| a novel carotenoid 1,2-hydratase (cruf) from two species of the non-photosynthetic bacterium deinococcus. | a novel carotenoid 1,2-hydratase (cruf) responsible for the c-1',2' hydration of gamma-carotene was identified in the non-photosynthetic bacteria deinococcus radiodurans r1 and deinococcus geothermalis dsm 11300. gene expression and disruption experiments demonstrated that dr0091 and dgeo2309 encode cruf in d. radiodurans and d. geothermalis, respectively. their homologues were also found in the genomes of cyanobacteria, and exhibited little homology to the hydroxyneurosporene synthase (crtc) pr ... | 2009 | 19443548 |
| recx is involved in the switch between dna damage response and normal metabolism in d. radiodurans. | apart from inhibiting reca activity through protein-protein interactions, deinococcus radiodurans recx inhibits the expression of reca and two other anti-oxidant proteins. to identify the repertoire of proteins regulated by recx, comparative proteomic studies were undertaken on a wild-type strain (r1) and recx null mutant (recx(-)). two-dimensional electrophoresis followed by maldi-tof identification revealed 35 differentially expressed proteins, including 12 up-regulated and 23 down-regulated p ... | 2009 | 19443693 |
| antioxidants used by deinococcus radiodurans and implications for antioxidant drug discovery. | | 2009 | 19444250 |
| [bacterial diversity of disused thermal vents in tibetan yangbajing region]. | to study the bacterial diversity in sediment and water from two disused thermal vents in yangbajing, tibet, china. | 2009 | 19445178 |
| salt shield: intracellular salts provide cellular protection against ionizing radiation in the halophilic archaeon, halobacterium salinarum nrc-1. | the halophilic archaeon halobacterium salinarum nrc-1 was used as a model system to investigate cellular damage induced by exposure to high doses of ionizing radiation (ir). oxidative damages are the main lesions from ir and result from free radicals production via radiolysis of water. this is the first study to quantify dna base modification in a prokaryote, revealing a direct relationship between yield of dna lesions and ir dose. most importantly, our data demonstrate the significance of dna r ... | 2009 | 19452594 |
| a conserved motif of vertebrate y rnas essential for chromosomal dna replication. | noncoding y rnas are required for the reconstitution of chromosomal dna replication in late g1 phase template nuclei in a human cell-free system. y rna genes are present in all vertebrates and in some isolated nonvertebrates, but the conservation of y rna function and key determinants for its function are unknown. here, we identify a determinant of y rna function in dna replication, which is conserved throughout vertebrate evolution. vertebrate y rnas are able to reconstitute chromosomal dna rep ... | 2009 | 19474146 |
| enzymatic synthesis of salicin glycosides through transglycosylation catalyzed by amylosucrases from deinococcus geothermalis and neisseria polysaccharea. | amylosucrase (asase, ec 2.4.1.4) is a member of family 13 of the glycoside hydrolases that catalyze the synthesis of an alpha-(1-->4)-linked glucan polymer from sucrose instead of an expensive activated sugar, such as adp- or udp-glucose. transglycosylation reactions mediated by the asases of deinococcus geothermalis (dgas) and neisseria polysaccharea (npas) were applied to the synthesis of salicin glycosides with sucrose serving as the glucopyranosyl donor and salicin as the acceptor molecule. ... | 2009 | 19482267 |
| radiation resistance of deinococcus radiodurans r1 with respect to growth phase. | deinococcus species exhibit an extraordinary ability to withstand ionizing radiation (ir). most of the studies on radiation resistance have been carried out with exponential phase cells. the studies on radiation resistance of deinococcus radiodurans r1 with respect to different phases of growth showed that late stationary phase cells of d. radiodurans r1 were fourfold more sensitive to ir and heat as compared with exponential or early stationary phase cells. the increased sensitivity of d. radio ... | 2009 | 19490129 |
| mechanistic basis of 5'-3' translocation in sf1b helicases. | superfamily 1b (sf1b) helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. however, structural analyses to date have focused on how sf1a helicases achieve 3'-5' movement along nucleic acids. we present crystal structures of the complex between the sf1b helicase recd2 from deinococcus radiodurans and ssdna in the presence and absence of an atp analog. these snapshots of the reaction pathway reveal a nucleotide binding-induced c ... | 2009 | 19490894 |
| [molecular basis of the conscious and eternal life]. | | 2009 | 19492522 |
| mechanism for attenuation of dna binding by marr family transcriptional regulators by small molecule ligands. | members of the multiple antibiotic resistance regulator (marr) family control gene expression in a variety of metabolic processes in bacteria and archaea. hypothetical uricase regulator (hucr), which belongs to the ligand-responsive branch of the marr family, regulates uricase expression in deinococcus radiodurans by binding a shared promoter region between uricase and hucr genes. we show here that hucr responds only to urate and, to a lesser extent, to xanthine by attenuated dna binding, compar ... | 2009 | 19501097 |
| deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium. | a gram-positive, non-motile, spherical, red-pigmented and facultatively anaerobic bacterium, designated strain i-0(t), was isolated from a sand sample of the gobi desert in xinjiang autonomous region, china. phylogenetic analysis based on 16s rrna gene sequences indicated that this isolate represents a novel member of the genus deinococcus, with low sequence similarities (<94 %) to recognized deinococcus species. the major cellular fatty acids were c(16 : 1)omega7c and c(16 : 0). its polar lipid ... | 2009 | 19502345 |
| directed evolution of ionizing radiation resistance in escherichia coli. | we have generated extreme ionizing radiation resistance in a relatively sensitive bacterial species, escherichia coli, by directed evolution. four populations of escherichia coli k-12 were derived independently from strain mg1655, with each specifically adapted to survive exposure to high doses of ionizing radiation. d(37) values for strains isolated from two of the populations approached that exhibited by deinococcus radiodurans. complete genomic sequencing was carried out on nine purified stra ... | 2009 | 19502398 |
| development of versatile shuttle vectors for deinococcus grandis. | to develop new shuttle vectors for deinococcus species, the nucleotide sequence of the small cryptic plasmid pue30 from deinococcus radiopugnans atcc19172 was determined. the 2467-bp plasmid possesses two open reading frames, one encoding 88 amino acid residues (orf1) and the other encoding 501 amino acid residues (orf2). the predicted amino acid sequence encoded by orf1 exhibits similarity to the n-terminal regions of replication proteins encoded by repabc-type plasmids of a-proteobacteria. on ... | 2009 | 19504653 |
