| the kinetic mechanism of manganese-containing superoxide dismutase from deinococcus radiodurans: a specialized enzyme for the elimination of high superoxide concentrations. | deinococcus radiodurans (drad), a bacterium with an extraordinary capacity to tolerate high levels of ionizing radiation, produces only a manganese-containing superoxide dismutase (mnsod). as mnsod has been shown to remove superoxide radical with varying efficiency depending upon its cellular origin, a comparison of the drad mnsod efficiency with that of both human and escherichia coli mnsods was undertaken. pulse radiolysis studies demonstrate that, under identical ratios of enzyme to superoxid ... | 2008 | 18247479 |
| a novel oxyr sensor and regulator of hydrogen peroxide stress with one cysteine residue in deinococcus radiodurans. | in bacteria, oxyr is a peroxide sensor and transcription regulator, which can sense the presence of reactive oxygen species and induce antioxidant system. when the cells are exposed to h(2)o(2), oxyr protein is activated via the formation of a disulfide bond between the two conserved cysteine residues (c199 and c208). in deinococcus radiodurans, a previously unreported special characteristic of droxyr (dr0615) is found with only one conserved cysteine. dr0615 gene mutant is hypersensitive to h(2 ... | 2008 | 18270589 |
| protein oxidation: key to bacterial desiccation resistance? | for extremely ionizing radiation-resistant bacteria, survival has been attributed to protection of proteins from oxidative damage during irradiation, with the result that repair systems survive and function with far greater efficiency during recovery than in sensitive bacteria. here we examined the relationship between survival of dry-climate soil bacteria and the level of cellular protein oxidation induced by desiccation. bacteria were isolated from surface soils of the shrub-steppe of the us d ... | 2008 | 18273068 |
| lineage-specific amino acid substitutions in region 2 of the rna polymerase sigma subunit affect the temperature of promoter opening. | highly conserved amino acid residues in region 2 of the rna polymerase sigma subunit are known to participate in promoter recognition and opening. we demonstrated that nonconserved residues in this region collectively determine lineage-specific differences in the temperature of promoter opening. | 2008 | 18281402 |
| physiological and phylogenetic study of an ammonium-oxidizing culture at high nitrite concentrations. | oxidation of high-strength ammonium wastewater can lead to exceptionally high nitrite concentrations; therefore, the effect of high nitrite concentration (> 400 mm) was studied using an ammonium-oxidizing enrichment culture in a batch reactor. ammonium was fed to the reactor in portions of 40-150 mm until ammonium oxidation rates decreased and finally stopped. activity was restored by replacing half of the medium, while biomass was retained by a membrane. the ammonium-oxidizing population obtain ... | 2008 | 18289820 |
| analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers. | to assess soil bacterial diversity, pcr systems consisting of several slightly different reverse primers together with forward primer f968-gc were used along with subsequent denaturing gradient gel electrophoresis (dgge) or clone library analyses. in this study, a set of 13 previously used and novel reverse primers was tested with the canonical forward primer as to the dgge fingerprints obtained from grassland soil. analysis of these dgge profiles by gelcompar showed that they all fell into two ... | 2008 | 18310425 |
| junction ribonuclease: a ribonuclease hii orthologue from thermus thermophilus hb8 prefers the rna-dna junction to the rna/dna heteroduplex. | the genome of an extremely thermophilic bacterium, thermus thermophilus hb8, contains a single orf (open reading frame) encoding an rnase-hii-like sequence. despite the presence of significant amino acid sequence identities with rnase (ribonuclease) hii enzymes, the orf ttha0198 could not suppress the temperature-sensitive growth defect of an rnase-h-deficient escherichia coli mutant and the purified recombinant protein could not cleave an rna strand of an rna/dna heteroduplex, suggesting that t ... | 2008 | 18318663 |
| the phy domain is required for conformational stability and spectral integrity of the bacteriophytochrome from deinococcus radiodurans. | bacteriophytochrome from deinococcus radiodurans (drbphp) is a plant phytochrome homolog. to investigate the interaction of chromophore and protein structure, we purified recombinant drbphp and performed biochemical analyses. differences of apo- and holo-protein in electrophoretic properties in native gels and their susceptibility to trypsin indicate changes in both the conformation and surface topography of this protein as a result of chromophore assembly. furthermore, proteolysis to pr and pfr ... | 2008 | 18331835 |
| [construction of the gene drb0099 deleted mutant and adversity analysis in the extremely radioresistant bacterium deinococcus radiodurans]. | deinococcus radiodurans r1 has extraordinary resistance to radiation. drb0099 might play an important role in protecting the bacterium against radiation. to verify the inference, we deleted drb0099 and constructed the mutant. comparing with the wild type, the mutant grew more slowly in the beginning cultivation stage (0-16 h) under normal conditions. after being cultivated for 16 h, the mutant grew faster than the wild type. the biomass concentration of the wild type was always higher than that ... | 2008 | 18338577 |
| involvement of recq in the ultraviolet damage repair pathway in deinococcus radiodurans. | deinococcus radiodurans is a bacterium which can survive extremely dna damage. to investigate the relationship between recq and the ultraviolet radiation (uv) damage repair pathway, we created a four mutant strain by constructing recq knockout mutants in uvra1, uvra2, and uvse backgrounds. using the rpob/rif(r) system, we measured the mutation frequencies and rates in wild type, recq (mq), uvse uvra1 uvra2 (tnk006), and uvse uvra1 uvra2 recq (tq). we then isolated rif(r) mutants of these strains ... | 2008 | 18343459 |
| extreme resistance of bdelloid rotifers to ionizing radiation. | rotifers of class bdelloidea are common invertebrate animals with highly unusual characteristics, including apparently obligate asexuality, the ability to resume reproduction after desiccation at any life stage, and a paucity of transposable genetic elements of types not prone to horizontal transmission. we find that bdelloids are also extraordinarily resistant to ionizing radiation (ir). reproduction of the bdelloids adineta vaga and philodina roseola is much more resistant to ir than that of e ... | 2008 | 18362355 |
| a widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. | we have identified a highly conserved rna motif located upstream of genes encoding molybdate transporters, molybdenum cofactor (moco) biosynthesis enzymes, and proteins that utilize moco as a coenzyme. bioinformatics searches have identified 176 representatives in gamma-proteobacteria, delta-proteobacteria, clostridia, actinobacteria, deinococcus-thermus species and dnas from environmental samples. using genetic assays, we demonstrate that a moco rna in escherichia coli associated with the moco ... | 2008 | 18363797 |
