesis pathway in the non-photosynthetic and extremely radioresistant bacterium deinococcus radiodurans was deleted from the genome. the colorless mutant obtained was designated as m61. survival rates of mutant strain and wild type strain were investigated under different doses of gamma-radiation and hydrog ... | 2006 | 16736578 |
| [effects of ppri and recx on antioxidant activity of deinococcus radiodurans]. | effects of mutations of pprl (dr0167) and recx (dr1310), which are relative to radioresistance, on reactive oxygen species scavenging activities in deinococcus radiodurans were investigated using gene mutation, chemiluminescence measurement and enzyme activity analysis. their possible regulating functions on the activities of antioxidant enzymes was evaluated. results show that mutant that lacks ppri is remarkably sensitive to reactive oxygen species and its enzyme activities of catalase and sup ... | 2006 | 16736584 |
| the crystal structure of the transcriptional regulator hucr from deinococcus radiodurans reveals a repressor preconfigured for dna binding. | we report here the 2.3 a resolution structure of the hypothetical uricase regulator (hucr) from deinococcus radiodurans r1. hucr, a member of the marr family of dna-binding proteins, was previously shown to repress its own expression as well as that of a uricase, a repression that is alleviated both in vivo and in vitro upon binding uric acid, the substrate for uricase. as uric acid is a potent scavenger of reactive oxygen species, and as d. radiodurans is known for its remarkable resistance to ... | 2006 | 16750221 |
| chromophore structure in the photocycle of the cyanobacterial phytochrome cph1. | the chromophore conformations of the red and far red light induced product states "pfr" and "pr" of the n-terminal photoreceptor domain cph1-n515 from synechocystis 6803 have been investigated by nmr spectroscopy, using specific 13c isotope substitutions in the chromophore. 13c-nmr spectroscopy in the pfr and pr states indicated reversible chemical shift differences predominantly of the c(4) carbon in ring a of the phycocyanobilin chromophore, in contrast to differences of c15 and c5, which were ... | 2006 | 16751241 |
| self-assembly of dendrimer-encapsulated nanoparticle arrays using 2-d microbial s-layer protein biotemplates. | we investigated the formation of self-assembled two-dimensional (2-d) arrays of dendrimer-encapsulated platinum nanoparticles (pt-dens) using prokaryotic surface-layer (s-layer) proteins as biomacromolecular templates. the pt-dens (mean core diameter 1.8 +/- 0.5 nm) were synthesized by chemical reduction of metal ion species complexed within the interior of fourth-generation, hydroxyl-terminated, starburst poly(amidoamine) dendrimers (g4 pamam-oh). detailed structural and elemental composition a ... | 2006 | 16768411 |
| novel thermostable single-stranded dna-binding protein (ssb) from deinococcus geothermalis. | to study the biochemical properties of single-stranded dna-binding (ssb) protein from deinococcus geothermalis (dgessb), we have cloned the ssb gene obtained by pcr and developed an overexpression system. the gene consists of an open reading frame of 900 nucleotides encoding a protein of 300 amino acids with a calculated molecular weight of 32.45 kda. the amino acid sequence exhibits 43, 44 and 75% identity with thermus aquaticus, thermus thermophilus and deinococcus radiodurans ssbs, respective ... | 2006 | 16802171 |
| modulating radiation resistance: insights based on defenses against reactive oxygen species in the radioresistant bacterium deinococcus radiodurans. | the classical dogma of radiation biology asserts that the cytotoxic effects of ionizing radiation (ir) are principally the result of dna damage. yet many organisms that encode a complement of dna repair functions are killed by ir doses that cause little dna damage. instead, proteins likely are the first major class of molecules damaged by ir. this article presents a new perspective on extreme ir resistance in the eubacterium deinococcus radiodurans, reevaluates the role of superoxide (02*-) ions ... | 2006 | 16815462 |
| crystal structure of dps-1, a functionally distinct dps protein from deinococcus radiodurans. | dna protection during starvation (dps) proteins play an important role in protecting cellular macromolecules from damage by reactive oxygen species (ros). unlike most orthologs that protect dna by a combination of dna binding and prevention of hydroxyl radical formation by ferroxidation and sequestration of iron, dps-1 from the radiation-resistant deinococcus radiodurans fails to protect dna from hydroxyl radical-mediated cleavage through a mechanism inferred to involve continuous release of iro ... | 2006 | 16828801 |