| ddrb protein, an alternative deinococcus radiodurans ssb induced by ionizing radiation. | deinococcus radiodurans exhibits an extraordinary resistance to the effects of exposure to ionizing radiation (ir). ddrb is one of five proteins induced to high levels in deinococcus following extreme ir exposure and that play a demonstrable role in genome reconstitution. although homology is limited, ddrb is a bacterial single-stranded dna-binding protein. ddrb features a stable core with a putative ob-fold, and a c-terminal segment with properties consistent with other bacterial ssbs. in solut ... | 2009 | 19515845 |
| dna polymerase x from deinococcus radiodurans implicated in bacterial tolerance to dna damage is characterized as a short patch base excision repair polymerase. | the deinococcus radiodurans r1 genome encodes an x-family dna repair polymerase homologous to eukaryotic dna polymerase beta. the recombinant deinococcal polymerase x (polx) purified from transgenic escherichia coli showed deoxynucleotidyltransferase activity. unlike the klenow fragment of e. coli, this enzyme showed short patch dna synthesis activity on heteropolymeric dna substrate. the recombinant enzyme showed 5'-deoxyribose phosphate (5'-drp) lyase activity and base excision repair function ... | 2009 | 19542005 |
| molecular identification and dynamics of microbial communities in reactor treating organic household waste. | the prokaryotic diversity associated with organic household waste (ohw), leachate (start-up inoculum), and mesophilic anaerobic digestion processes in the degradation of ohw for 44 and 90 days was investigated using a culture-independent approach. bacterial and archaeal 16s rrna and mcra gene clone libraries were constructed from community dna preparations. bacterial clones were affiliated with 13 phyla, of which firmicutes, proteobacteria, and bacteroidetes were represented in all libraries, wh ... | 2009 | 19551378 |
| deep into the red. | | 2009 | 19555017 |
| microbial diversity of a sulfide black smoker in main endeavour hydrothermal vent field, juan de fuca ridge. | submarine hydrothermal vents are among the least-understood habitats on earth but have been the intense focus of research in the past 30 years. an active hydrothermal sulfide chimney collected from the dudley site in the main endeavour vent field (mef) of juan de fuca ridge was investigated using mineralogical and molecular approaches. mineral analysis indicated that the chimney was composed mainly of fe-, zn-and cu-rich sulfides. according to phylogenetic analysis, within the crenarchaeota, clo ... | 2009 | 19557339 |
| deinococcus aerius sp. nov., isolated from the high atmosphere. | an orange-pigmented, non-motile, coccoid bacterial strain, designated tr0125t, was isolated from dust samples collected in the high atmosphere above japan. phylogenetic analysis based on 16s rrna gene sequences showed that the strain was within the radiation of deinococcus species. the major peptidoglycan amino acids were d-glutamic acid, glycine, d-alanine, l-alanine and ornithine. the predominant fatty acids were iso-c17:0, iso-c17:1omega9c and iso-c15:0. strong resistance to desiccation, uv-c ... | 2009 | 19567578 |
| the essential histone-like protein hu plays a major role in deinococcus radiodurans nucleoid compaction. | the nucleoid of radioresistant bacteria, including d. radiodurans, adopts a highly condensed structure that remains unaltered after exposure to high doses of irradiation. this structure may contribute to radioresistance by preventing the dispersion of dna fragments generated by irradiation. in this report, we focused our study on the role of hu protein, a nucleoid-associated protein referred to as a histone-like protein, in the nucleoid compaction of d. radiodurans. we demonstrate, using a new s ... | 2009 | 19570109 |
| bacillithiol is an antioxidant thiol produced in bacilli. | glutathione is a nearly ubiquitous, low-molecular-mass thiol and antioxidant, but it is conspicuously absent from most gram-positive bacteria. we identify here the structure of bacillithiol, a newly described and abundant thiol produced by bacillus species, staphylococcus aureus and deinococcus radiodurans. bacillithiol is the alpha-anomeric glycoside of l-cysteinyl-d-glucosamine with l-malic acid and most probably functions as an antioxidant. bacillithiol, like the structurally similar mycothio ... | 2009 | 19578333 |
| nutrition induced pleomorphism and budding mode of reproduction in deinococcus radiodurans. | morphological adaptation is an important biological function of a microorganism to cope with its environment. pleomorphism (to exist in a number of morphological forms) took centre stage in many discussions wherein a bacterium exhibits morphological transition and altered mode of reproduction in response to an environmental condition. | 2009 | 19583846 |
| molecular cloning and functional expression of a new amylosucrase from alteromonas macleodii. | the presence of amylosucrase in 12 alteromonas and pseudoalteromonas strains was examined. two alteromonas species (alteromonas addita kctc 12195 and alteromonas macleodii kctc 2957) possessed genes that had high sequence homology to known amylosucrases. genomic clones containing the asase analogs were obtained from a. addita and a. macleodii, and the deduced amino acid sequences of the corresponding genes (aaas and amas, respectively) revealed that they were highly similar to the asases of neis ... | 2009 | 19584557 |
| disruption of manganese ions [mn(ii)] transporter genes dr1709 or dr2523 in extremely radio-resistant bacterium deinococcus radiodurans. | the primary objective of this study was to identify whether the manganese ions [mn(ii)] transporter genes dr1709 and dr2523 played roles in deinococcus radiodurans's radiation resistance. the second objective was to study the relationships among manganese ions, manganese ions transporter genes and the bacterial radioresistance. | 2009 | 19621629 |
| deinococcus piscis sp. nov., a radiation-resistant bacterium isolated from a marine fish. | a radiation-resistant, gram-stain-positive, non-motile, non-sporulating, aerobic, coccoid bacterium, strain 3ax(t), was isolated from a marine fish (black pomfret, parastromateus niger), with radiation as a selective pressure. phylogenetic analysis based on 16s rrna gene sequences showed that strain 3ax(t) exhibited highest similarity (97.9 %) with deinococcus proteolyticus dsm 20540(t). the deltat(m) for dna-dna hybridization of d. proteolyticus dsm 20540(t) and strain 3ax(t) was 15.3 degrees c ... | 2009 | 19625434 |
| the deinococcus radiodurans smc protein is dispensable for cell viability yet plays a role in dna folding. | deinococcus radiodurans contains a highly condensed nucleoid that remains to be unaltered following the exposure to high doses of gamma-irradiation. proteins belonging to the structural maintenance of chromosome protein (smc) family are present in all organisms and were shown to be involved in chromosome condensation, pairing, and/or segregation. here, we have inactivated the smc gene in the radioresistant bacterium d. radiodurans, and, unexpectedly, found that smc null mutants showed no discern ... | 2009 | 19629621 |