| architecture of deinococcus geothermalis biofilms on glass and steel: a lectin study. | deinococcus geothermalis is resistant to chemical and physical stressors and forms tenuous biofilms in paper industry. the architecture of its biofilms growing on glass and on stainless acid proof steel was studied with confocal laser scanning microscopy and fluorescent lectins and nanobeads as in situ probes. hydrophobic nanobeads adhered to the biofilms but did not penetrate to biofilm interior. in contrast, the biofilms were readily permeable towards many different lectins. a skeletal network ... | 2008 | 18373677 |
| microbial community composition in soils of northern victoria land, antarctica. | biotic communities and ecosystem dynamics in terrestrial antarctica are limited by an array of extreme conditions including low temperatures, moisture and organic matter availability, high salinity, and a paucity of biodiversity to facilitate key ecological processes. recent studies have discovered that the prokaryotic communities in these extreme systems are highly diverse with patchy distributions. investigating the physical and biological controls over the distribution and activity of microbi ... | 2008 | 18373679 |
| involvement of a protein kinase activity inducer in dna double strand break repair and radioresistance of deinococcus radiodurans. | transgenic bacteria producing pyrroloquinoline quinone, a known cofactor for dehydrogenases and an inducer of a periplasmic protein kinase activity, show resistance to both oxidative stress and protection from nonoxidative effects of radiation and dna-damaging agents. deinococcus radiodurans r1 encodes an active pyrroloquinoline quinone synthase, and constitutive synthesis of pyrroloquinoline quinone occurred in wild-type bacteria. disruption of a genomic copy of pqqe resulted in cells that lack ... | 2008 | 18375565 |
| three-dimensional architecture of inorganic nanoarrays electrodeposited through a surface-layer protein mask. | transmission electron microscopy was used to analyze the three-dimensional (3d) architecture of cuprous oxide electrochemically deposited through the pores of the hexagonally packed intermediate surface-layer protein from deinococcus radiodurans sark. imaging at multiple tilt angles and averaging from five different samples allowed approximately 3 nm computed 3d reconstructions of the inorganic deposit and protein template. we show that the electrodeposition process used here was able to fully a ... | 2008 | 18376869 |
| microbe repelling coated stainless steel analysed by field emission scanning electron microscopy and physicochemical methods. | coating of stainless steel with diamond-like carbon or certain fluoropolymers reduced or almost eliminated adhesion and biofilm growth of staphylococcus epidermidis, deinococcus geothermalis, meiothermus silvanus and pseudoxanthomonas taiwanensis. these species are known to be pertinent biofilm formers on medical implants or in the wet-end of paper machines. field emission scanning electron microscopic analysis showed that staph. epidermidis, d. geothermalis and m. silvanus grew on stainless ste ... | 2008 | 18379832 |
| resistance of deinococcus radiodurans to mutagenesis is facilitated by pentose phosphate pathway in the muts1 mutant background. | muts1 is a key protein involved in mismatch repair system for ensuring fidelity of replication and recombination in deinococcus radiodurans. the zwf gene encodes glucose-6-phosphate dehydrogenase (g6pd) in the pentose phosphate (pp) pathway, which provides adequate metabolites as precursors of dna repair. in this study, muts1 and zwf were disrupted by homologous recombination. the zwf mutant (deltazwf) and the zwf/muts1 double mutant (deltazwf/muts1) were sensitive to ultraviolet (uv) light, h(2 ... | 2008 | 18389309 |
| translational regulation via l11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. | the thiopeptide class of antibiotics targets the gtpase-associated center (gac) of the ribosome to inhibit translation factor function. using x-ray crystallography, we have determined the binding sites of thiostrepton (thio), nosiheptide (nosi), and micrococcin (micro), on the deinococcus radiodurans large ribosomal subunit. the thiopeptides, by binding within a cleft located between the ribosomal protein l11 and helices 43 and 44 of the 23s rrna, overlap with the position of domain v of ef-g, t ... | 2008 | 18406324 |
| structure and function of the regulatory c-terminal hrdc domain from deinococcus radiodurans recq. | recq helicases are critical for maintaining genome integrity in organisms ranging from bacteria to humans by participating in a complex network of dna metabolic pathways. their diverse cellular functions require specialization and coordination of multiple protein domains that integrate catalytic functions with dna-protein and protein-protein interactions. the recq helicase from deinococcus radiodurans (drrecq) is unusual among recq family members in that it has evolved to utilize three 'helicase ... | 2008 | 18411208 |
| isolation of novel bacteria, including a candidate division, from geothermal soils in new zealand. | we examined bacterial diversity of three geothermal soils in the taupo volcanic zone of new zealand. phylogenetic analysis of 16s rrna genes recovered directly from soils indicated that the bacterial communities differed in composition and richness, and were dominated by previously uncultured species of the phyla actinobacteria, acidobacteria, chloroflexi, proteobacteria and candidate division op10. aerobic, thermophilic, organotrophic bacteria were isolated using cultivation protocols that invo ... | 2008 | 18422642 |
| complex oligomeric structure of a truncated form of ddra: a protein required for the extreme radiotolerance of deinococcus. | in order to preserve their genome integrity, organisms have developed elaborate tactics for genome protection and repair. the deinococcus radiodurans bacteria famous for their extraordinary tolerance toward high doses of radiations or long period of desiccation, possess some specific genes with unknown function which are related to their survival in such extreme conditions. among them, ddra is an orphan gene specific of deinococcus genomes. ddra, the product of this gene was suggested to be a co ... | 2008 | 18424274 |
| crystal structure of dfa0005 complexed with alpha-ketoglutarate: a novel member of the icl/pepm superfamily from alkali-tolerant deinococcus ficus. | the crystal structure of the dfa0005 protein complexed with alpha-ketoglutarate (akg) from an alkali-tolerant bacterium deinococcus ficus has been determined to a resolution of 1.62 a. the monomer forms an incomplete alpha7/beta8 barrel with a protruding alpha8 helix that interacts extensively with another subunit to form a stable dimer of two complete alpha8/beta8 barrels. the dimer is further stabilized by four glycerol molecules situated at the interface. one unique akg ligand binding pocket ... | 2008 | 18433062 |
| description of four novel psychrophilic, ionizing radiation-sensitive deinococcus species from alpine environments. | five psychrophilic bacterial strains were isolated from soil samples collected above the treeline of alpine environments. phylogenetic analysis based on 16s rrna gene sequences indicated that these organisms represent four novel species of the genus deinococcus; levels of sequence similarity to the type strains of recognized deinococcus species were in the range 89.3-94.7 %. strains po-04-20-132t, po-04-20-144, po-04-19-125t, me-04-01-32t and me-04-04-52t grew aerobically, with optimum growth at ... | 2008 | 18450723 |