| dynamics of deinococcus radiodurans under controlled growth conditions. | deinococcus radiodurans is a potent radiation resistant bacterium with immense potential in nuclear waste treatment. in this investigation, the translational and rotational dynamics of dilute suspensions of d. radiodurans cultured under controlled growth conditions was studied by the polarized and depolarized dynamic light-scattering (dls) techniques. additionally, confocal laser scanning microscopy was used for characterizing the cultured samples and also for identification of d. radiodurans di ... | 2006 | 16829564 |
| deinococcus radiodurans engineered for complete toluene degradation facilitates cr(vi) reduction. | toluene and other fuel hydrocarbons are commonly found in association with radionuclides at numerous us department of energy sites, frequently occurring together with cr(vi) and other heavy metals. in this study, the extremely radiation-resistant bacterium deinococcus radiodurans, which naturally reduces cr(vi) to the less mobile and less toxic cr(iii), was engineered for complete toluene degradation by cloned expression of tod and xyl genes of pseudomonas putida. the recombinant tod/xyl strain ... | 2006 | 16849809 |
| the crystal structure of deinococcus radiodurans dps protein (dr2263) reveals the presence of a novel metal centre in the n terminus. | the crystal structure of a dna-binding protein from starved cells (dps) (dr2263) from deinococcus radiodurans was determined in two states: a native form, to 1.1-a resolution, and one soaked in an iron solution, to 1.6-a resolution. in comparison with other dps proteins, dr2263 has an extended n-terminal extension, in both structures presented here, a novel metal binding site was identified in this n-terminal extension and was assigned to bound zinc. the zinc is tetrahedrally coordinated and the ... | 2006 | 16855817 |
| characterization of intact subcellular bodies in whole bacteria by cryo-electron tomography and spectroscopic imaging. | we illustrate the combined use of cryo-electron tomography and spectroscopic difference imaging in the study of subcellular structure and subcellular bodies in whole bacteria. we limited our goal and focus to bodies with a distinct elemental composition that was in a sufficiently high concentration to provide the necessary signal-to-noise level at the relatively large sample thicknesses of the intact cell. this combination proved very powerful, as demonstrated by the identification of a phosphor ... | 2006 | 16872430 |
| expression, purification, crystallization and preliminary x-ray crystallographic studies of deinococcus radiodurans thioredoxin reductase. | deinococcus radiodurans, a gram-positive bacterium capable of withstanding extreme ionizing radiation, contains two thioredoxins (trx and trx1) and a single thioredoxin reductase (trxr) as part of its response to oxidative stress. thioredoxin reductase is a member of the family of pyridine nucleotide-disulfide oxidoreductase flavoenzymes. recombinant d. radiodurans trxr with a his tag at the n-terminus was expressed in escherichia coli and purified by metal-affinity chromatography. the protein w ... | 2006 | 16880549 |
| a highly thermostable, homodimeric single-stranded dna-binding protein from deinococcus radiopugnans. | we report the identification and characterization of the single-stranded dna-binding protein (ssb) from the mesophile and highly radiation-resistant deinococcus radiopugnans (drpssb). pcr-derived dna fragment containing the complete structural gene for drpssb protein was cloned and expressed in escherichia coli. the gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated molecular weight of 32.45 kda and pi 5.34. the amino acids sequence ... | 2006 | 16896528 |
| characterization of the mn2+-stimulated (di)adenosine polyphosphate hydrolase encoded by the deinococcus radiodurans dr2356 nudix gene. | the dr2356 nudix hydrolase gene from deinococcus radiodurans has been cloned and the product expressed as an 18 kda histidine-tagged protein. the enzyme hydrolysed adenosine and diadenosine polyphosphates, always generating atp as one of the initial products. atp and other (deoxy)nucleoside triphosphates were also substrates, yielding (d)ndp and pi as products. the dr2356 protein was most active at ph 8.6-9.0 and showed a strong preference for mn(2+) as activating cation. mg(2+) ions at 15 mm su ... | 2006 | 16900379 |
| [ribosome recycling revisited]. | ribosome recycling involves the coordinated action of the ribosome recycling factor (rrf), elongation factor ef-g and initiation factor if3 to disassemble the post-termination complex, recycling the components for the next round of translation. the crystal structure of domain i of rrf (rrf-di) in complex with the large ribosomal subunit from the eubacteria deinococcus radiodurans at high resolution reveals the nature and details of the interactions between this protein factor and rrna/protein co ... | 2006 | 16913233 |
| ring-like nucleoids and dna repair through error-free nonhomologous end joining in deinococcus radiodurans. | | 2006 | 16923869 |
| study of the deinococcus radiodurans nucleoid by cryoelectron microscopy of vitreous sections: supplementary comments. | | 2006 | 16923871 |
