Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| an inventory of genes encoding rna polymerase sigma factors in 31 completely sequenced eubacterial genomes. | sigma factors are important elements involved in transcriptional regulation of gene expression by conferring promoter specificity to rna polymerase. the number of sigma factor encoding genes in 31 completely sequenced bacterial genomes were compared. two unrelated families of sigma factors, the sigma70- and the sigma54-family were identified previously. the sigma70-family can be further subdivided into two distantly related groups: the sigma70 subfamily and the poorly characterized ecf subfamily ... | 2002 | 11763973 |
| mechanisms of biofilm formation in paper machine by bacillus species: the role of deinococcus geothermalis. | mechanisms for the undesired persistence of bacillus species in paper machine slimes were investigated. biofilm formation was measured for industrial bacillus isolates under paper machine wet-end-simulating conditions (white water, ph 7, agitated at 45 degrees c for 1-2 days). none of the 40 tested strains of seven bacillus species formed biofilm on polished stainless steel or on polystyrene surfaces as a monoculture. under the same conditions, deinococcus geothermalis e50051 covered all test su ... | 2001 | 11773998 |
| recovery of deinococcus radiodurans from radiation damage was enhanced under microgravity. | effect of microgravity on recovery of bacterial cells from radiation damage was examined on the iml-2 mission in 1994 using extremely radioresistant bacterium deinococcus radiodurans. the cells were lyophilized and exposed to 60co gamma-rays with doses 2 to 12 kgy before the space flight. at the end of the mission, the cells were mixed on board with liquid nutrient medium to allow the cells to start recovery process from the radiation damage. afterwards the cells were stored at 4 degrees c until ... | 1996 | 11785538 |
| genetic evidence that the uvse gene product of deinococcus radiodurans r1 is a uv damage endonuclease. | an in vitro transposition system, developed to facilitate gene disruption in deinococcus radiodurans r1, has been used to inactivate the gene designated dr1819 in uvra-1(+) and uvra-1 backgrounds. dr1819 encodes a protein with homology to a uv dna damage endonuclease expressed by schizosaccharomyces pombe. interruption of dr1819 greatly sensitizes the uvra-1 strain but not the uvra-1(+) strain to uv light, indicating that the dr1819 gene product is a component in a dna repair pathway that can co ... | 2002 | 11807060 |
| molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium thermus thermophilus strain hb27. | thermus thermophilus hb27, an extremely thermophilic bacterium, exhibits high competence for natural transformation. to identify genes of the natural transformation machinery of t. thermophilus hb27, we performed homology searches in the partially completed t. thermophilus genomic sequence for conserved competence genes. these analyses resulted in the detection of 28 open reading frames (orfs) exhibiting significant similarities to known competence proteins of gram-negative and gram-positive bac ... | 2002 | 11823215 |
| a poxvirus-like type ib topoisomerase family in bacteria. | we report that diverse species of bacteria encode a type ib dna topoisomerase that resembles vaccinia virus topoisomerase. deinococcus radiodurans topoisomerase ib (dratopib), an exemplary member of this family, relaxes supercoiled dna in the absence of a divalent cation or atp. dratopib has a compact size (346 aa) and is a monomer in solution. mutational analysis shows that the active site of dratopib is composed of the same constellation of catalytic side chains as the vaccinia enzyme. sequenc ... | 2002 | 11830640 |
| inactivation of two homologues of proteins presumed to be involved in the desiccation tolerance of plants sensitizes deinococcus radiodurans r1 to desiccation. | mutational inactivation of the genes designated dr1172 and drb0118 in deinococcus radiodurans r1 greatly sensitizes this species to desiccation, but not to ionizing radiation. these genes encode proteins that share features with the desiccation-induced lea76 proteins of many plants and the pcc13-62 protein of craterostigma plantagineum, suggesting that d. radiodurans may serve as a useful model for the study of desiccation tolerance in higher organisms. | 2001 | 11846468 |
| enhanced immune protection by a liposome-encapsulated recombinant respiratory syncytial virus (rsv) vaccine using immunogenic lipids from deinococcus radiodurans. | the radiation-resistant bacterium, deinococcus radiodurans contains a variety of phospho-, glyco- and phosphoglycolipids, the structures of which appear to be largely unique in nature. we show here that such lipids are immunogenic when administered as liposomes intranasally in mice, as evidenced by the induction of serum antibodies which recognize d. radiodurans lipids but not other lipids by thin layer chromatographic immunostaining. by modifying a liposomal vaccine against respiratory syncytia ... | 2002 | 11858866 |
| hunc93b1: a novel human gene representing a new gene family and encoding an unc-93-like protein. | we have identified a novel human gene unc93b1 encoding a protein related to unc-93 of caenorhabditis elegans. the combined sequence derived from several cdna clones is 2282 bp and comparison with genomic sequence shows that the gene contains 11 exons. the longest open reading frame encodes a deduced sequence of 597 amino acids. homology analysis shows that the hunc93b1 gene is highly conserved and related to sequences in arabidopsis thaliana, c. elegans, drosophila melanogaster, chicken and mous ... | 2002 | 11867227 |
| reca protein from the extremely radioresistant bacterium deinococcus radiodurans: expression, purification, and characterization. | the reca protein of deinococcus radiodurans (reca(dr)) is essential for the extreme radiation resistance of this organism. the reca(dr) protein has been cloned and expressed in escherichia coli and purified from this host. in some respects, the reca(dr) protein and the e. coli reca (reca(ec)) proteins are close functional homologues. reca(dr) forms filaments on single-stranded dna (ssdna) that are similar to those formed by the reca(ec). the reca(dr) protein hydrolyzes atp and datp and promotes ... | 2002 | 11872716 |
| transfer rna-dependent amino acid biosynthesis: an essential route to asparagine formation. | biochemical experiments and genomic sequence analysis showed that deinococcus radiodurans and thermus thermophilus do not possess asparagine synthetase (encoded by asna or asnb), the enzyme forming asparagine from aspartate. instead these organisms derive asparagine from asparaginyl-trna, which is made from aspartate in the trna-dependent transamidation pathway [becker, h. d. & kern, d. (1998) proc. natl. acad. sci. usa 95, 12832-12837; and curnow, a. w., tumbula, d. l., pelaschier, j. t., min, ... | 2002 | 11880622 |