| chromophore heterogeneity and photoconversion in phytochrome crystals and solution studied by resonance raman spectroscopy. | | 2008 | 18484576 |
| unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context. | the phosphoenolpyruvate phosphotransferase system (pts) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. the pts couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (pep) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme ii complexes which catalyze the uptake and phosphorylation of solutes. previous studies have suggested that the evolution of the constituents ... | 2008 | 18485189 |
| functional and structural characterization of dr_0079 from deinococcus radiodurans, a novel nudix hydrolase with a preference for cytosine (deoxy)ribonucleoside 5'-di- and triphosphates. | the genome of the extremely radiation resistant bacterium deinococcus radiodurans encodes 21 nudix hydrolases, of which only two have been characterized in detail. here we report the activity and crystal structure for dr_0079, the first nudix hydrolase observed to have a marked preference for cytosine ribonucleoside 5'-diphosphate (cdp) and cytosine ribonucleoside 5'-triphosphate (ctp). after cdp and ctp, the next most preferred substrates for dr_0079, with a relative activity of <50%, were the ... | 2008 | 18512963 |
| cloning, purification and characterization of a thermostable amylosucrase from deinococcus geothermalis. | amylosucrase is a transglucosidase that catalyses the synthesis of an amylose-type polymer from sucrose, an abundant agro-resource. here we describe a novel thermostable amylosucrase from the moderate thermophile deinococcus geothermalis (dgas). the dgas gene was cloned and expressed in escherichia coli. the encoded enzyme was purified and characterized. dgas displays a specific activity of 44 u mg(-1), an optimal temperature of 50 degrees c and a half-life of 26 h at 50 degrees c. moreover, it ... | 2008 | 18522649 |
| molecular characterization of the diversity and distribution of a thermal spring microbial community by using rrna and metabolic genes. | the diversity and distribution of a bacterial community from coffee pots hot spring, a thermal spring in yellowstone national park with a temperature range of 39.3 to 74.1 degrees c and ph range of 5.75 to 6.91, were investigated by sequencing cloned pcr products and quantitative pcr (qpcr) of 16s rrna and metabolic genes. the spring was inhabited by three aquificae genera--thermocrinis, hydrogenobaculum, and sulfurihydrogenibium--and members of the alpha-, beta-, and gammaproteobacteria, firmic ... | 2008 | 18539788 |
| high-resolution structure of the antibiotic resistance protein nima from deinococcus radiodurans. | many anaerobic human pathogenic bacteria are treated using 5-nitroimidazole-based (5-ni) antibiotics, a class of inactive prodrugs that contain a nitro group. the nitro group must be activated in an anaerobic one-electron reduction and is therefore dependent on the redox system in the target cells. antibiotic resistance towards 5-ni drugs is found to be related to the nim genes (nima, nimb, nimc, nimd, nime and nimf), which are proposed to encode a reductase that is responsible for converting th ... | 2008 | 18540048 |
| structure of deinococcus radiodurans tunicamycin-resistance protein (tmrd), a phosphotransferase. | the open-reading frame (orf) dr_1419 in the deinococcus radiodurans genome is annotated as a representative of the wide family of tunicamycin-resistance proteins as identified in a range of bacterial genomes. the d. radiodurans orf dr_1419 was cloned and expressed; the protein tmrd was crystallized and its x-ray crystal structure was determined to 1.95 a resolution. the structure was determined using single-wavelength anomalous diffraction with selenomethionine-derivatized protein. the refined s ... | 2008 | 18540055 |
| deinococcus radiodurans: what belongs to the survival kit? | deinococcus radiodurans, one of the most radioresistant organisms known to date, is able to repair efficiently hundreds of dna double- and single-strand breaks as well as other types of dna damages promoted by ionizing or ultraviolet radiation. we review recent discoveries concerning several aspects of radioresistance and survival under high genotoxic stress. we discuss different hypotheses and possibilities that have been suggested to contribute to radioresistance and propose that d. radioduran ... | 2008 | 18568848 |
| basal dna repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria. | ionizing-radiation-resistant bacteria (irrb) show a surprising capacity for adaptation to ionizing radiation and desiccation. positive darwinian selection is expected to play an important role in this trait, but no data are currently available regarding the role of positive adaptive selection in resistance to ionizing-radiation and tolerance of desiccation. we analyzed the four known genome sequences of irrb (deinococcus geothermalis, deinococcus radiodurans, kineococcus radiotolerans, and rubro ... | 2008 | 18570673 |
| structural principles from large rnas. | since the year 2000 a number of large rna three-dimensional structures have been determined by x-ray crystallography. structures composed of more than 100 nucleotide residues include the signal recognition particle rna, group i intron, the glms ribozyme, rnasep rna, and ribosomal rnas from haloarcula morismortui, escherichia coli, thermus thermophilus, and deinococcus radiodurans. these large rnas are constructed from the same secondary and tertiary structural motifs identified in smaller rnas b ... | 2008 | 18573090 |
| a novel serralysin metalloprotease from deinococcus radiodurans. | a hypothetical protein (dr2310) from the radiation resistant organism deinococcus radiodurans harbors highly conserved zn+2-binding (hexxh) domain and met-turn (svmsy), characteristic of the serralysin family of secreted metalloproteases from gram negative bacteria. deletion mutagenesis of dr2310 confirmed that the orf is expressed in deinococcus radiodurans as a secreted protease of 85 kda. biochemical analysis revealed dr2310 to be a ca+2 and zn+2-requiring metalloprotease. unique features suc ... | 2008 | 18590838 |
| analysis of rna cleavage by rna polymerases from escherichia coli and deinococcus radiodurans. | rna polymerase can both synthesize and cleave rna. both reactions occur at the same catalytic center containing two magnesium ions bound to three aspartic acid residues of the absolutely conserved nadfdgd motif of the rna polymerase beta subunit. we have demonstrated that rna polymerase from deinococcus radiodurans possesses much higher rate of intrinsic rna cleavage than rna polymerase from escherichia coli (the difference in the rates is about 15-fold at 20 degrees c). however, these rna polym ... | 2008 | 18620540 |
| advanced mass spectrometric methods for the rapid and quantitative characterization of proteomes. | progress is reviewed towards the development of a global strategy that aims to extend the sensitivity, dynamic range, comprehensiveness and throughput of proteomic measurements based upon the use of high performance separations and mass spectrometry. the approach uses high accuracy mass measurements from fourier transform ion cyclotron resonance mass spectrometry (fticr) to validate peptide 'accurate mass tags' (amts) produced by global protein enzymatic digestions for a specific organism, tissu ... | 2002 | 18628837 |