| structure-based and random mutagenesis approaches increase the organophosphate-degrading activity of a phosphotriesterase homologue from deinococcus radiodurans. | an enzyme from the amidohydrolase family from deinococcus radiodurans (dr-oph) with homology to phosphotriesterase has been shown to exhibit activity against both organophosphate (op) and lactone compounds. we have characterized the physical properties of dr-oph and have found it to be a highly thermostable enzyme, remaining active after 3 h of incubation at 60 degrees c and withstanding incubation at temperatures up to 70 degrees c. in addition, it can withstand concentrations of at least 200 m ... | 2009 | 19631223 |
| [construction of deinococcal bacteria-escherichia coli shuttle vector and expression of luciferase gene]. | to express luciferase gene in escherichia coli through developed deinococcal bacteria-e. coli shuttle expression vector. | 2009 | 19637564 |
| purification of the large ribosomal subunit via its association with the small subunit. | we have developed an affinity purification of the large ribosomal subunit from deinococcus radiodurans that exploits its association with flag-tagged 30s subunits. thus, capture is indirect so that no modification of the 50s is required and elution is achieved under mild conditions (low magnesium) that disrupt the association, avoiding the addition of competitor ligands or coelution of common contaminants. efficient purification of highly pure 50s is achieved, and the chromatography simultaneous ... | 2009 | 19646947 |
| expression, purification and preliminary x-ray crystallographic analysis of udp-galactopyranose mutase from deinococcus radiodurans. | udp-galactopyranose mutase (ugm) catalyzes the interconversion of udp-galactopyranose and udp-galactofuranose. a ugm-substrate complex from deinococccus radiodurans has been expressed, purified and crystallized. crystals were obtained by the microbatch-under-oil method at room temperature. the crystals diffracted to 2.36 a resolution at the canadian light source. the space group was found to be p2(1)2(1)2(1), with unit-cell parameters a = 134.0, b = 176.6, c = 221.6 a. the initial structure solu ... | 2009 | 19652355 |
| deinococcus aetherius sp. nov., isolated from the stratosphere. | a pink-red pigmented, non-motile, coccoid bacterial strain, st0316(t), was isolated from dust samples collected from the stratosphere in japan. phylogenetic analysis based on 16s rrna gene sequences showed that it belonged to the genus deinococcus. dna g+c content (69.8 mol%), desiccation tolerance, and resistance to gamma-rays [d(10) (dose required to reduce the bacterial population by 10-fold) >8 kgy] and uv radiation (d(10) 1000 j m(-2)) supported the affiliation of strain st0316(t) to the ge ... | 2010 | 19656935 |
| deinococcus aerolatus sp. nov. and deinococcus aerophilus sp. nov., isolated from air samples. | two strains of pink-coloured bacteria, 5516t-9(t) and 5516t-11(t), were isolated from an air sample collected in korea. the taxonomic status of these novel strains was investigated by means of a polyphasic approach. the novel strains were gram-positive, aerobic, non-spore-forming and coccus-shaped bacteria. the dna g+c contents of strains 5516t-9(t) and 5516t-11(t) were 61.0 and 59.3 mol%, respectively. the major isoprenoid quinone for both strains was mk-8. strain 5516t-9(t) contained summed fe ... | 2010 | 19667390 |
| a model of interactions between radiation-induced oxidative stress, protein and dna damage in deinococcus radiodurans. | ionizing radiation triggers oxidative stress, which can have a variety of subtle and profound biological effects. here we focus on mathematical modeling of potential synergistic interactions between radiation damage to dna and oxidative stress-induced damage to proteins involved in dna repair/replication. when sensitive sites on these proteins are attacked by radiation-induced radicals, correct repair of dangerous dna lesions such as double strand breaks (dsbs) can be compromised. in contrast, i ... | 2009 | 19679136 |
| pleiotropic effects of recq in deinococcus radiodurans. | in deinococcus radiodurans, there is a unique recq homolog (dr1289) with three-tandem hrdc domains. deletion of drrecq resulted in a low doubling rate and sensitivity to hydrogen peroxide. here, we used cdna microarray and biochemical assays to explore the physiological changes in the drrecq mutant. the expressions of genes with predicted functions involved in iron homeostasis, antioxidant system, electron transport, and energy metabolism were significantly altered in response to drrecq disrupti ... | 2009 | 19679178 |
| mutagenic lesion bypass and two functionally different reca proteins in deinococcus deserti. | reca is essential for extreme radiation tolerance in deinococcus radiodurans. interestingly, sahara bacterium deinococcus deserti has three reca genes (reca(c), reca(p1), reca(p3)) that code for two different reca proteins (reca(c), reca(p)). moreover, and in contrast to other sequenced deinococcus species, d. deserti possesses homologues of translesion synthesis (tls) dna polymerases, including imuy and dnae2. together with a lexa homologue, imuy and dnae2 form a gene cluster similar to a wides ... | 2009 | 19703105 |
| the thermus thermophilus dead box helicase hera contains a modified rna recognition motif domain loosely connected to the helicase core. | dead box family helicases consist of a helicase core that is formed by two flexibly linked reca-like domains. the helicase activity can be regulated by n- or c-terminal extensions flanking the core. thermus thermophilus heat resistant rna-dependent atpase (hera) is the first dead box helicase that forms a dimer using a unique dimerization domain. in addition to the dimerization domain, hera contains a c-terminal rna binding domain (rbd) that shares sequence homology only to uncharacterized prote ... | 2009 | 19710183 |
| d-matrix: a web tool for constructing weight matrix of conserved dna motifs. | despite considerable efforts to date, dna motif prediction in whole genome remains a challenge for researchers. currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. considering this, we developed a d-matrix tool which predicts the different types of weight matrix based on u ... | 2009 | 19759861 |
| involvement of recg in h2o2-induced damage repair in deinococcus radiodurans. | deinococcus radiodurans (ex raj et al. 1960) brooks and murray 1981 is well known for its efficient repair of various types of physically or chemically induced dna damage caused by ionizing and ultraviolet radiation or h2o2. recg codes for a helicase that is known to be involved in repairing oxidative damage in other bacterium. in this work, we constructed a drrecg deletion mutant and investigated its possible role in h2o2-induced damage. the results showed that the deletion of drrecg resulted i ... | 2009 | 19767856 |