| the use of accurate mass tags for high-throughput microbial proteomics. | we describe and review progress towards a global strategy that aims to extend the sensitivity, dynamic range, comprehensiveness, and throughput of proteomic measurements for microbial systems based upon the use of polypeptide accurate mass tags (amts) produced by global protein enzymatic digestions. the two-stage strategy exploits high accuracy mass measurements using fourier transform ion cyclotron resonance mass spectrometry (fticr) to validate polypeptide amts for a specific organism, from po ... | 2002 | 11881835 |
| an exported rhodanese-like protein is induced during growth of acidithiobacillus ferrooxidans in metal sulfides and different sulfur compounds. | by proteomic analysis we found a 21-kda protein (p21) from acidithiobacillus ferrooxidans atcc 19859 whose synthesis was greatly increased by growth of the bacteria in pyrite, thiosulfate, elemental sulfur, cus, and zns and was almost completely repressed by growth in ferrous iron. after we determined the n-terminal amino acid sequence of p21, we used the available preliminary genomic sequence of a. ferrooxidans atcc 23270 to isolate the dna region containing the p21 gene. the nucleotide sequenc ... | 2002 | 11916703 |
| bacteriophage mu genome sequence: analysis and comparison with mu-like prophages in haemophilus, neisseria and deinococcus. | we report the complete 36,717 bp genome sequence of bacteriophage mu and provide an analysis of the sequence, both with regard to the new genes and other genetic features revealed by the sequence itself and by a comparison to eight complete or nearly complete mu-like prophage genomes found in the genomes of a diverse group of bacteria. the comparative studies confirm that members of the mu-related family of phage genomes are genetically mosaic with respect to each other, as seen in other groups ... | 2002 | 11922669 |
| firm but slippery attachment of deinococcus geothermalis. | bacterial biofilms impair the operation of many industrial processes. deinococcus geothermalis is efficient primary biofilm former in paper machine water, functioning as an adhesion platform for secondary biofilm bacteria. it produces thick biofilms on various abiotic surfaces, but the mechanism of attachment is not known. high-resolution field-emission scanning electron microscopy and atomic force microscopy (afm) showed peritrichous adhesion threads mediating the attachment of d. geothermalis ... | 2002 | 11948162 |
| an accurate mass tag strategy for quantitative and high-throughput proteome measurements. | we describe and demonstrate a global strategy that extends the sensitivity, dynamic range, comprehensiveness, and throughput of proteomic measurements based upon the use of peptide "accurate mass tags" (amts) produced by global protein enzymatic digestion. the two-stage strategy exploits fourier transform-ion cyclotron resonance (ft-icr) mass spectrometry to validate peptide amts for a specific organism, tissue or cell type from "potential mass tags" identified using conventional tandem mass spe ... | 2002 | 11987125 |
| low-energy collision-induced dissociation fragmentation analysis of cysteinyl-modified peptides. | the development of methods to chemically modify and isolate cysteinyl-residue-containing peptides (cys-peptides) for lc-ms/ms analysis has generated considerable interest in the field of proteomics. methods using isotope-coded affinity tags (icat) and (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine (iodoacetyl-peo-biotin) employ similar cys-modifying reagents that contain a thiolate-specific biotin group to modify and isolate cys-containing peptides in conjunction with immobilized avidin. for ... | 2002 | 12038753 |
| the reca proteins of deinococcus radiodurans and escherichia coli promote dna strand exchange via inverse pathways. | the reca protein of escherichia coli, and all filament-forming homologues identified to date, promote dna strand exchange by a common, ordered pathway. a filament is first formed on single-stranded dna, followed by uptake of the duplex substrate. these proteins are thereby targeted to single-strand gaps and tails where recombinational dna repair is required. the observed course of dna strand exchange promoted by the reca protein from the extremely radioresistant bacterium deinococcus radiodurans ... | 2002 | 12048253 |
| the branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. | the presence of shared conserved inserts and deletions (indels or signature sequences) in proteins provides a powerful means for understanding the evolutionary relationships among the bacteria. using such indels, all of the main groups within the bacteria can be defined in clear molecular terms and it has become possible to deduce that they branched from a common ancestor in the following order: low g + c gram-positive --> high g+c gram-positive --> deinococcus thermus --> cyanobacteria --> spir ... | 2001 | 12051562 |
| h(2)o(2), which causes macrophage-related stress, triggers induction of expression of virulence-associated plasmid determinants in rhodococcus equi. | the response of the intracellular pathogen rhodococcus equi to h(2)o(2) treatment, a situation potentially encountered after the oxidative burst of alveolar macrophages, was analyzed. compared to other bacteria, including deinococcus radiodurans, r. equi showed exceptionally high resistance to this stress. a proteomic approach showed that four polypeptides present in the wild-type strain (85f) are missing in the plasmid-cured strain 85f(p-), and by using a dna macroarray, we identified two plasm ... | 2002 | 12065520 |
| deinococcus radiodurans catb gene cloning and expression in escherichia coli. | a 1 611 bp length complete coding sequence of the catalase (cat) was obtained through bioimformatical analysis of the database of d.radiodurans genome, and then was amplified from d. radiodurans genomic dna by polymerase chain reaction. the amplified gene was cloned into pkk223-3 vector and transformed into e.coli um2, a cat-deficient mutant. staining of non-denaturing polyacrylamide gels for cat activity demonstrated that pkk223-3 insert encoded a cat that co-migrated with the catb found in d.r ... | 2000 | 12075436 |
| sequence and structural conservation in rna ribose zippers. | the "ribose zipper", an important element of rna tertiary structure, is characterized by consecutive hydrogen-bonding interactions between ribose 2'-hydroxyls from different regions of an rna chain or between rna chains. these tertiary contacts have previously been observed to also involve base-backbone and base-base interactions (a-minor type). we searched for ribose zipper tertiary interactions in the crystal structures of the large ribosomal subunit rnas of haloarcula marismortui and deinococ ... | 2002 | 12096903 |