| isolation and characterization of deinococcus geothermalis t27, a slightly thermophilic and organic solvent-tolerant bacterium able to survive in the presence of high concentrations of ethyl acetate. | a solvent-tolerant, slightly thermophilic bacterium was isolated at 45 degrees c in the presence of toluene vapor provided as the sole carbon source. strain t27 was identified as deinococcus geothermalis t27. it could tolerate high concentrations of solvent provided as a nonaqueous layer (5% and 20%, v/v) to a cell suspension and had a remarkable ability to tolerate a broad range of solvents having log p(ow) values ranging from 5.6 of n-decane to as low as 0.7 of ethyl acetate. it was also able ... | 2008 | 18647360 |
| identification of pink-pigmented bacteria isolated from environmental water samples and their biofilm formation abilities. | sixty-seven strains of pink-pigmented bacteria, which were isolated from environmental water samples collected nationwide, were identified by partial 16s rdna sequence analysis. in addition, the biofilm formation ability of the isolates was experimentally investigated. we could identify only 2 strains at the species level: pedobacter roseus hs-38 and runella slithyformis hs-77. the results showed that of the strains tested, 22 strains (32.8%) were pedobacter spp., which was most frequently ident ... | 2008 | 18661678 |
| dna binding to recd: role of the 1b domain in sf1b helicase activity. | the molecular mechanism of superfamily 1balpha helicases remains unclear. we present here the crystal structure of the recd2 helicase from deinococcus radiodurans at 2.2-a resolution. the structure reveals the folds of the 1b and 2b domains of recd that were poorly ordered in the structure of the escherichia coli recbcd enzyme complex reported previously. the 2b domain adopts an sh3 fold which, although common in eukaryotes, is extremely rare in bacterial systems. in addition, the d. radiodurans ... | 2008 | 18668125 |
| the stable, functional core of ddra from deinococcus radiodurans r1 does not restore radioresistance in vivo. | ddra protein binds to and protects 3' dna ends and is essential for preserving the genome integrity of deinococcus radiodurans following treatment by gamma radiation in an environment lacking nutrients. limited proteolysis was used to identify a stable and functional protein core, designated ddra157, consisting of the first 157 residues of the protein. in vitro, the biochemical differences between wild-type and mutant proteins were modest. ddra exhibits a strong bias in binding dna with 3' exten ... | 2008 | 18676665 |
| extracellular proteome changes of deinococcus radiodurans under gamma-irradiation stress conditions. | to analysis the change of deinococcus radiodurans extracellular proteins recovering from gamma-irradiation, we examined extracellular proteome changes using two-dimensional polyacrylamide gel electrophoresis. twenty-six spots on the gel of irradiated sample were showed significant changes compared with spots on the control gel. using peptide mass fingerprinting via matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof-ms), 21 different proteins could be distingu ... | 2008 | 18680455 |
| biochemical characterization of two dna ligases from deinococcus radiodurans. | two genes encoding a nad(+)-dependent dna ligase (liga) and an atp-dependent dna ligase (ligb) were identified in the genome of the extremely radioresistant bacterium, deinococcus radiodurans (dr). the recombinant enzymes expressed in escherichia coli, were purified to homogeneity and characterized. the optimal temperature and ph value of the two dna ligases were 60 ( degrees )c and 7.0, respectively. their optimal concentration of mgcl(2) was 5mm. their half-lifes of heat inactivation at 100 ( ... | 2008 | 18680457 |
| isolation and identification of a thermophilic strain producing trehalose synthase from geothermal water in china. | a slightly thermophilic strain, cbs-01, producing trehalose synthase (tres), was isolated from geothermal water in this study. according to the phenotypic characteristics and phylogenetic analysis of the 16s rrna gene sequence, it was identified as meiothermus ruber. the trehalose synthase gene of meiothermus ruber cbs-01 was cloned by polymerase chain reaction and sequenced. the tres gene consisted of 2,895 nucleotides, which specified a 964-amino-acid protein. this novel tres catalyzed reversi ... | 2008 | 18685210 |
| synonymous codon usage bias dependent on local nucleotide context in the class deinococci. | to study the evolution of mutation biased synonymous codon usage, we examined nucleotide co-occurrence patterns in the deinococcus radiodurans, d. geothermalis, and thermus thermophilus genomes for nucleotide replacement dependent on the surrounding nucleotide context. nucleotides on the third codon site were found to be strongly correlated with nucleotide sites at most six nucleotides away in all three species, where abundance patterns were dependent on whether two nucleotides share the same pu ... | 2008 | 18696025 |
| role of premature stop codons in bacterial evolution. | when the stop codons tga, taa, and tag are found in the second and third reading frames of a protein-encoding gene, they are considered premature stop codons (psc). deinococcus radiodurans disproportionately favored tga more than the other two triplets as a psc. the tga triplet was also found more often in noncoding regions and as a stop codon, though the bias was less pronounced. we investigated this phenomenon in 72 bacterial species with widely differing chromosomal gc contents. although tga ... | 2008 | 18708500 |
| quantitative contributions of bacteria and of deinococcus geothermalis to deposits and slimes in paper industry. | deinococcus geothermalis has frequently been isolated from pink colored deposits of paper industry processes. laboratory studies have shown that d. geothermalis is capable of forming on nonliving surfaces patchy biofilms that are resistant to adverse agents such as extreme ph, desiccation, solubilising detergents and biocides. this study was done to quantitatively assess the role of d. geothermalis as a biofouler in paper industry. colored deposits were collected from 24 european and north ameri ... | 2008 | 18726625 |
| the oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect trna positioning. | the oxazolidinones represent the first new class of antibiotics to enter into clinical usage within the past 30 years, but their binding site and mechanism of action has not been fully characterized. we have determined the crystal structure of the oxazolidinone linezolid bound to the deinococcus radiodurans 50s ribosomal subunit. linezolid binds in the a site pocket at the peptidyltransferase center of the ribosome overlapping the aminoacyl moiety of an a-site bound trna as well as many clinical ... | 2008 | 18757750 |
| crystal structure of escherichia coli rnk, a new rna polymerase-interacting protein. | sequence-based searches identified a new family of genes in proteobacteria, named rnk, which shares high sequence similarity with the c-terminal domains of the gre factors (grea and greb) and the thermus/deinococcus anti-gre factor gfh1. we solved the x-ray crystal structure of escherichia coli regulator of nucleoside kinase (rnk) at 1.9 a resolution using the anomalous signal from the native protein. the rnk structure strikingly resembles those of e. coli grea and greb and thermus gfh1, all of ... | 2008 | 18760284 |