| overexpression and characterization of a thermostable trehalose synthase from meiothermus ruber. | a thermostable trehalose synthase (tres) gene from meiothermus ruber cbs-01 was cloned and overexpressed in escherichia coli. the purified recombinant tres could utilize maltose to produce trehalose, and showed an optimum ph and temperature of 6.5 and 50 degrees c, respectively. kinetic analysis showed that the enzyme had a twofold higher catalytic efficiency (k (cat)/k (m)) for maltose than for trehalose, indicating maltose as the preferred substrate. the tres also had a weak hydrolytic propert ... | 2010 | 19779856 |
| effects of carotenoids from deinococcus radiodurans on protein oxidation. | to evaluate the antioxidant effect of carotenoids from deinococcus radiodurans on protein. | 2009 | 19780959 |
| structural-dynamical properties of the deinococcus radiodurans topoisomerase ib in absence of dna: correlation with the human enzyme. | a molecular dynamics simulation of the deinococcus radiodurans topoisomerase ib crystallized in absence of dna has been carried out. the protein stably maintains its initial conformation with the n- and c-terminal domains slightly oscillating around their initial positions, being their relative orientations stabilized by two inter-domain interactions, arg4:glu228 and glu63:arg91. a charge perturbation has then been introduced to destabilize the protein from its local minimum. the simulation carr ... | 2009 | 19795914 |
| deinococcus wulumuqiensis sp. nov., and deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil. | the taxonomic positions of two gamma- and uv-ray-resistant strains isolated from radiation-polluted soil in north-west china were determined in a polyphasic study. the organisms, designated r12(t) and r13(t), were gram-stain-positive, non-spore-forming cocci, which contained mk-8 as the major respiratory quinone and c(16 : 1)omega7c and c(16 : 0) as major fatty acids. the cell walls of strains r12(t) and r13(t) contained ornithine. phylogenetic analysis based on 16s rrna gene sequences and dna-d ... | 2010 | 19801390 |
| catalase and superoxide dismutase double staining zymogram technique for deinococcus and kocuria species exposed to multiple stresses. | superoxide dismutase (sod) and catalase expression is associated with oxidative stress. existing techniques for the individual staining of sod and catalase have been described in the past. the objective of this study was to achieve a simple and rapid technique for the double staining of bacterial sod and catalase on the same polyacrylamide gel. sod detection was carried out using nitro-blue tetrazolium (nbt) dye reduction followed by ferricyanide precipitation for negative staining of the catala ... | 2009 | 19810043 |
| functional analysis of gamma-carotene ketolase involved in the carotenoid biosynthesis of deinococcus radiodurans. | deinococcus radiodurans strain r1 synthesizes a unique ketocarotenoid product named deinoxanthin. the detailed steps involved in the biosynthesis of deinoxanthin remain unresolved. a carotene ketolase homologue encoded by dr0093 was inactivated by gene mutation to verify its function in the native host d. radiodurans. analysis of the carotenoids in the resultant mutant r1deltacrto demonstrated that dr0093 encodes gamma-carotene ketolase (crto) catalysing the introduction of one keto group into t ... | 2009 | 19832905 |
| structural basis of substrate binding to udp-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with udp-galactopyranose and udp. | d-galactofuranose (galf) residues are found in the cell walls of pathogenic microbes such as mycobacterium tuberculosis, and are essential for viability. udp-galactopyranose mutase (ugm) is a unique flavo-enzyme that catalyzes the reversible conversion of udp-galactopyranose (udp-galp) and udp-galactofuranose (udp-galf). udp-galf is the active precursor of galf residues found in cell walls. despite the wealth of biochemical/mechanistic data generated for ugm, the structural basis of substrate bi ... | 2009 | 19836401 |
| evolution of double mutt/nudix domain-containing proteins: similar domain architectures from independent gene duplication-fusion events. | the mutt/nudix superfamily proteins repair dna damage and play a role in human health and disease. in this study, we examined two different cases of double mutt/nudix domain-containing proteins from eukaryotes and prokaryotes. firstly, these double domain proteins were discovered in drosophila, but only single nudix domain proteins were found in other animals. the phylogenetic tree was constructed based on the protein sequence of nudix_n and nudix_c from drosophila, and nudix from other animals. ... | 2009 | 19840758 |
| endogenous nitric oxide regulates the recovery of the radiation-resistant bacterium deinococcus radiodurans from exposure to uv light. | deinococcus radiodurans (dr) withstands desiccation, reactive oxygen species, and doses of radiation that would be lethal to most organisms. deletion of a gene encoding a homolog of mammalian nitric oxide synthase (nos) severely compromises the recovery of dr from ultraviolet (uv) radiation damage. the deltanos defect can be complemented with recombinant nos, rescued by exogenous nitric oxide (no) and mimicked in the wild-type strain with an no scavenging compound. uv radiation induces both upre ... | 2009 | 19841256 |
| the evolution of recd outside of the recbcd complex. | the common understanding of the function of recd, as derived predominantly from studies in escherichia coli, is that recd is one of three enzymes in the recbcd double-stranded break repair dna recombination complex. however, comparative genomics has revealed that many organisms possess a recd gene even though the other members of the complex, recb and recc, are not present. further, bioinformatic analyses have shown that there is substantial sequence dissimilarity between recd genes associated w ... | 2009 | 19841849 |
| bacterial community in the east rongbuk glacier, mt. qomolangma (everest) by culture and culture-independent methods. | the abundance of total and culturable bacteria deposited into the east rongbuk ice core was investigated, and the bacterial content was examined through culture and culture-independent approaches. total counts of bacteria in the ice core ranged from 0.02 x 10(3) to 6.4 x 10(3) cells ml(-1). viable bacteria varied between 0 and 5.6 cfu ml(-1) on pygv and r2a media. the phylogenetic trees placed the culturable bacteria into four major groups: actinobacteria, firmicutes, proteobacteria and deinococ ... | 2010 | 19853425 |
| allosteric control of catalysis by the f loop of rna polymerase. | bacterial rna polymerases (rnaps) undergo coordinated conformational changes during catalysis. in particular, concerted folding of the trigger loop and rearrangements of the bridge helix at the rnap active center have been implicated in nucleotide addition and rnap translocation. at moderate temperatures, the rate of catalysis by rnap from thermophilic thermus aquaticus is dramatically reduced compared with its closest mesophilic relative, deinococcus radiodurans. here, we show that a part of th ... | 2009 | 19855007 |