| a phylogenomic study of the general stress response sigma factor sigmab of bacillus subtilis and its regulatory proteins. | regulation of expression of the general stress regulon of bacillus subtilis is mediated by the activation of the alternative sigma factor sigmab. activation of sigmab is accomplished by a complex regulatory network involving protein-protein interactions and reversible protein phosphorylation. psi-blast searches were performed and phylogenetic trees for sigmab and its regulatory proteins were constructed. occurrence of sigmab is restricted to a small group of gram-positive bacteria (bacillus, sta ... | 2002 | 12125823 |
| cysteine activation is an inherent in vitro property of prolyl-trna synthetases. | aminoacyl-trna synthetases are well known for their remarkable precision in substrate selection during aminoacyl-trna formation. some synthetases enhance the accuracy of this process by editing mechanisms that lead to hydrolysis of incorrectly activated and/or charged amino acids. prolyl-trna synthetases (prorss) can be divided into two structurally divergent groups, archaeal-type and bacterial-type enzymes. a striking difference between these groups is the presence of an insertion domain (appro ... | 2002 | 12130657 |
| regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. | the riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. a model for regulation based on formation of alternative rna structures involving the rfn elements is suggested. in gram-positive bacteria including actinomycetes, thermotoga, thermus and deinococcus, the riboflavin metabolism and transport genes are predicted to be regulated by transcriptional attenuation, whereas in most gram-negative bacteria, the riboflavin biosynthesis ... | 2002 | 12136096 |
| critical issues in bacterial phylogeny. | to understand bacterial phylogeny, it is essential that the following two critical issues be resolved: (i) development of well-defined (molecular) criteria for identifying the main groups within bacteria, and (ii) to understand how the different main groups are related to each other and how they branched off from a common ancestor. these issues are not resolved at present. we have recently described a new approach, based on shared conserved inserts and deletions (indels or signature sequences) f ... | 2002 | 12167362 |
| studies on etching and damage action of low energy ion beam on icrobial cells. | the action of 20 kev n(+) ion on deinococcus radiodurans and e. coli was investigated by means of scanning electron microscope(sem) and electron spin resonance(esr). the results showed that ion implantation exerted direct etching damage and indirect free radicals action by energy deposition on the cells of the two microbes. the dna damage and biological mutation resulted mainly from the etching action of injected ions; the free radicals resulted chiefly in the damage of peroxidation of biologica ... | 1998 | 12167990 |
| global analysis of the deinococcus radiodurans proteome by using accurate mass tags. | understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. to this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by fourier transform ion cy ... | 2002 | 12177431 |
| new technology may reveal mechanisms of radiation resistance in deinococcus radiodurans. | 2002 | 12177454 | |
| disruption analysis of dr1420 and/or dr1758 in the extremely radioresistant bacterium deinococcus radiodurans. | the extremely radioresistant bacterium deinococcus radiodurans encodes two genes that are homologous to those involved in bacterial lysine biosynthesis. in lysine biosynthesis, these genes are involved in the aminoadipate pathway and the diaminopimelate (dap) pathway. dr1420 is homologous to lysz, which is essential for bacterial lysine biosynthesis via the aminoadipate pathway, and dr1758 is homologous to lysa, which is essential for lysine biosynthesis via the dap pathway. in this study, dr142 ... | 2002 | 12213936 |
| l22 ribosomal protein and effect of its mutation on ribosome resistance to erythromycin. | the ribosomal protein l22 is a core protein of the large ribosomal subunit interacting with all domains of the 23s rrna. the triplet met82-lys83-arg84 deletion in l22 from escherichia coli renders cells resistant to erythromycin which is known as an inhibitor of the nascent peptide chain elongation. the crystal structure of the thermus thermophilus l22 mutant with equivalent triplet leu82-lys83-arg84 deletion has been determined at 1.8a resolution. the superpositions of the mutant and the wild-t ... | 2002 | 12225755 |
| quantification of reca protein in deinococcus radiodurans reveals involvement of reca, but not lexa, in its regulation. | reca protein is essential for the very high level of resistance of deinococcus radiodurans to dna damage induced by ionizing radiation or other dna-damaging agents. since the mechanism(s) involved in the control of reca expression and the extent of reca induction following dna damage in this species are still unclear, we have performed a genetic analysis of the reca locus and quantified the basal and induced levels of reca protein in wild type, reca, and lexa mutants. we found that the two genes ... | 2002 | 12242496 |
| bacterial hemoglobins and flavohemoglobins for alleviation of nitrosative stress in escherichia coli. | escherichia coli mg1655 cells expressing novel bacterial hemoglobin and flavohemoglobin genes from a medium-copy-number plasmid were grown in shake flask cultures under nitrosative and oxidative stress. e. coli cells expressing these proteins display enhanced resistance against the no(.) releaser sodium nitroprusside (snp) relative to that of the control strain bearing the parental plasmid. expression of bacterial hemoglobins originating from campylobacter jejuni (chb) and vitreoscilla sp. (vhb) ... | 2002 | 12324328 |
| meiothermus taiwanensis sp. nov., a novel filamentous, thermophilic species isolated in taiwan. | two novel filamentous bacterial isolates, strains wr-30t and wr-220, with an optimum growth temperature of approximately 55-60 degrees c were isolated from wu-rai hot springs in the northern part of taiwan. these isolates were aerobic, thermophilic, non-sporulating, red-pigmented and heterotrophic and formed extremely long, filamentous trichomes from cells of different lengths. phylogenetic analysis of 16s rdna, dna-dna hybridization, morphological and biochemical features and fatty acid composi ... | 2002 | 12361269 |
| high-resolution structures of large ribosomal subunits from mesophilic eubacteria and halophilic archaea at various functional states. | structural analysis of the recently determined high resolution structures of the small and the large ribosomal subunits from three bacterial sources, assisted by the medium resolution structure of a complex of the entire ribosome with three trnas, led to a quantum jump in our understanding of the process of the translation of the genetic code into proteins. results of these studies highlighted dynamic aspects of protein biosynthesis; illuminated the modes of action of several antibiotics; indica ... | 2002 | 12370012 |