| factors accelerating pyrimidine production in deinococcus radiophilus. | in studying the pyrimidine synthesising pathway in deinococcus radiophilus two instances of anomalous behaviour were observed. one was the strikingly different results obtained for two types of assay for carbamoyl phosphate synthetase. both depend on the fixation of 14c from the substrate bicarbonate to give radioactive products. in the coupled assay the carbamoyl phosphate product of the enzyme is converted to carbamoyl aspartate in the presence of aspartate and aspartate transcarbamoylase. in ... | 2009 | 18807014 |
| deinococcus aquaticus sp. nov., isolated from fresh water, and deinococcus caeni sp. nov., isolated from activated sludge. | the taxonomic positions of two environmental isolates from south korea were established using a combination of genotypic and phenotypic data. the organisms, designated pb314(t) and ho-08(t), were gram-negative, rod-shaped and non-spore-forming and had chemotaxonomic properties consistent with their classification in the genus deinococcus 16s rrna gene tree, the highest sequence similarities being shown to the type strains of deinococcus grandis (96.3-96.7 %) and deinococcus indicus (96.3-96.4 %) ... | 2008 | 18842854 |
| structure of the stress response protein dr1199 from deinococcus radiodurans: a member of the dj-1 superfamily. | the expression level of protein dr1199 is observed to increase considerably in the radio-resistant bacterium deinococcus radiodurans following irradiation. this protein belongs to the dj-1 superfamily, which includes proteins with diverse functions, such as the archaeal proteases phpi and pfpi, the bacterial chaperone hsp31 and hyperosmotic stress protein yhbo, and the human parkinson's disease-related protein dj-1. all members of the superfamily are oligomeric, and the oligomerization interface ... | 2008 | 18850720 |
| identification of a dna processing complex from deinococcus radiodurans. | an efficient dna strand break repair contributes to the radioresistance of deinococcus radiodurans, which harbors the dna repair pathways nearly identical to escherichia coli. the molecular mechanisms of these proteins functioning in 2 diverse classes of bacteria seem to be different. the macromolecular interactions and formation of multiprotein complexes in vivo have gained significant importance in explaining the mechanism of the complex cellular processes. here, we report the identification o ... | 2008 | 18923546 |
| the fungal phytochrome fpha from aspergillus nidulans. | the red light-sensing photoreceptor fpha from aspergillus nidulans is involved in the regulation of developmental processes in response to light. here we present extended biochemical and spectroscopic characterization of recombinant fpha using a synthetic gene with host-adapted codon usage. the recombinant photosensory domain fphan753 was shown to display all features of a bona fide phytochrome. it covalently binds biliverdin as chromophore and undergoes red/far-red light-inducible photoconversi ... | 2008 | 18931394 |
| deinococcus radiodurans ppri switches on dna damage response and cellular survival networks after radiation damage. | preliminary findings indicate that ppri is a regulatory protein that stimulates transcription and translation of reca and other dna repair genes in response to dna damage in the extremely radioresistant bacterium deinococcus radiodurans. to define the repertoire of proteins regulated by ppri and investigate the in vivo regulatory mechanism of ppri in response to gamma radiation, we performed comparative proteomics analyses on wild type (r1) and a ppri knock-out strain (yr1) under conditions of i ... | 2009 | 18953020 |
| a major clade of prokaryotes with ancient adaptations to life on land. | evolutionary trees of prokaryotes usually define the known classes and phyla but less often agree on the relationships among those groups. this has been attributed to the effects of horizontal gene transfer, biases in sequence change, and large evolutionary distances. furthermore, higher level clades of prokaryote phyla rarely are supported by information from ecology and cell biology. nonetheless, common patterns are beginning to emerge as larger numbers of species are analyzed with sophisticat ... | 2009 | 18988685 |
| tracking the influence of long-term chromium pollution on soil bacterial community structures by comparative analyses of 16s rrna gene phylotypes. | bacterial community structures of highly chromium-polluted industrial landfill sites (g1 and g2) and a nearby control site (g3) were assessed using cultivation-dependent and cultivation-independent analyses. sequencing of 16s rrna genes discerned a total of 141 distinct operational taxonomic units (otus). twelve different bacterial phyla were represented amongst 35, 34 and 72 different bacterial genera retrieved from sites g1, g2 and g3, respectively. the bacterial community of site g1 consisted ... | 2009 | 18996186 |
| recr-mediated modulation of recf dimer specificity for single- and double-stranded dna. | recf pathway proteins play an important role in the restart of stalled replication and dna repair in prokaryotes. following dna damage, recf, recr, and reco initiate homologous recombination (hr) by loading of the reca recombinase on single-stranded (ss) dna, protected by ssdna-binding protein. the specific role of recf in this process is not well understood. previous studies have proposed that recf directs the recor complex to boundaries of damaged dna regions by recognizing single-stranded/dou ... | 2009 | 19017635 |
| high diversity of cultivable heterotrophic bacteria in association with cyanobacterial water blooms. | cyanobacterial mass occurrences (water blooms) cause ecological, economic and health problems worldwide. still, little is known about heterotrophic bacteria associated with cyanobacteria and the interactions between those organisms. we isolated 460 bacterial strains from more than 40 lakes and rivers (151 samples), baltic sea (32 samples) and treated drinking water of seven treatment plants (29 samples). the water bodies and the raw water of the treatment plants were frequently dominated by high ... | 2009 | 19020559 |
| the enzymology of nitric oxide in bacterial pathogenesis and resistance. | mammalian noss (nitric oxide synthases) are haem-based monoxygenases that oxidize the amino acid arginine to the intracellular signal and protective cytotoxin nitric oxide (no). certain strains of mostly gram-positive bacteria contain homologues of the mammalian nos catalytic domain that can act as noss when suitable reductants are supplied. crystallographic analyses of bacterial noss, with substrates and haem-ligands, have disclosed important features of assembly and active-centre chemistry, bo ... | 2008 | 19021514 |
| masdet-a fast and user-friendly multiplatform software for mass determination by dark-field electron microscopy. | electron microscopy has been used to measure the mass of biological nanoparticles since the early 60s, and is the only way to obtain the mass of large structures or parameters such as the mass-per-length of filaments. the ability of this method to sort heterogeneous samples both in terms of mass and shape promises to make it a key tool for proteomics down to the single cell level. a new multiplatform software package, masdet, that can be run under matlab or as a standalone program is described. ... | 2009 | 19041401 |