| isolation and identification of a new radiation-resistant bacterium deinococcus guangriensis sp.nov. and analysis of its radioresistant character. | to isolate and identify a new ionizing-radiation resistant strain capable of surviving under highly ionizing radiation conditions as uv and gamol/la radiation and to characterize its radioresistant properties. | 2009 | 19873756 |
| proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. | deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ... | 2010 | 19875382 |
| roles of ppra, irre, and reca in the resistance of deinococcus radiodurans to germicidal and environmentally relevant uv radiation. | to study the role of different dna repair genes in the resistance of deinococcus radiodurans to mono- and polychromatic uv radiation, wild-type strain and knockout mutants in reca, ppra, and irre of d. radiodurans were irradiated with uv-c (254 nm), uv-(a + b) (280-400 nm) and uv-a (315-400 nm) radiation, and survival was monitored. the strain deficient in reca was highly sensitive to uv-c radiation compared to the wild-type, but showed no loss of resistance against irradiation with uv-(a + b) a ... | 2009 | 19882142 |
| characteristics of nuclease activity of the sbccd complex from deinococcus radiodurans. | the bacterium deinococcus radiodurans is extremely resistant to the intense ionizing irradiation which causes extensive dna double-strand breaks (dsbs). the deinococcal sbccd complex (drsbccd) is required for dsb repair. the drsbcc and drsbcd genes were cloned and overexpressed in escherichia coli cells, respectively. the nearly homogeneous drsbcc and drsbcd proteins were purified and reconstituted to form a stable complex in vitro. the drsbccd complex has an atp-independent 3'-->5' exonuclease ... | 2010 | 19897571 |
| decomposition of intact chicken feathers by a thermophile in combination with an acidulocomposting garbage-treatment process. | in order to develop a practical method for the decomposition of intact chicken feathers, a moderate thermophile strain, meiothermus ruber h328, having strong keratinolytic activity, was used in a bio-type garbage-treatment machine working with an acidulocomposting process. the addition of strain h328 cells (15 g) combined with acidulocomposting in the garbage machine resulted in 70% degradation of intact chicken feathers (30 g) within 14 d. this degradation efficiency is comparable to a previous ... | 2009 | 19897897 |
| structure of an n-terminally truncated nudix hydrolase dr2204 from deinococcus radiodurans. | nudix pyrophosphatases are a well represented protein family in the deinococcus radiodurans genome. these hydrolases, which are known to be enzymatically active towards nucleoside diphosphate derivatives, play a role in cleansing the cell pool of potentially deleterious damage products. here, the structure of dr2204, the only adp-ribose pyrophosphatase in the d. radiodurans genome that is known to be active towards flavin adenosine dinucleotide (fad), is presented at 2.0 angstrom resolution. | 2009 | 19923723 |
| thioredoxin system from deinococcus radiodurans. | this paper describes the cloning, purification, and characterization of thioredoxin (trx) and thioredoxin reductase (trxr) and the structure determination of trxr from the ionizing radiation-tolerant bacterium deinococcus radiodurans strain r1. the genes from d. radiodurans encoding trx and trxr were amplified by pcr, inserted into a pet expression vector, and overexpressed in escherichia coli. the overexpressed proteins were purified by metal affinity chromatography, and their activity was demo ... | 2010 | 19933368 |
| two-dimensional proteome reference map for the radiation-resistant bacterium deinococcus geothermalis. | 2-de reference maps for deinococcus geothermalis cytosolic and cell envelope proteomes were constructed. in total, 403 spots were identified as 299 different proteins. unique in the proteomes were four subunits of v-type atpase and deinococcus specific proteins constituting one-fourth of cell envelope proteome. the cytoplasmic proteome included enzymes of the central carbon metabolism, chaperones, enzymes of protein and dna repair, and oxidative stress. a total of 34 abundant proteins with unkno ... | 2010 | 19941306 |
| analysis of the recj gene and protein from deinococcus radiodurans. | the mechanism by which double-strand dna breaks are repaired in the radiation-resistant bacterium deinococcus radiodurans is not well understood. this organism lacks the recbcd helicase/nuclease, which processes broken dna ends in other bacteria. the recf pathway is an alternative pathway for recombination and dna repair in e. coli, when recbcd is absent due to mutation, and d. radiodurans may rely on enzymes of this pathway for double-strand break repair. the recj exonuclease is thought to proc ... | 2010 | 19944654 |
| [expression of gene reca of deinococcus radiodurans in escherichia coli cells]. | plasmids pks5 and pksrec30 carrying normal and mutant alleles of deinococcus radiodurans reca gene controlled by the lactose promoter slightly increase radioresistance of escherichia coli cells with mutations at genes reca and ssb. the reca protein of d. radiodurans is expressed in e. coli cells, and its synthesis can be supplementary induced. the radioprotective effect of the xenologic protein does not exceed 1.5 times and is essentially to the contribution of plasmid puc 19-reca1.1 harboring t ... | 2009 | 19947546 |
| dynamics of the base of ribosomal a-site finger revealed by molecular dynamics simulations and cryo-em. | helix 38 (h38) of the large ribosomal subunit, with a length of 110 a, reaches the small subunit through intersubunit bridge b1a. previous cryo-em studies revealed that the tip of h38 moves by more than 10 a from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible h38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. we investigate a region including the elbow-shaped kink-turn (kt-38) i ... | 2010 | 19952067 |
| bioremediation of endocrine disruptor di-n-butyl phthalate ester by deinococcus radiodurans and pseudomonas stutzeri. | di-n-butyl phthalate (dbp) is a group of phthalate esters (paes) that are widely used in cosmetics, perfumes, and plasticizers. due to its high production and application figures, dbp is commonly found in wastewater, sewage sludge, and aquatic environments. it has been classified as suspected endocrine disruptors by most countries. in this study, we isolated two dbp degradable strains from activated sludge. the strains were identified with their 16s rrna as deinococcus radiodurans and pseudomona ... | 2010 | 19959202 |
| a systematic study of 50s ribosomal subunit purification enabling robust crystallization. | a systematic analysis was undertaken to seek correlations between the integrity, purity and activity of 50s ribosomal subunit preparations from deinococcus radiodurans and their ability to crystallize. conditions of fermentation, purification and crystallization were varied in a search for crystals that could reliably supply an industrial x-ray crystallography program for the structure-based design of ribosomal antibiotics. a robust protocol was obtained to routinely obtain crystals that gave di ... | 2009 | 19966413 |