| nudix hydrolases that degrade dinucleoside and diphosphoinositol polyphosphates also have 5-phosphoribosyl 1-pyrophosphate (prpp) pyrophosphatase activity that generates the glycolytic activator ribose 1,5-bisphosphate. | a total of 17 nudix hydrolases were tested for their ability to hydrolyze 5-phosphoribosyl 1-pyrophosphate (prpp). all 11 enzymes that were active toward dinucleoside polyphosphates with 4 or more phosphate groups as substrates were also able to hydrolyze prpp, whereas the 6 that could not and that have coenzyme a, ndp-sugars, or pyridine nucleotides as preferred substrates did not degrade prpp. the products of hydrolysis were ribose 1,5-bisphosphate and p(i). active prpp pyrophosphatases includ ... | 2002 | 12370170 |
| closely related cc- and a-adding enzymes collaborate to construct and repair the 3'-terminal cca of trna in synechocystis sp. and deinococcus radiodurans. | the 3'-terminal cca sequence of trna is faithfully constructed and repaired by the cca-adding enzyme (atp(ctp):trna nucleotidyltransferase) using ctp and atp as substrates but no nucleic acid template. until recently, all cca-adding enzymes from all three kingdoms appeared to be composed of a single kind of polypeptide with dual specificity for adding both ctp and atp; however, we recently found that in aquifex aeolicus, which lies near the deepest root of the eubacterial 16 s rrna-based phyloge ... | 2002 | 12370185 |
| asymmetric directional mutation pressures in bacteria. | when there are no strand-specific biases in mutation and selection rates (that is, in the substitution rates) between the two strands of dna, the average nucleotide composition is theoretically expected to be a = t and g = c within each strand. deviations from these equalities are therefore evidence for an asymmetry in selection and/or mutation between the two strands. by focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced b ... | 2002 | 12372146 |
| fold-recognition detects an error in the protein data bank. | 2002 | 12376384 | |
| microbial survival of space vacuum and extreme ultraviolet irradiation: strain isolation and analysis during a rocket flight. | we have recovered new isolates from hot springs, in yellowstone national park and the kamchatka peninsula, after gamma-irradiation and exposure to high vacuum (10(-6) pa) of the water and sediment samples. the resistance to desiccation and ionizing radiation of one of the isolates, bacillus sp. strain ps3d, was compared to that of the mesophilic bacterium, deinococcus radiodurans, a species well known for its extraordinary resistance to desiccation and high doses of ionizing radiation. survival ... | 2002 | 12393217 |
| involvement of two putative alternative sigma factors in stress response of the radioresistant bacterium deinococcus radiodurans. | two genes bearing similarity to alternative sigma factors were identified in the deinococcus radiodurans genome sequence and designated sig1 and sig2. these genes were cloned and inactivated, and both were found to be important for survival during heat and ethanol stress, although the sig1 mutants displayed a more severe phenotype than the sig2 mutants. reporter gene fusions to the groesl and dnakj operons transformed into these mutant backgrounds indicated that sig1 is required for the heat sho ... | 2002 | 12399488 |
| the irre protein of deinococcus radiodurans r1 is a novel regulator of reca expression. | irs24 is a dna damage-sensitive strain of deinococcus radiodurans strain 302 carrying a mutation in an uncharacterized locus designated irre. five overlapping cosmids capable of restoring ionizing radiation resistance to irs24 were isolated from a genomic library. the ends of each cloned insert were sequenced, and these sequences were used to localize irre to a 970-bp region on chromosome i of d. radiodurans r1. the irre gene corresponds to coding sequence dr0167 in the r1 genome. the irre gene ... | 2002 | 12399492 |
| protein splicing of the deinococcus radiodurans strain r1 snf2 intein. | adjacent intein fragments fused to a snf2/rad54 helicase-related protein and snf2/rad54 helicase were reported for deinococcus radiodurans r1, leading to the speculation that a frameshift was required for splicing or that trans splicing occurred. however, a type strain (atcc 13939, rf18410) yielded a single protein that splices by the ala1 protein splicing pathway, with splicing dependent on adjacent residues. | 2002 | 12399510 |
| primegens: robust and efficient design of gene-specific probes for microarray analysis. | motivation: dna microarray is a powerful high-throughput tool for studying gene function and regulatory networks. due to the problem of potential cross hybridization, using full-length genes for microarray construction is not appropriate in some situations. a bioinformatic tool, primegens, has recently been developed for the automatic design of pcr primers using dna fragments that are specific to individual open reading frames (orfs). results: primegens first carries out a blast search for each ... | 2002 | 12424113 |
| gene expression profiling using advanced mass spectrometric approaches. | in the era of systems biology, computational and high-throughput experimental biological approaches are increasingly being combined to provide global snapshots of entire genomes and proteomes under tissue- and disease-specific conditions. the aim is to identify proteins changing in concentration and/or post-translational state and/or location, and develop a better molecular level understanding of the operation of biological systems. here we describe an approach for comparative proteomics that bu ... | 2002 | 12489076 |
| distribution of microorganisms in the subsurface of the manus basin hydrothermal vent field in papua new guinea. | the distribution of microorganisms in the subsurfaces of hydrothermal vents was investigated by using subvent rock core samples. microbial cells and atp were detected from cores taken at depths of less than 99.4 and 44.8 m below the seafloor (mbsf), respectively. cores from various depths were incubated anaerobically with a heterotrophic medium. growth at 60 and 90 degrees c was ascribed to a geobacillus sp. in the 448.6- to 99.4-mbsf cores and a deinococcus sp. in the 64.8- to 128.9-mbsf cores, ... | 2003 | 12514053 |
| structure of the l1 protuberance in the ribosome. | the l1 protuberance of the 50s ribosomal subunit is implicated in the release/disposal of deacylated trna from the e site. the apparent mobility of this ribosomal region has thus far prevented an accurate determination of its three-dimensional structure within either the 50s subunit or the 70s ribosome. here we report the crystal structure at 2.65 a resolution of ribosomal protein l1 from sulfolobus acidocaldarius in complex with a specific 55-nucleotide fragment of 23s rrna from thermus thermop ... | 2003 | 12514741 |
| ringlike structure of the deinococcus radiodurans genome: a key to radioresistance? | the bacterium deinococcus radiodurans survives ionizing irradiation and other dna-damaging assaults at doses that are lethal to all other organisms. how d. radiodurans accurately reconstructs its genome from hundreds of radiation-generated fragments in the absence of an intact template is unknown. here we show that the d. radiodurans genome assumes an unusual toroidal morphology that may contribute to its radioresistance. we propose that, because of restricted diffusion within the tightly packed ... | 2003 | 12522252 |