| carotenoid 3',4'-desaturase is involved in carotenoid biosynthesis in the radioresistant bacterium deinococcus radiodurans. | deinococcus radiodurans strain r1 synthesizes deinoxanthin, a unique carotenoid product, which contributes to cell resistance following various stresses. the biosynthetic pathway of deinoxanthin is unclear, although several enzymes are presumed to be involved. the gene (dr2250) predicted by gene homologue analysis to encode carotenoid 3',4'-desaturase (crtd) was deleted to investigate its function. a mutant deficient in the gene homologue of crtlm (dr0801) was also constructed to verify the cata ... | 2008 | 19047737 |
| survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of kineococcus radiotolerans srs30216. | kineococcus radiotolerans srs30216 was isolated from a high-level radioactive environment at the savannah river site (srs) and exhibits gamma-radiation resistance approaching that of deinococcus radiodurans. the genome was sequenced by the u.s. department of energy's joint genome institute which suggested the existence of three replicons, a 4.76 mb linear chromosome, a 0.18 mb linear plasmid, and a 12.92 kb circular plasmid. southern hybridization confirmed that the chromosome is linear. the k. ... | 2008 | 19057647 |
| deinococcus aquatilis sp. nov., isolated from water. | a pale-pink strain (ccug 53370(t)) from water was investigated by a polyphasic taxonomic approach. the cells stained gram-positive and were rod-shaped and non-spore-forming. analyses using the 16s rrna gene sequence of the isolate showed that the organism belongs to the genus deinococcus, with the highest sequence similarities to the type strains of deinococcus ficus (94.4 %), deinococcus navajonensis (94.3 %) and deinococcus mumbaiensis (94.3 %). chemotaxonomic data revealed that ccug 53370(t) ... | 2008 | 19060062 |
| time-resolved binding of azithromycin to escherichia coli ribosomes. | azithromycin is a semisynthetic derivative of erythromycin that inhibits bacterial protein synthesis by binding within the peptide exit tunnel of the 50s ribosomal subunit. nevertheless, there is still debate over what localization is primarily responsible for azithromycin binding and as to how many molecules of the drug actually bind per ribosome. in the present study, kinetic methods and footprinting analysis are coupled together to provide time-resolved details of the azithromycin binding pro ... | 2009 | 19071138 |
| molecular bacterial diversity and distribution in waste from a steel plant. | we characterized the bacterial diversity of newly produced steelmaking wastes (npsw) and steelmaking wastes deposited (swd) in a restricted land area, generated by the siderurgic industry, using the 16s rdna clone library approach. a total of 212 partial-length sequences were analyzed, revealing 123 distinct operational taxonomic units (otus) determined by the dotur program to 97% sequence similarity. phylogenetic analysis of bacterial 16s rdna sequences from the npsw and swd libraries demonstra ... | 2008 | 19096454 |
| structural basis for cross-resistance to ribosomal ptc antibiotics. | clinically relevant antibiotics that target the ribosomal peptidyl transferase center (ptc), a highly conserved ribosomal region, exert their inhibitory action by exploiting the flexibility of ptc nucleotides, which trigger modulations of the shape of the antibiotic binding pocket. resistance to these antibiotics was observed clinically and in vitro. based on the crystal structures of the large ribosomal subunit from eubacterium suitable to represent pathogens in complex with these antibiotics, ... | 2008 | 19098107 |
| the subcellular distribution of an rna quality control protein, the ro autoantigen, is regulated by noncoding y rna binding. | the ro autoantigen is a ring-shaped rna-binding protein that binds misfolded rnas in nuclei and is proposed to function in quality control. in the cytoplasm, ro binds noncoding rnas, called y rnas, that inhibit access of ro to other rnas. ro also assists survival of mammalian cells and at least one bacterium after uv irradiation. in mammals, ro undergoes dramatic localization changes after uv irradiation, changing from mostly cytoplasmic to predominantly nuclear. here, we report that a second ro ... | 2009 | 19116308 |
| an initial characterization of the mercury resistance (mer) system of the thermophilic bacterium thermus thermophilus hb27. | the evolutionary origin of the broadly distributed mer system, which plays an important role in mercury detoxification and biogeochemistry, is presently unknown. the phylum deinococcus/thermus was found to be one of the deepest-branching bacterial lineage to have a homolog of mera, which specifies reduction of ionic to elemental mercury, and the mercuric reductase (mera) of thermus thermophilus hb27 was found to be basal to all bacterial mera when this protein's phylogeny was constructed. a mera ... | 2009 | 19120462 |
| molecular dynamics simulations of the chromophore binding site of deinococcus radiodurans bacteriophytochrome using new force field parameters for the phytochromobilin chromophore. | the conformational flexibility of the tetrapyrrolic phytochromobilin (pphib) chromophore of the bacteriophytochrome deinococcus radiodurans (drcbd) in the pr state has been investigated by molecular dynamics simulations. because these simulations require accurate force field parameters for the prosthetic group, in the present work we developed new empirical force field parameters for the pphib molecule that are compatible with the charmm22 force field for proteins. for this reason, the new force ... | 2009 | 19123828 |
| deinococcus aquiradiocola sp. nov., isolated from a radioactive site in japan. | a gamma- and uv-radiation-tolerant, pale-pink strain (tdma-uv53t) was isolated from a freshwater sample collected at misasa (tottori, japan), after exposure of the water sample to uv radiation. the cells stained gram-positive and were non-motile, rod-shaped and non-spore-forming. the dna g+c content of the strain was 69.1 mol%. phylogenetic analysis based on 16s rrna gene sequences indicated that strain tdma-uv53t belongs to the genus deinococcus, the highest sequence similarities being found wi ... | 2009 | 19126739 |
| high cell density production of deinococcus radiodurans under optimized conditions. | deinococcus radiodurans is a bacterium being investigated for mechanisms of extreme radiation resistance and for bioremediation of environmental radioactive waste sites. in both fundamental and applied research settings, methods for large-scale production of d. radiodurans are needed. in this study, a systematic investigation was carried out to optimize d. radiodurans production at the 20-l fermentor scale. in defined medium, the phosphate buffer typically used was found to be inhibitory to d. r ... | 2009 | 19137334 |
| the unique branching patterns of deinococcus glycogen branching enzymes are determined by their n-terminal domains. | glycogen branching enzymes (gbe) or 1,4-alpha-glucan branching enzymes (ec 2.4.1.18) introduce alpha-1,6 branching points in alpha-glucans, e.g., glycogen. to identify structural features in gbes that determine their branching pattern specificity, the deinococcus geothermalis and deinococcus radiodurans gbe (gbe(dg) and gbe(dr), respectively) were characterized. compared to other gbes described to date, these deinococcus gbes display unique branching patterns, both transferring relatively short ... | 2009 | 19139240 |