| increased synthesis of signaling molecules coincides with reversible inhibition of nucleolytic activity during postirradiation recovery of deinococcus radiodurans. | deinococcus radiodurans tolerates extensive dna damage and exhibits differential expression of various genes associated with the growth of the organism and dna repair. in cells treated with gamma radiation, the levels of cyclic amp (camp) and atp increased rapidly by differentially regulating adenylyl cyclase (ac) and 2'3' camp phosphodiesterase. the levels of camp, atp, ac and protein kinases were high when phosphodiesterase activity was low. these cells exhibited in vivo inhibition of nucleoly ... | 2010 | 20015337 |
| quantitative biological imaging by ptychographic x-ray diffraction microscopy. | recent advances in coherent x-ray diffractive imaging have paved the way to reliable and quantitative imaging of noncompact specimens at the nanometer scale. introduced a year ago, an advanced implementation of ptychographic coherent diffractive imaging has removed much of the previous limitations regarding sample preparation and illumination conditions. here, we apply this recent approach toward structure determination at the nanoscale to biological microscopy. we show that the projected electr ... | 2010 | 20018650 |
| route 66: investigations into the organisation and distribution of the is66 family of prokaryotic insertion sequences. | we have analysed a large number of members of the is66 family of prokaryotic insertion sequences which include three orfs (a, b and c) and we show that these are closely related to a second group (isbst12) which includes only orfc, encoding the transposase tnpc. these two is groups are also related by their terminal inverted repeats (ir) which show significant conservation. we propose that both groups be included in the same family, the is66 family. we have also identified members of both is gro ... | 2010 | 20079432 |
| the structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics. | crystallographic analysis revealed that the 17-member polyketide antibiotic lankacidin produced by streptomyces rochei binds at the peptidyl transferase center of the eubacterial large ribosomal subunit. biochemical and functional studies verified this finding and showed interference with peptide bond formation. chemical probing indicated that the macrolide lankamycin, a second antibiotic produced by the same species, binds at a neighboring site, at the ribosome exit tunnel. these two antibiotic ... | 2010 | 20080686 |
| rising from the ashes: dna repair in deinococcus radiodurans. | | 2010 | 20084105 |
| a major role of the recfor pathway in dna double-strand-break repair through esdsa in deinococcus radiodurans. | in deinococcus radiodurans, the extreme resistance to dna-shattering treatments such as ionizing radiation or desiccation is correlated with its ability to reconstruct a functional genome from hundreds of chromosomal fragments. the rapid reconstitution of an intact genome is thought to occur through an extended synthesis-dependent strand annealing process (esdsa) followed by dna recombination. here, we investigated the role of key components of the recf pathway in esdsa in this organism naturall ... | 2010 | 20090937 |
| irradiation-induced deinococcus radiodurans genome fragmentation triggers transposition of a single resident insertion sequence. | stress-induced transposition is an attractive notion since it is potentially important in creating diversity to facilitate adaptation of the host to severe environmental conditions. one common major stress is radiation-induced dna damage. deinococcus radiodurans has an exceptional ability to withstand the lethal effects of dna-damaging agents (ionizing radiation, uv light, and desiccation). high radiation levels result in genome fragmentation and reassembly in a process which generates significa ... | 2010 | 20090938 |
| biophysical characterization and mutational analysis of the antibiotic resistance protein nima from deinococcus radiodurans. | metronidazole (mtz) is an antibiotic commonly used to treat anaerobic bacterial infections in humans and animals. antibiotic resistance toward this class of 5-nitroimidazole (5-ni) drug derivatives has been related to the nim genes thought to encode a reductase. here we report the biophysical characteristics of the nima protein from deinococcus radiodurans (drnima) binding to mtz and three other 5-ni drugs. the interaction energies of the protein and antibiotic are studied by isothermal titratio ... | 2010 | 20096385 |
| epitaxy of ge nanowires grown from biotemplated au nanoparticle catalysts. | semiconductor nanowires (nws) are being actively investigated due to their unique functional properties which result from their quasi-one-dimensional structure. however, control over the crystallographic growth direction, diameter, location, and morphology of high-density nws is essential to achieve the desirable properties and to integrate these nws into miniaturized devices. this article presents evidence for the suitability of a biological templated catalyst approach to achieve high-density, ... | 2010 | 20128609 |
| the structure of ddrb from deinococcus: a new fold for single-stranded dna binding proteins. | deinococcus spp. are renowned for their amazing ability to recover rapidly from severe genomic fragmentation as a result of exposure to extreme levels of ionizing radiation or desiccation. despite having been originally characterized over 50 years ago, the mechanism underlying this remarkable repair process is still poorly understood. here, we report the 2.8 a structure of ddrb, a single-stranded dna (ssdna) binding protein unique to deinococcus spp. that is crucial for recovery following dna da ... | 2010 | 20129942 |
| conservation of the lexa repressor binding site in deinococcus radiodurans. | the lexa protein is a transcriptional repressor of the bacterial sos dna repair system, which comprises a set of dna repair and cellular survival genes that are induced in response to dna damage. its varied dna binding motifs have been characterized and reported in the escherichia coli, bacillus subtilis, rhizobia family members, marine magnetotactic bacterium, salmonella typhimurium and recently in mycobacterium tuberculosis and this motifs information has been used in our theoretical analysis ... | 2008 | 20134056 |
| the sbccd complex of deinococcus radiodurans contributes to radioresistance and dna strand break repair in vivo and exhibits mre11-rad50 type activity in vitro. | deinococcus radiodurans lacks a homologue of the recb and recc genes, and the sbca/b genes, of escherichia coli. thus, dna strand break repair in deinococcus proceeds by pathways that do not utilize these proteins. unlike e. coli, the absence of recbc and sbca/sbcb, and presence of only sbcc and sbcd in deinococcus, indicates an enigmatic role of sbccd in this bacterium. studies on sbccd mutation in deinococcus showed nearly a 100-fold increase in gamma radiation sensitivity as compared to wild ... | 2010 | 20144564 |