| acyl-homoserine lactone acylase from ralstonia strain xj12b represents a novel and potent class of quorum-quenching enzymes. | n-acylhomoserine lactones (ahls) are used as signal molecules by many quorum-sensing proteobacteria. diverse plant and animal pathogens use ahls to regulate infection and virulence functions. these signals are subject to biological inactivation by ahl-lactonases and ahl-acylases. previously, little was known about the molecular details underlying the latter mechanism. an ahl signal-inactivating bacterium, identified as a ralstonia sp., was isolated from a mixed-species biofilm. the signal inacti ... | 2003 | 12535081 |
| structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression. | crystal structures of trna mimics complexed with the large ribosomal subunit of deinococcus radiodurans indicate that remote interactions determine the precise orientation of trna in the peptidyl-transferase center (ptc). the ptc tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. sparsomycin binds to a2602 and alters the ptc conformation. h69, the intersubunit-bridge connecting the ptc and deco ... | 2003 | 12535524 |
| [the effect of n+ implantation on sod activity of deinococcus radiodurans and induction of mn-sod]. | the induction of mn-sod and effect of n+ of 20 kev implantation on sod activity of d. radiodurans were investigated. the results were as follows: (1) sod activity of d. radiodurans had a little change when implantation dose was less than 8 x 10(14) n+/cm2, and increased gradually from 8 x 10(14) to 60 x 10(14) n+/cm2, and then decreased rapidly; (2) the test of adding h2o2 and chcl3-ch3ch2oh which could inhibit different types of sod showed that most sod activity of d. radiodurans was constitute ... | 1999 | 12555577 |
| citrate synthase from thermus aquaticus: a thermostable bacterial enzyme with a five-membered inter-subunit ionic network. | a bacterial thermostable citrate synthase has been analyzed to investigate the structural basis of its thermostability, and to compare such features with those previously identified in archaeal citrate synthases. the gene encoding the citrate synthase from thermus aquaticus was identified from a gene library by screening with a pcr fragment amplified from genomic dna using a primer based on the determined n-terminal amino acid sequence and a citrate synthase consensus primer. apart from high seq ... | 2003 | 12579375 |
| high mass measurement accuracy determination for proteomics using multivariate regression fitting: application to electrospray ionization time-of-flight mass spectrometry. | important factors that limit the mass measurement accuracy from a mass spectrometer are related to (1) the type of mass analyzer used and (2) the data processing/calibration methods used to obtain mass values from the raw data. here, two data processing methods are presented that correct for systematic deviations when the mass of ions is measured using a time-of-flight (tof) mass spectrometer. the first fitting method is one where m/z values are obtained from fitting peak distributions using dou ... | 2003 | 12585471 |
| structural basis for the antibiotic activity of ketolides and azalides. | the azalide azithromycin and the ketolide abt-773, which were derived by chemical modifications of erythromycin, exhibit elevated activity against a number of penicillin- and macrolide-resistant pathogenic bacteria. analysis of the crystal structures of the large ribosomal subunit from deinococcus radiodurans complexed with azithromycin or abt-773 indicates that, despite differences in the number and nature of their contacts with the ribosome, both compounds exert their antimicrobial activity by ... | 2003 | 12623020 |
| use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. | the use of artificial neural networks (anns) is described for predicting the reversed-phase liquid chromatography retention times of peptides enzymatically digested from proteome-wide proteins. to enable the accurate comparison of the numerous lc/ms data sets, a genetic algorithm was developed to normalize the peptide retention data into a range (from 0 to 1), improving the peptide elution time reproducibility to approximately 1%. the network developed in this study was based on amino acid resid ... | 2003 | 12641221 |
| a novel complexity measure for comparative analysis of protein sequences from complete genomes. | analysis of sequence complexities of proteins is an important step in the characterization and classification of new genomes. a new measure has been proposed to compute sequence complexity in protein sequences based on linguistic complexity. the algorithm requires a single parameter, is computationally simple and provides a framework for comparative genomic analysis. protein sequences were classified into groups of high or low complexity based on a quantitative measure termed f(c), which is prop ... | 2003 | 12643768 |
| enrichment of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry. | an increasing number of proteomic strategies rely on liquid chromatography-tandem mass spectrometry (lc-ms/ms) to detect and identify constituent peptides of enzymatically digested proteins obtained from various organisms and cell types. however, sample preparation methods for isolating membrane proteins typically involve the use of detergents and chaotropes that often interfere with chromatographic separation and/or electrospray ionization. to address this problem, a sample preparation method c ... | 2002 | 12645891 |
| transcriptome dynamics of deinococcus radiodurans recovering from ionizing radiation. | deinococcus radiodurans r1 (deira) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. to define the repertoire of deira genes responding to acute irradiation (15 kgy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using dna microarrays covering approximately 94% of its predicted genes. at least at one time point ... | 2003 | 12651953 |
| 1h, (13)c, and (15)n nmr assignments of the hypothetical nudix protein dr0079 from the extremely radiation-resistant bacterium deinococcus radiodurans. | 2003 | 12652130 | |
| purification, crystallization and preliminary x-ray analysis of two nudix hydrolases from deinococcus radiodurans. | two nudix hydrolases from deinococcus radiodurans have been purified and crystallized. diffraction data have been collected to 1.4 and 1.9 a resolution for dr1025 and dr0079, respectively. dr1025 belongs to space group p4(1)2(1)2/p4(3)2(1)2, with unit-cell parameters a = b = 53.2, c = 122.6 a (unit-cell volume 346 883 a(3), v(m) = 2.5 a(3) da(-1), solvent content 50.2%). dr0079 belongs to space group c222(1), with unit-cell parameters a = 34.1, b = 157.2, c = 126.5 a (unit-cell volume 677 308 a( ... | 2003 | 12657797 |