| crystal structure of the irre protein, a central regulator of dna damage repair in deinococcaceae. | deinococcaceae are famous for their extreme radioresistance. transcriptome analysis in deinococcus radiodurans revealed a group of genes up-regulated in response to desiccation and ionizing radiation. irre, a novel protein initially found in d. radiodurans, was shown to be a positive regulator of some of these genes. deinococcus deserti irre is able to restore radioresistance in a d. radiodurans deltairre mutant. the d. deserti irre crystal structure reveals a unique combination of three domains ... | 2009 | 19150362 |
| functional annotation and three-dimensional structure of dr0930 from deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. | dr0930, a member of the amidohydrolase superfamily in deinococcus radiodurans, was cloned, expressed, and purified to homogeneity. the enzyme crystallized in the space group p3121, and the structure was determined to a resolution of 2.1 a. the protein folds as a (beta/alpha)7beta-barrel, and a binuclear metal center is found at the c-terminal end of the beta-barrel. the purified protein contains a mixture of zinc and iron and is intensely purple at high concentrations. the purple color was deter ... | 2009 | 19159332 |
| residues clustered in the light-sensing knot of phytochrome b are necessary for conformer-specific binding to signaling partner pif3. | the bhlh transcription factor, phytochrome interacting factor 3 (pif3), interacts specifically with the photoactivated, pfr, form of arabidopsis phytochrome b (phyb). this interaction induces pif3 phosphorylation and degradation in vivo and modulates phyb-mediated seedling deetiolation in response to red light. to identify missense mutations in the phyb n-terminal domain that disrupt this interaction, we developed a yeast reverse-hybrid screen. fifteen individual mutations identified in this scr ... | 2009 | 19165330 |
| a new perspective on radiation resistance based on deinococcus radiodurans. | in classical models of radiation toxicity, dna is the molecule that is most affected by ionizing radiation (ir). however, recent data show that the amount of protein damage caused during irradiation of bacteria is better related to survival than to dna damage. in this opinion article, a new model is presented in which proteins are the most important target in the hierarchy of macromolecules affected by ir. a first line of defence against ir in extremely radiation-resistant bacteria might be the ... | 2009 | 19172147 |
| ribosomal proteins of deinococcus radiodurans: their solvent accessibility and reactivity. | the structure of proteins in native ribosomes from deinococcus radiodurans r1 was probed by s-methylthioacetimidate (smta) modification of amino groups. the extent of protein labeling was quantified using top down methods, and modified positions were identified using bottom up experiments. each protein's reactivity was predicted by examination of the crystal structures of the d. radiodurans 50s subunit and the t. thermophilus hb8 30s subunit. the close phylogenetic relation between d. radioduran ... | 2009 | 19178299 |
| characterization in vitro and in vivo of the dna helicase encoded by deinococcus radiodurans locus dr1572. | deinococcus radiodurans survives extremely high doses of ionizing and ultraviolet radiation and treatment with various dna-damaging chemicals. as an effort to identify and characterize proteins that function in dna repair in this organism, we have studied the protein encoded by locus dr1572. this gene is predicted to encode a superfamily i dna helicase, except that genome sequencing indicated that it has a one-base frameshift and would not encode a complete helicase. we have cloned the gene from ... | 2009 | 19179120 |
| sustainable and practical degradation of intact chicken feathers by cultivating a newly isolated thermophilic meiothermus ruber h328. | the sustainable and practical degradation of intact chicken feathers by a newly isolated thermophilic bacterium meiothermus ruber h328 was presented with extensive data. aerobic cultivation with moderately thermophilic strain h328 at 55 degrees c for 6 days led to the apparently complete decay of the truly intact feathers and provided 1.89 mmol free amino acids and 7.32 mmol acid-hydrolyzed amino acids from 50 ml of culture containing 3% (w/v) intact chicken feathers. the amino acid components i ... | 2009 | 19194700 |
| deinococcus mumbaiensis shashidhar and bandekar 2006 is a later heterotypic synonym of deinococcus ficus lai et al. 2006. | deinococcus mumbaiensis dsm 17424(t) was compared with deinococcus ficus cc-fr2-10(t) to clarify the taxonomic relationship between the two species. 16s rrna gene sequence comparisons demonstrated that these strains share 99.5 % sequence similarity. investigation of fatty acid patterns and substrate utilization profiles displayed no striking differences between the type strains of the two species. dna-dna hybridizations between the two strains showed 75.4 % (76.6 %) relatedness. therefore, the r ... | 2009 | 19196779 |
| irre, a global regulator of extreme radiation resistance in deinococcus radiodurans, enhances salt tolerance in escherichia coli and brassica napus. | globally, about 20% of cultivated land is now affected by salinity. salt tolerance is a trait of importance to all crops in saline soils. previous efforts to improve salt tolerance in crop plants have met with only limited success. bacteria of the genus deinococcus are known for their ability to survive highly stressful conditions, and therefore possess a unique pool of genes conferring extreme resistance. in deinococcus radiodurans, the irre gene encodes a global regulator responsible for extre ... | 2009 | 19204796 |
| tightening the knot in phytochrome by single-molecule atomic force microscopy. | a growing number of proteins have been shown to adopt knotted folds. yet the biological roles and biophysical properties of these knots remain poorly understood. we used protein engineering and atomic force microscopy to explore the single-molecule mechanics of the figure-eight knot in the chromophore-binding domain of the red/far-red photoreceptor, phytochrome. under load, apo phytochrome unfolds at forces of approximately 47 pn, whereas phytochrome carrying its covalently bound tetrapyrrole ch ... | 2009 | 19217867 |
| identification of pprm: a modulator of the ppri-dependent dna damage response in deinococcus radiodurans. | deinococcus radiodurans possesses a dna damage response mechanism that acts via the ppri protein to induce reca and ppra proteins, both of which are necessary in conferring extreme radioresistance. in an effort to further delineate the nature of the dna damage response mechanism in d. radiodurans, we set out to identify novel components of the ppri-dependent signal transduction pathway in response to radiation stress. here we demonstrate the discovery of a novel regulatory protein, pprm (a modul ... | 2009 | 19242651 |
| the family x dna polymerase from deinococcus radiodurans adopts a non-standard extended conformation. | deinococcus radiodurans is an extraordinarily radioresistant bacterium that is able to repair hundreds of radiation-induced double-stranded dna breaks. one of the players in this pathway is an x family dna polymerase (polx(dr)). deletion of polx(dr) has been shown to decrease the rate of repair of double-stranded dna breaks and increase cell sensitivity to gamma-rays. a 3'-->5' exonuclease activity that stops cutting close to dna loops has also been demonstrated. the present crystal structure of ... | 2009 | 19251692 |