| circular dichroism studies on the deinococcus radiodurans nudix hydrolase dr_0079: an atypical thermal melt. | the crystal structure for the deinococcus radiodurans nudix protein dr_0079 was recently determined in the metal-free form at 1.9 a resolution (2o5f). the protein adopts the fundamental fold common to the nudix family of proteins, a large mixed b-sheet sandwiched between the a-helix of the "nudix box" and a second a-helix. the protein's physical properties were further characterized by circular dichroism (cd) spectroscopy. a cd thermal melt at 220 nm identifies an inflection point at approximate ... | 2010 | 20156187 |
| a role for a bacterial ortholog of the ro autoantigen in starvation-induced rrna degradation. | cellular adaptations to stress often involve changes in rna metabolism. one rna-binding protein that has been implicated in rna handling during environmental stress in both animal cells and prokaryotes is the ro autoantigen. however, the function of ro in stress conditions has been unknown. we report that a ro protein in the radiation-resistant eubacterium deinococcus radiodurans participates in ribosomal rna (rrna) degradation during growth in stationary phase, a form of starvation. levels of t ... | 2010 | 20160119 |
| a probabilistic framework for microarray data analysis: fundamental probability models and statistical inference. | gene expression studies generate large quantities of data with the defining characteristic that the number of genes (whose expression profiles are to be determined) exceed the number of available replicates by several orders of magnitude. standard spot-by-spot analysis still seeks to extract useful information for each gene on the basis of the number of available replicates, and thus plays to the weakness of microarrays. on the other hand, because of the data volume, treating the entire data set ... | 2010 | 20170665 |
| antimicrobial drug resistance. | this chapter provides an overview of our current understanding of the mechanisms associated with the development of antimicrobial drug resistance, international differences in definitions of resistance, ongoing efforts to track shifts in drug susceptibility, and factors that can influence the selection of therapeutic intervention. the latter presents a matrix of complex variables that includes the mechanism of drug action, the pharmacokinetics (pk) of the antimicrobial agent in the targeted pati ... | 2010 | 20204590 |
| bacterial diversity at different stages of the composting process. | composting is an aerobic microbiological process that is facilitated by bacteria and fungi. composting is also a method to produce fertilizer or soil conditioner. tightened eu legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. however, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. in this study we examine the bacterial species r ... | 2010 | 20350306 |
| self-sufficient control of urate homeostasis in mice by a synthetic circuit. | synthetic biology has shown that the metabolic behavior of mammalian cells can be altered by genetic devices such as epigenetic and hysteretic switches, timers and oscillators, biocomputers, hormone systems and heterologous metabolic shunts. to explore the potential of such devices for therapeutic strategies, we designed a synthetic mammalian circuit to maintain uric acid homeostasis in the bloodstream, disturbance of which is associated with tumor lysis syndrome and gout. this synthetic device ... | 2010 | 20351688 |
| kinetics of dna unwinding by the recd2 helicase from deinococcus radiodurans. | recd2 from deinococcus radiodurans is a superfamily 1 dna helicase that is homologous to the escherichia coli recd protein but functions outside the context of recbcd enzyme. we report here on the kinetics of dna unwinding by recd2 under single and multiple turnover conditions. there is little unwinding of 20-bp substrates by preformed recd2-dsdna complexes when excess ssdna is present to trap enzyme molecules not bound to the substrate. a shorter 12-bp substrate is unwound rapidly under single ... | 2010 | 20360003 |
| recn is a cohesin-like protein that stimulates intermolecular dna interactions in vitro. | the bacterial recn protein is involved in the recombinational repair of dna double-stranded breaks, and recn mutants are sensitive to dna-damaging agents. little is known about the biochemical function of recn. protein sequence analysis suggests that recn is related to the smc (structural maintenance of chromosomes) family of proteins, predicting globular n- and c-terminal domains connected by an extensive coil-coiled domain. the n- and c-domains contain the nucleotide-binding sequences walker a ... | 2010 | 20360008 |
| cryogenic x-ray diffraction microscopy for biological samples. | x-ray diffraction microscopy (xdm) is well suited for nondestructive, high-resolution biological imaging, especially for thick samples, with the high penetration power of x rays and without limitations imposed by a lens. we developed nonvacuum, cryogenic (cryo-) xdm with hard x rays at 8 kev and report the first frozen-hydrated imaging by xdm. by preserving samples in amorphous ice, the risk of artifacts associated with dehydration or chemical fixation is avoided, ensuring the imaging condition ... | 2009 | 20365956 |
| de novo sequencing of tryptic peptides derived from deinococcus radiodurans ribosomal proteins using 157 nm photodissociation maldi tof/tof mass spectrometry. | vacuum ultraviolet photodissociation of peptide ions in a matrix assisted laser desorption ionization (maldi) tandem time-of-flight (tof) mass spectrometer is used to characterize peptide mixtures derived from deinococcus radiodurans ribosomal proteins. tryptic peptides from 52 proteins were separated by reverse-phase liquid chromatography and spotted onto a maldi plate. from 192 sample spots, 492 peptide ions were isolated, fragmented by both photodissociation and postsource decay (psd), and th ... | 2010 | 20377247 |
| deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a finnish paper mill. | a rod-shaped, non-spore-forming, non-motile, aerobic, oxidase and catalase-positive and radiation-resistant bacterium (designated strain k4.1(t)) was isolated from biofilm collected from a finnish paper mill. the bacterium grew as pale pink colonies on oligotrophic medium at 12 to 50 °c (optimum 37 to 45 °c) and at ph 6 to 10.3. the dna g+c content of the strain was 66.8 l%. according to 16s rrna gene sequence analysis, strain k4.1(t) was distantly related to the genus deinococcus, sharing highe ... | 2011 | 20382794 |
| crystallization and preliminary x-ray characterization of a catalytic and atp-binding domain of a putative phor histidine kinase from the gamma-radioresistant bacterium deinococcus radiodurans. | the gene product of histidine kinase dr2244 (putative phor) encoded by deinococcus radiodurans has been suggested to be involved in the phor-phob two-component regulatory system. this two-component signalling system is activated upon phosphate starvation in several bacteria, including d. radiodurans. single crystals were obtained from a recombinant preparation of the catalytic/atp-binding (ca) domain of d. radiodurans phor (79-224) overexpressed in escherichia coli. the crystals belonged to spac ... | 2010 | 20383008 |