| structural insight into the role of the ribosomal tunnel in cellular regulation. | nascent proteins emerge out of ribosomes through an exit tunnel, which was assumed to be a firmly built passive path. recent biochemical results, however, indicate that the tunnel plays an active role in sequence-specific gating of nascent chains and in responding to cellular signals. consistently, modulation of the tunnel shape, caused by the binding of the semi-synthetic macrolide troleandomycin to the large ribosomal subunit from deinococcus radiodurans, was revealed crystallographically. the ... | 2003 | 12665853 |
| colored moderately thermophilic bacteria in paper-machine biofilms. | biofilms cause several problems in papermaking. this report describes a microbiological survey of colored biofilms in six paper and board machines, including two case studies of outbreaks of colored slimes in which the causative bacteria were found. a total of 95 pink-, red-, orange- or yellow-pigmented strains were isolated. nearly all (99%) of the strains grew at 52 degrees c, 72% grew at 56 degrees c, but only 30% grew at 28 degrees c, indicating that most of the strains were moderately therm ... | 2003 | 12700951 |
| affinity labeling of highly hydrophobic integral membrane proteins for proteome-wide analysis. | the ability to identify and quantitate integral membrane proteins is an analytical challenge for mass spectrometry-based proteomics. the use of surfactants to solubilize and facilitate derivatization of these proteins can suppress peptide ionization and interfere with chromatographic separations during microcapillary reversed-phase liquid chromatography-electrospray-tandem mass spectrometry. to circumvent the use of surfactants and increase proteome coverage, an affinity labeling method has been ... | 2003 | 12716129 |
| cloning of structural gene of deinococcus radiodurans uv-endonuclease beta. | to characterize its enzymic property we cloned and sequenced the gene of deinococcus radiodurans encoding uv-endonuclease beta, an alternative enzyme to uvrabc repairing damaged dna. amino acid substitutions were found in uv-sensitive mutants. the putative amino acid sequence had some similarity with those of eukaryotic uv-endonucleases and with a sequence found in a protein data base of bacillus subtilis. | 2003 | 12723611 |
| characterization of class 1 integron resistance gene cassettes and the identification of a novel is-like element in acinetobacter baumannii. | based on hybridization studies, 21/32 multi-resistant clinical isolates of acinetobacter baumannii contain class 1 integrons. amplification products were obtained from 20 of the hybridization-positive strains. a single dfra7 cassette was identified in 18 of the isolates and an integron with two cassettes (aadb-aada4) was found in only one strain. amplicons were not obtained from one of the hybridization positive strains. dna sequence analysis of a 6.080-kb fragment, cloned from this strain, iden ... | 2003 | 12726770 |
| nmr structure of the ribosomal protein l23 from thermus thermophilus. | the ribosomal protein l23 is a component of the large ribosomal subunit in which it is located close to the peptide exit tunnel. in this position l23 plays a central role both for protein secretion and folding. we have determined the solution structure of l23 from thermus thermophilus. uncomplexed l23 consists of a well-ordered part, with four anti-parallel beta-strands and three alpha-helices connected as beta-alpha-beta-alpha-beta-beta-alpha, and a large and flexible loop inserted between the ... | 2003 | 12766408 |
| on peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. derived on 20 october 2002 at the 28th febs meeting in istanbul. | high-resolution crystal structures of large ribosomal subunits from deinococcus radiodurans complexed with trna-mimics indicate that precise substrate positioning, mandatory for efficient protein biosynthesis with no further conformational rearrangements, is governed by remote interactions of the trna helical features. based on the peptidyl transferase center (ptc) architecture, on the placement of trna mimics, and on the existence of a two-fold related region consisting of about 180 nucleotides ... | 2003 | 12787020 |
| the dna excision repair system of the highly radioresistant bacterium deinococcus radiodurans is facilitated by the pentose phosphate pathway. | deinococcus radiodurans is highly resistant to radiation and mutagenic chemicals. mutants defective in the putative glucose-6-phosphate dehydrogenase gene (zwf-) and the aldolase gene (fda-) were generated by homologous recombination. these mutants were used to test the cells' resistance to agents that cause dimer formation and dna strand breaks. the zwf - mutants were more sensitive to agents that induce dna excision repair, such as uv irradiation and h2o2, but were as resistant to dna strand b ... | 2003 | 12787358 |
| production of superoxide dismutase by deinococcus radiophilus. | the production of superoxide dismutase (sod) varied in deinococcus radiophilus, the uv resistant bacterium, depending upon different phases of growth, uv irradiation, and superoxide treatment. a gradual increase in total sod activity occurred up to the stationary phases. the electrophoretic resolution of the sod in cell extracts of d. radiophilus at each growth phase revealed the occurrence of mnsod throughout the growth phases. the sod profiles of d. radiophilus at the exponential phase receive ... | 2003 | 12787483 |
| a lupus-like syndrome develops in mice lacking the ro 60-kda protein, a major lupus autoantigen. | antibodies against a conserved rna-binding protein, the ro 60-kda autoantigen, occur in 24-60% of all patients with systemic lupus erythematosus. anti-ro antibodies are correlated with photosensitivity and cutaneous lesions in these patients and with neonatal lupus, a syndrome in which mothers with anti-ro antibodies give birth to children with complete congenital heart block and photosensitive skin lesions. in higher eukaryotes, the ro protein binds small rnas of unknown function known as y rna ... | 2003 | 12788971 |
| impact of low-temperature plasmas on deinococcus radiodurans and biomolecules. | the effects of cold plasma on deinococcus radiodurans, plasmid dna, and model proteins were assessed using microbiological, spectrometric, and biochemical techniques. in low power o(2) plasma (approximately 25 w, approximately 45 mtorr, 90 min), d. radiodurans, a radiation-resistant bacterium, showed a 99.999% reduction in bioburden. in higher power o(2) plasma (100 w and 500 mtorr), the reduction rate increased about 10-fold and observation by atomic force microscopy showed significant damage t ... | 2003 | 12790638 |
| genomic dna of nostoc commune (cyanobacteria) becomes covalently modified during long-term (decades) desiccation but is protected from oxidative damage and degradation. | genomic dna of nostoc commune (cyanobacteria) became covalently modified during decades of desiccation. amplification of gene loci from desiccated cells required pretreatment of dna with n-phenacylthiazolium bromide, a reagent that cleaves dna- and protein-linked advanced glycosylation end-products. dna from 13 year desiccated cells did not show any higher levels of the commonly studied oxidatively modified dna damage biomarkers 8-hydroxyguanine, 8-hydroxyadenine and 5-hydroxyuracil, compared to ... | 2003 | 12799425 |