| biochemical features and functional implications of the rna-based t-box regulatory mechanism. | the t-box mechanism is a common regulatory strategy used for modulating the expression of genes of amino acid metabolism-related operons in gram-positive bacteria, especially members of the firmicutes. t-box regulation is usually based on a transcription attenuation mechanism in which an interaction between a specific uncharged trna and the 5' region of the transcript stabilizes an antiterminator structure in preference to a terminator structure, thereby preventing transcription termination. alt ... | 2009 | 19258532 |
| q&a: poetry in the genes. interview by krista zala. | | 2009 | 19262657 |
| the complete genome and proteome of laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. | laribacter hongkongensis is a newly discovered gram-negative bacillus of the neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. the complete genome sequence of l. hongkongensis hlhk9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with g+c content of 62.35%. genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish ... | 2009 | 19283063 |
| extreme genome repair. | slade et al. (2009) describe in this issue how the genome of the bacterium deinococcus radiodurans gets reassembled after being shattered by high-dose radiation. in contrast to the extreme nature of the damage, the steps of repair appear surprisingly ordinary. so, why can't all organisms carry out extreme genome repair? | 2009 | 19303843 |
| recombination and replication in dna repair of heavily irradiated deinococcus radiodurans. | deinococcus radiodurans' extreme resistance to ionizing radiation, desiccation, and dna-damaging chemicals involves a robust dna repair that reassembles its shattered genome. the repair process requires diploidy and commences with an extensive exonucleolytic erosion of dna fragments. liberated single-stranded overhangs prime strand elongation on overlapping fragments and the elongated complementary strands reestablish chromosomal contiguity by annealing. we explored the interdependence of the dn ... | 2009 | 19303848 |
| deinococcus xinjiangensis sp. nov., isolated from desert soil. | a gram-positive-staining, spherical-shaped and faintly pink-pigmented bacterial strain, x-82(t), was isolated from soil samples collected from a desert in xinjiang, china. the organism was found to be resistant to uv radiation but sensitive to gamma radiation and desiccation. the optimum growth ph, nacl concentration and temperature were ph 7.0, 0-1 % nacl and 30 degrees c. phylogenetic analysis based on the 16s rrna gene sequence indicated that strain x-82(t) is member of a novel species belong ... | 2009 | 19329593 |
| deciphering peculiar protein-protein interacting modules in deinococcus radiodurans. | interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (irrb) might be a part of the answer to the question as to how irrb, particularly deinococcus radiodurans r1 (deira), resist ionizing radiation. here, using the database of interacting proteins (dip) and the protein structural interactome (psi)-base server for psi map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in deira and other irrb, but which are abse ... | 2009 | 19356244 |
| the chromophore structure of the cyanobacterial phytochrome cph1 as predicted by time-dependent density functional theory. | the uv-vis absorption spectra of the photoreceptor chromophores biliverdin (bv) in the zzzssa conformation and the phycocyanobilin (pcb) with conformations zzzssa and zzzasa have been investigated by means of time-dependent density functional theory (td-dft) with a polarized continuum model. the three systems are studied in different conditions to include protonation, solvation- and protein-environmental effects on gas phase and available x-ray structures. the crystal structures of bv in bacteri ... | 2008 | 19368024 |
| structural and mutational analyses of deinococcus radiodurans uvra2 provide insight into dna binding and damage recognition by uvras. | uvra proteins are key actors in dna damage repair and play an essential role in prokaryotic nucleotide excision repair (ner), a pathway that is unique in its ability to remove a broad spectrum of dna lesions. understanding the dna binding and damage recognition activities of the uvra family is a critical component for establishing the molecular basis of this process. here we report the structure of the class ii uvra2 from deinococcus radiodurans in two crystal forms. these structures, coupled wi ... | 2009 | 19368888 |
| alliance of proteomics and genomics to unravel the specificities of sahara bacterium deinococcus deserti. | to better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, deinococcus deserti vcd115, isolated from sahara surface sand. its genome consists of a 2.8-mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. from the large corpus of ms/ms spectra recorded, 1,348 proteins w ... | 2009 | 19370165 |
| synthesis of nitric oxide by the nos-like protein from deinococcus radiodurans: a direct role for tetrahydrofolate. | genes encoding for proteins with high sequence homology to the heme-containing, oxygenase domain of mammalian nitric oxide synthase (nos) have been identified in a number of bacteria. many of these species of bacteria do not contain the genes that encode for the synthetic machinery to produce tetrahydrobiopterin (h(4)b), a cofactor of nos required for no synthesis. these bacteria have the genes for the synthesis of tetrahydrofolate (h(4)f) which contains the redox-active pteridine ring of h(4)b. ... | 2009 | 19388666 |
| a perfect genome annotation is within reach with the proteomics and genomics alliance. | high-throughput identification of proteins and their accurate partial sequencing by shotgun nanolc-ms/ms are now feasible for any cellular model at a full genomic scale. proteogenomics is the integration of these data with the genome. mining microbial proteomes allows validation of predicted orphan genes and correction of genome annotation errors such as discovery of unannotated genes, reversal of reading frames and identification of translational start sites, stop codon read-throughs or program ... | 2009 | 19410500 |
| iso-superoxide dismutase in deinococcus grandis, a uv resistant bacterium. | deinococcus grandis possesses two types of superoxide dismutase (sod, e. c. 1.15.1.1.) that show distinct electrophoretic behavior, one that migrates slowly and the other that migrates rapidly (sod-1 and sod-2, respectively). in this study, sod-1 was uniformly and abundantly detected, regardless of growth phase, whereas sod-2 was not detected during early growth, but was detectable from the exponential growth phase. in addition, a substantial increase in sod-2 was observed in cells that were tre ... | 2009 | 19412601 |
| diversity of 23s rrna genes within individual prokaryotic genomes. | the concept of ribosomal constraints on rrna genes is deduced primarily based on the comparison of consensus rrna sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rrna operons. | 2009 | 19415112 |
| mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. | visibly fluorescent proteins (fps) from jellyfish and corals have revolutionized many areas of molecular and cell biology, but the use of fps in intact animals, such as mice, has been handicapped by poor penetration of excitation light. we now show that a bacteriophytochrome from deinococcus radiodurans, incorporating biliverdin as the chromophore, can be engineered into monomeric, infrared-fluorescent proteins (ifps), with excitation and emission maxima of 684 and 708 nm, respectively; extincti ... | 2009 | 19423828 |