| 23s rrna 2058a-->g alteration mediates ketolide resistance in combination with deletion in l22. | resistance to macrolides and ketolides occurs mainly via alterations in rna moieties of the drug-binding site. using an a2058g mutant of mycobacterium smegmatis, additional telithromycin resistance was acquired via deletion of 15 residues from protein l22. molecular modeling, based on the crystal structure of the large ribosomal subunit from deinococcus radiodurans complexed with telithromycin, shows that the telithromycin carbamate group is located in the proximity of the tip of the l22 hairpin ... | 2006 | 16923950 |
| amt tag approach to proteomic characterization of deinococcus radiodurans and shewanella oneidensis. | | 2006 | 16929677 |
| nucleoid organization and the maintenance of dna integrity in e. coli, b. subtilis and d. radiodurans. | for enzymatic activities to be effectively carried out, basic prerequisites must be met. many enzymatic tasks require continuous consumption and dissipation of energy, sometimes in massive amounts. some activities, such as dna replication, transcription, and repair through homologous recombination rely upon templates that provide the information required for these transactions. yet, circumstances where intracellular energy pools are severely depleted, or where intact templates are not available, ... | 2006 | 16935006 |
| involvement of the s-layer proteins hpi and slpa in the maintenance of cell envelope integrity in deinococcus radiodurans r1. | the potential functions have been investigated of two proteins in deinococcus radiodurans r1 predicted to be involved in the maintenance and integrity of the s layer: the hexagonally packed intermediate (hpi) protein, and slpa (dr2577), a homologue of an s-layer slpa protein in thermus thermophilus. deletion of the hpi gene had little effect on the structure of the cell envelope or on shear- or solvent-induced stress responses. however, deletion of the slpa gene caused substantial alterations in ... | 2006 | 16946272 |
| occurrence of thioredoxin reductase in deinococcus species, the uv resistant bacteria. | the occurrence of thioredoxin reductase (nad(p)h: oxidized-thioredoxin reductase, ec 1.6.4.5, trxr) in five mesophilic species of deinococcus was investigated by page. each species possessed a unique trxr pattern, for example, a single trxr characterized d. radiopugnans while multiple forms of trxr occurred in other deinococcal spp. most of trxrs occurring in deinococcus showed dual cofactor specificity, active with either nadh or nadph, although the nadph specific-trxr was observed in d. radiop ... | 2006 | 16953184 |
| coexistence of two protein folding states in the crystal structure of ribosomal protein l20. | the recent finding of intrinsically unstructured proteins defies the classical structure-function paradigm. however, owing to their flexibility, intrinsically unstructured proteins generally escape detailed structural investigations. consequently little is known about the extent of conformational disorder and its role in biological functions. here, we present the x-ray structure of the unbound ribosomal protein l20, the long basic amino-terminal extension of which has been previously interpreted ... | 2006 | 16977336 |
| characterization of adhesion threads of deinococcus geothermalis as type iv pili. | deinococcus geothermalis e50051 forms tenuous biofilms on paper machine surfaces. field emission electron microscopy analysis revealed peritrichous appendages which mediated cell-to-surface and cell-to-cell interactions but were absent in planktonically grown cells. the major protein component of the extracellular extract of d. geothermalis had an n-terminal sequence similar to the fimbrial protein pilin annotated in the d. geothermalis dsm 11300 draft sequence. it also showed similarity to the ... | 2006 | 16980504 |
| repair dependent radiation survival: a stochastic model with euler gamma function solutions. | the probability of survival of cells or viruses exposed to various forms of radiation is expressed as a function of the probability that a given cell will receive a certain number of lethal damages, the average probability that each such damage is repairable, and an upper bound on the repair capacity of each cell. all lethal damages are presumed induced as a linear function of dose. the probability of survival is found to be the product of a single exponential, which reflects inactivation by unr ... | 2006 | 16985277 |
| the nmr structure of an internal loop from 23s ribosomal rna differs from its structure in crystals of 50s ribosomal subunits. | internal loops play an important role in structure and folding of rna and in recognition of rna by other molecules such as proteins and ligands. an understanding of internal loops with propensities to form a particular structure will help predict rna structure, recognition, and function. the structures of internal loops 5' 1009cuaag1013 3'/3' 1168gaagc1164 5' and 5' 998cuaag1002 3'/3' 1157gaagc1153 5' from helix 40 of the large subunit rrna in deinococcus radiodurans and escherichia coli, respec ... | 2006 | 17002278 |