| ppri: a general switch responsible for extreme radioresistance of deinococcus radiodurans. | deinococcus radiodurans exhibits an extraordinary ability to withstand the lethal and mutagenic effects of dna damaging agents, particularly, ionizing radiation. available evidence indicates that efficient repair of dna damage and protection of the chromosomal structure are mainly responsible for the radioresistance. little is known about the biochemical basis for this phenomenon. we have identified a unique gene, ppri, as a general switch for downstream dna repair and protection pathways, from ... | 2003 | 12804570 |
| structure of a coenzyme a pyrophosphatase from deinococcus radiodurans: a member of the nudix family. | gene dr1184 from deinococcus radiodurans codes for a nudix enzyme (dr-coase) that hydrolyzes the pyrophosphate moiety of coenzyme a (coa). nudix enzymes with the same specificity have been found in yeast, humans, and mice. the three-dimensional structure of dr-coase, the first of a nudix hydrolase with this specificity, reveals that this enzyme contains, in addition to the fold observed in other nudix enzymes, insertions that are characteristic of a coa-hydrolyzing nudix subfamily. the structure ... | 2003 | 12837785 |
| structural insight into the antibiotic action of telithromycin against resistant mutants. | the crystal structure of the ketolide telithromycin bound to the deinococcus radiodurans large ribosomal subunit shows that telithromycin blocks the ribosomal exit tunnel and interacts with domains ii and v of the 23s rna. comparisons to other clinically relevant macrolides provided structural insights into its enhanced activity against macrolide-resistant strains. | 2003 | 12837804 |
| microbial diversity of cryptoendolithic communities from the mcmurdo dry valleys, antarctica. | in the mcmurdo dry valleys of antarctica, microorganisms colonize the pore spaces of exposed rocks and are thereby protected from the desiccating environmental conditions on the surface. these cryptoendolithic communities have received attention in microscopy and culture-based studies but have not been examined by molecular approaches. we surveyed the microbial biodiversity of selected cryptoendolithic communities by analyzing clone libraries of rrna genes amplified from environmental dna. over ... | 2003 | 12839754 |
| improved peptide sequencing using isotope information inherent in tandem mass spectra. | we demonstrate here the use of natural isotopic 'labels' in peptides to aid in the identification of peptides with a de novo algorithm. using data from ion trap tandem mass spectrometric (ms/ms) analysis of 102 tryptic peptides, we have analyzed multiple series of peaks within lcq ms/ms spectra that 'spell' peptide sequences. isotopic peaks from naturally abundant isotopes are particularly prominent even after peak centroiding on y- and b-series ions and lead to increased confidence in the ident ... | 2003 | 12872285 |
| deinococcus radiodurans. | deinococcus radiodurans (deira) is a remarkable organism. its properties of extreme resistance to environmental damage and ionising radiation command the attention of the cancer research community for the insights which it may bring to the understanding of cytotoxic and radiotherapy treatment resistance. | 2003 | 12875865 |
| vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family thermaceae from a deep-sea hot vent. | a novel thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium designated strain tr(t) was isolated from a sample of a deep-sea hydrothermal chimney collected at the rainbow vent field on the mid-atlantic ridge (36 degrees 14'n). gram-negative, non-spore-forming, non-motile rods occurred singly or in pairs. the organism grew in the temperature range 37-80 degrees c with an optimum at 70 degrees c and at ph 5.5-8.4 with an optimum around 6.7. the nacl range for growth was ... | 2003 | 12892142 |
| engineering deinococcus geothermalis for bioremediation of high-temperature radioactive waste environments. | deinococcus geothermalis is an extremely radiation-resistant thermophilic bacterium closely related to the mesophile deinococcus radiodurans, which is being engineered for in situ bioremediation of radioactive wastes. we report that d. geothermalis is transformable with plasmids designed for d. radiodurans and have generated a hg(ii)-resistant d. geothermalis strain capable of reducing hg(ii) at elevated temperatures and in the presence of 50 gy/h. additionally, d. geothermalis is capable of red ... | 2003 | 12902245 |
| complete resonance assignments for the nudix hydrolase dr2356 of deinococcus radiodurans. | 2003 | 12913415 | |
| cloning of an alkaline phosphatase gene from the moderately thermophilic bacterium meiothermus ruber and characterization of the recombinant enzyme. | a gene that codes for an alkaline phosphatase was cloned from the thermophilic bacterium meiothermus ruber, and its nucleotide sequence was determined. the deduced amino acid sequence indicates that the enzyme precursor including the putative signal sequence is composed of 503 amino acid residues and has an estimated molecular mass of 54,229 da. comparison of the peptide sequence with that of the prototype alkaline phosphatase from escherichia coli revealed conservation of the regions in the vic ... | 2003 | 12928867 |
| [identification of the horizontal gene transfer based on phylogenetic data]. | we suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. the search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. numeric values are introduced to measure the discrepancy between the trees. this approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. this resulted in a list of the candidate genes ... | 2003 | 12942641 |
| using dna microarray data to understand the ionizing radiation resistance of deinococcus radiodurans. | in a recent paper, liu et al. documented the changes in gene expression as stationary phase deinococcus radiodurans cultures recover from acute exposure to gamma radiation. given that the biochemical details of the response of d. radiodurans to ionizing radiation are poorly understood, this work represents an important first step towards achieving an understanding of the ionizing radiation resistance in this species. | 2003 | 12948669 |
| evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. | shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire opero ... | 2003 | 12952534 |
| deinoccocus radiodurans: getting a better fix on dna repair. | 2003 | 12953078 | |