| involvement of recf in 254 nm ultraviolet radiation resistance in deinococcus radiodurans and escherichia coli. | recf is a critical gene involved in the recfor pathway of dna repair in deinococcus radiodurans (d. radiodurans). to investigate the role of recf in uv-c radiation resistance, we generated the recf-deficient d. radiodurans strain r1, expressed recf in escherichia coli (e. coli) bl21 cells, and compared the ability of each to resist uv-c radiation by f (10), inactivation constant (ic), and extrapolation number (n). the mutation of recf in d. radiodurans r1 resulted in characteristic slow growth a ... | 2010 | 20386912 |
| dr2539 is a novel dtxr-like regulator of mn/fe ion homeostasis and antioxidant enzyme in deinococcus radiodurans. | transcriptional regulators of the diphtheria toxin repressor (dtxr) family control the expression of genes involved in the uptake of iron and manganese, which is not only necessitous nutrients but also was suggested to be essential for intracellular redox cycling of microorganisms. we identified a unique dtxr homologue (dr2539) with special characteristics from deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. the dr2539 mutant showed higher resistance ... | 2010 | 20417183 |
| repression of reca induction by recx is independent of the reca protein in deinococcus radiodurans. | besides inhibiting reca activity at the protein level, deinococcus radiodurans recx can suppress reca induction at the transcriptional level. the regulation of recx on reca induction is independent of reca activity, and its n terminus is involved in this process. | 2010 | 20418393 |
| both ob folds of single-stranded dna-binding protein are essential for its ssdna binding activity in deinococcus radiodurans. | the single-stranded dna-binding proteins are crucial in all kinds of dna metabolic processes. deinococcus ssb-like proteins are homodimers in nature and contain two ob folds per monomer, in contrast to other bacterial ssb proteins that are functionally active as homotetramers. we generated four truncated variants of drassb protein, based on its crystal structure (pdb code: 1se8). gel filtration showed that drassb, dsct (lack c-tail) and dscc (lack c-tail and c-terminal ob) were mostly homodimers ... | 2010 | 20423318 |
| ddrb stimulates single-stranded dna annealing and facilitates reca-independent dna repair in deinococcus radiodurans. | the bacterium deinococcus radiodurans can survive extremely high exposure to ionizing radiation. the repair mechanisms involved in this extraordinary ability are still being investigated. ddrb is one gene that is highly up-regulated after irradiation, and it has been proposed to be involved in reca-independent repair in d. radiodurans. here we cloned, expressed and characterized ddrb in order to define its roles in the radioresistance of d. radiodurans. ddrb preferentially binds to single-strand ... | 2010 | 20451472 |
| evaluation of the role of enzymatic and nonenzymatic antioxidant systems in the radiation resistance of deinococcus. | antioxidant enzymes and antioxidant metabolites appear to have different roles in the oxidative stress resistance responses of radiation-resistant bacteria belonging to the deinococcus-thermus group. twelve distinct strains belonging to 7 deinococcus species were characterized for their responses to hydrogen peroxide, ciprofloxacin, and ionizing radiation. the levels of catalase and peroxidase activities in these strains showed a positive correlation with resistance to hydrogen peroxide and cipr ... | 2010 | 20453905 |
| genomic bipyrimidine nucleotide frequency and microbial reactions to germicidal uv radiation. | the role of the genomic bipyrimidine nucleotide frequency in pyrimidine dimer formation caused by germicidal uv radiation was studied in three microbial reference organisms (escherichia coli k12, deinococcus radiodurans r1, spores and cells of bacillus subtilis 168). the sensitive hplc tandem mass spectrometry assay was used to identify and quantify the different bipyrimidine photoproducts induced in the dna of microorganisms by germicidal uv radiation. the yields of photoproducts per applied fl ... | 2010 | 20454780 |
| biodegradation of di-n-butyl phthalate in a soil microcosm. | this study investigated the effects of various culture treatments on di-n-butyl phthalate (dbp) degradation and the survival conditions of dbp-degrading bacterial strains in a soil microcosm. in the previous study, a dbp-degrading strain was isolated from activated sludge and identified by 16s rrna as deinococcus radiodurans. in this study, we added d. radiodurans into a soil microcosm and analyzed the structure of the whole bacterial community of the soil using a polymerase chain reaction-denat ... | 2010 | 20512726 |
| the deinococcus radiodurans snf2 intein caught in the act: detection of the class 3 intein signature block f branched intermediate. | inteins are the protein equivalent of introns. they are remarkable and robust single turnover enzymes that splice out of precursor proteins during post-translational maturation of the host protein (extein). the deinococcus radiodurans snf2 intein is the second member of the recently discovered class 3 subfamily of inteins to be characterized. class 3 inteins have a unique sequence signature: (a) they start with residues other than the standard class 1 cys, ser or thr, (b) have a noncontiguous, c ... | 2010 | 20521254 |
| quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy. | phytochromes are a collection of dimeric photoreceptors that direct a diverse array of responses in plants and microorganisms through photoconversion between a red light-absorbing ground state pr, and a far-red light-absorbing photoactivated state pfr. photoconversion from pr to pfr is initiated by a light-driven rotation within the covalently attached bilin, which then triggers a series of protein conformational changes in the binding pocket. these movements ultimately affect an appended output ... | 2010 | 20534495 |
| crystal structure of a bacterial topoisomerase ib in complex with dna reveals a secondary dna binding site. | type ib dna topoisomerases (topib) are monomeric enzymes that relax supercoils by cleaving and resealing one strand of duplex dna within a protein clamp that embraces a approximately 21 dna segment. a longstanding conundrum concerns the capacity of topib enzymes to stabilize intramolecular duplex dna crossovers and form protein-dna synaptic filaments. here we report a structure of deinococcus radiodurans topib in complex with a 12 bp duplex dna that demonstrates a secondary dna binding site loca ... | 2010 | 20541510 |
| response of deinococcus radiodurans to low-pressure low-temperature plasma sterilization processes. | characterize the response of deinococcus radiodurans r1 cells to low-pressure low-temperature nitrogen-oxygen microwave plasma and identify repair processes during recovery. | 2010 | 20553346 |