| proteome analyses using accurate mass and elution time peptide tags with capillary lc time-of-flight mass spectrometry. | we describe the application of capillary liquid chromatography (lc) time-of-flight (tof) mass spectrometric instrumentation for the rapid characterization of microbial proteomes. previously (lipton et al., proc. natl. acad. sci. u.s.a. 2002, 99, 11049) the peptides from a series of growth conditions of deinococcus radiodurans have been characterized using capillary lc ms/ms and accurate mass measurements which are captured as an accurate mass and time (amt) tag database. using this amt tag datab ... | 2003 | 12954166 |
| unlocking radiation resistance mechanisms: still a long way to go. | 2003 | 13678857 | |
| [specificity of bacterial response to variation of isotopic composition of water]. | culture growth of bacteria with different membrane lipid composition was studied in liquid media with different isotope content of water. the concentration of deuterium in water was varied from 0.01 to 90%. it was shown that large concentrations of deuterium cause the inhibition of all cultures except deinococcus radiodurans, the most stable living cell. two cultures, methylobacterium organophilum and hyphomonas jannaschiana, showed a pronounced activation at a deuterium concentration of 0.01%. ... | 2003 | 14515487 |
| a dna pairing-enhanced conformation of bacterial reca proteins. | the reca proteins of escherichia coli (ec) and deinococcus radiodurans (dr) both promote a dna strand exchange reaction involving two duplex dnas. the four-strand exchange reaction promoted by the drreca protein is similar to that promoted by ecreca, except that key parts of the reaction are inhibited by ec single-stranded dna-binding protein (ssb). in the absence of ssb, the initiation of strand exchange is greatly enhanced by dsdna-ssdna junctions at the ends of dna gaps. this same trend is se ... | 2003 | 14530291 |
| mechanism of thermotolerance induction by split-dose hyperthermia in deinococcus radiodurans dna repair deficient mutants. | we examined the phenomenon of thermotolerance induction in the radioresistant prokaryote, deinococcus radiodurans, which was initially exposed to 30 min at 52 degrees c followed by various intervals up to 6 h at 30 degrees c in tgy medium and then re-exposed to 52 degrees c for various periods, i.e., split-dose hyperthermia. this thermotolerance induction was analyzed in dna repair deficient mutants (strain 302, 251, uvs25, rec30 and kh840) and the wild-type strain mr1. the strain uvs25 is a dou ... | 2003 | 14533003 |
| the trove module: a common element in telomerase, ro and vault ribonucleoproteins. | ribonucleoproteins carry out a variety of important tasks in the cell. in this study we show that a number of these contain a novel module, that we speculate mediates rna-binding. | 2003 | 14563212 |
| the structure of d. radiodurans. | 2003 | 14576403 | |
| sequence and genetic organization of the 19.3-kb erythromycin- and dalfopristin-resistance plasmid plme300 from lactobacillus fermentum rot1. | lactobacillus fermentum rot1 was isolated from a raw milk dairy product. it is resistant to novobiocin, tetracycline, erythromycin and dalfopristin. a chromosomal tetracycline-resistance determinant was identified as tetm. a 19,398-bp plasmid (plme300), present in several erythromycin-resistant strains of lb. fermentum, was isolated from strain rot1 and completely sequenced. based on putative open reading frames, plme300 contains at least four different functional regions. in region i, orf1 show ... | 2003 | 14597008 |
| pyrroloquinoline-quinone synthesized in escherichia coli by pyrroloquinoline-quinone synthase of deinococcus radiodurans plays a role beyond mineral phosphate solubilization. | deinococcus radiodurans, an extremely radioresistant bacterium, synthesizes coenzyme pyrroloquinoline-quinone (pqq) but exhibits a negative phenotype for mineral phosphate solubilization. gene for the putative pqq synthesizing protein was pcr amplified and cloned from deinococcus, sequenced, and expressed in escherichia coli, under an inducible e. coli promoter. the transgenic e. coli expressed pqq synthase protein of 42kda and complemented the mineral phosphate solubilization phenotype of e. co ... | 2003 | 14637137 |
| expression of deinococcus radiodurans ppri enhances the radioresistance of escherichia coli. | ppri, a newly identified gene switch responsible for extreme radioresistance of deinococcus radiodurans, plays a central regulatory role in multiple dna damage repair and protection pathways in response to radiation stress [biochem. biophy. res. commun. 306 (2003) 354]. to evaluate whether ppri also functions in the radioresistance in other organisms, d. radiodurans ppri protein (deira-ppri) was expressed in escherichia coli. the complemented e. coli strain showed an increase of approximately 1. ... | 2003 | 14642569 |
| nanoscale proteomics. | efforts to develop a liquid chromatography (lc)/mass spectrometry (ms) technology for ultra-sensitive proteomics studies (i.e., nanoscale proteomics) are described. the approach combines high-efficiency nanoscale lc (separation peak capacity of approximately 10(3); 15-microm-i.d. packed capillaries with flow rates of 20 nl min(-1), the optimal separation linear velocity) with advanced ms, including high-sensitivity and high-resolution fourier transform ion cyclotron resonance ms, to perform both ... | 2004 | 14647945 |
| analysis of thermal adaptation in the hsl enzyme family. | the recently solved three-dimensional (3d) structures of two thermostable members of the carboxylesterase/lipase hsl family, namely the alicyclobacillus (formerly bacillus) acidocaldarius and archaeoglobus fulgidus carboxylesterases (est2 and afest, respectively) were compared with that of the mesophilic homologous counterpart brefeldine a esterase from bacillus subtilis. since the 3d homology models of other members of the hsl family were also available, we performed a structural alignment with ... | 2004 | 14659763 |
| characterization and distribution of is8301 in the radioresistant bacterium deinococcus radiodurans. | the insertion sequence element is8301 isolated from the radiation resistant bacterium deinococcus radiodurans strain kd8301 was characterized. is8301 is comprised of 1,736-bp, lacks terminal inverted repeats and does not duplicate target dna upon its insertion. the amino acid sequence homology of two open reading frames encoded in is8301 indicates that this insertion sequence element belongs to the is200/is605 group. there were seven loci completely identical with the is8301 sequence in the publ ... | 2003 | 14676423 |
| cysteinyl-trna(cys) formation in methanocaldococcus jannaschii: the mechanism is still unknown. | most organisms form cys-trna(cys), an essential component for protein synthesis, through the action of cysteinyl-trna synthetase (cysrs). however, the genomes of methanocaldococcus jannaschii, methanothermobacter thermautotrophicus, and methanopyrus kandleri do not contain a recognizable cyss gene encoding cysrs. it was reported that m. jannaschii prolyl-trna synthetase (c. stathopoulos, t. li, r. longman, u. c. vothknecht, h. d. becker, m. ibba, and d. söll, science 287:479-482, 2000; r. s. lip ... | 2004 | 14679218 |