Publications

initiation factor 2 of myxococcus xanthus, a large version of prokaryotic translation initiation factor 2.	we have isolated the structural gene for translation initiation factor if2 (infb) from the myxobacterium myxococcus xanthus. the gene (3.22 kb) encodes a 1,070-residue protein showing extensive homology within its g domain and c terminus to the equivalent regions of if2 from escherichia coli. the protein cross-reacts with antibodies raised against e. coli if2 and was able to complement an e. coli infb mutant. the m. xanthus protein is the largest if2 known to date. this is essentially due to a l ...	2001	11114918
characterization and evolution of anthranilate 1,2-dioxygenase from acinetobacter sp. strain adp1.	the two-component anthranilate 1,2-dioxygenase of the bacterium acinetobacter sp. strain adp1 was expressed in escherichia coli and purified to homogeneity. this enzyme converts anthranilate (2-aminobenzoate) to catechol with insertion of both atoms of o(2) and consumption of one nadh. the terminal oxygenase component formed an alpha(3)beta(3) hexamer of 54- and 19-kda subunits. biochemical analyses demonstrated one rieske-type [2fe-2s] center and one mononuclear nonheme iron center in each larg ...	2001	11114907
rubrerythrin and rubredoxin oxidoreductase in desulfovibrio vulgaris: a novel oxidative stress protection system.	evidence is presented for an alternative to the superoxide dismutase (sod)-catalase oxidative stress defense system in desulfovibrio vulgaris (strain hildenborough). this alternative system consists of the nonheme iron proteins, rubrerythrin (rbr) and rubredoxin oxidoreductase (rbo), the product of the rbo gene (also called desulfoferrodoxin). a deltarbo strain of d. vulgaris was found to be more sensitive to internal superoxide exposure than was the wild type. unlike rbo, expression of plasmid- ...	2001	11114906
recombinant thermus aquaticus rna polymerase, a new tool for structure-based analysis of transcription.	the three-dimensional structure of dna-dependent rna polymerase (rnap) from thermophilic thermus aquaticus has recently been determined at 3.3 a resolution. currently, very little is known about t. aquaticus transcription and no genetic system to study t. aquaticus rnap genes is available. to overcome these limitations, we cloned and overexpressed t. aquaticus rnap genes in escherichia coli. overproduced t. aquaticus rnap subunits assembled into functional rnap in vitro and in vivo when coexpres ...	2001	11114902
evidence for horizontal gene transfer in evolution of elongation factor tu in enterococci.	the elongation factor tu, encoded by tuf genes, is a gtp binding protein that plays a central role in protein synthesis. one to three tuf genes per genome are present, depending on the bacterial species. most low-g+c-content gram-positive bacteria carry only one tuf gene. we have designed degenerate pcr primers derived from consensus sequences of the tuf gene to amplify partial tuf sequences from 17 enterococcal species and other phylogenetically related species. the amplified dna fragments were ...	2000	11092850
crystal structure of yeast initiation factor 4a, a dead-box rna helicase.	the eukaryotic translation initiation factor 4a (eif4a) is a member of the dea(d/h)-box rna helicase family, a diverse group of proteins that couples an atpase activity to rna binding and unwinding. previous work has provided the structure of the amino-terminal, atp-binding domain of eif4a. extending those results, we have solved the structure of the carboxyl-terminal domain of eif4a with data to 1.75 a resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, o ...	2000	11087862
aminoglycosides: perspectives on mechanisms of action and resistance and strategies to counter resistance.		2000	11083623
a dual-specificity aminoacyl-trna synthetase in the deep-rooted eukaryote giardia lamblia.	cysteinyl-trna (cys-trna) is essential for protein synthesis. in most organisms the enzyme responsible for the formation of cys-trna is cysteinyl-trna synthetase (cysrs). the only known exceptions are the euryarchaea methanococcus jannaschii and methanobacterium thermoautotrophicum, which do not encode a cysrs. deviating from the accepted concept of one aminoacyl-trna synthetase per amino acid, these organisms employ prolyl-trna synthetase as the enzyme that carries out cys-trna formation. to da ...	2000	11078517
crystal structure combined with genetic analysis of the thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch.	ribosome recycling factor (rrf), in concert with elongation factor ef-g, is required for disassembly of the posttermination complex of the ribosome after release of polypeptides. the crystal structure of thermus thermophilus rrf was determined at 2.6 a resolution. it is a trna-like l-shaped molecule consisting of two domains: a long three-helix bundle (domain 1) and a three-layer beta/alpha/beta sandwich (domain 2). although the individual domain structures are similar to those of thermotoga mar ...	2000	11073219
improved version 2.0 qualitative and quantitative amplicor reverse transcription-pcr tests for hepatitis c virus rna: calibration to international units, enhanced genotype reactivity, and performance characteristics.	version 2.0 qualitative and quantitative amplicor reverse transcription-pcr tests for hcv were designed to improve on the performance of first version of the hepatitis c virus (hcv) tests. the new tests were calibrated in international units, the new commonly accepted standard unit of measurement for hcv rna. the sensitivity of the qualitative tests was enhanced by modifying the specimen processing procedure to achieve a limit of detection 50 iu/ml. the limit of detection for the quantitative te ...	2000	11060086
trna aminoacylation by arginyl-trna synthetase: induced conformations during substrates binding.	the 2.2 a crystal structure of a ternary complex formed by yeast arginyl-trna synthetase and its cognate trna(arg) in the presence of the l-arginine substrate highlights new atomic features used for specific substrate recognition. this first example of an active complex formed by a class ia aminoacyl-trna synthetase and its natural cognate trna illustrates additional strategies used for specific trna selection. the enzyme specifically recognizes the d-loop and the anticodon of the trna, and the ...	2000	11060012
structural and mechanistic conservation in dna ligases.	dna ligases are enzymes required for the repair, replication and recombination of dna. dna ligases catalyse the formation of phosphodiester bonds at single-strand breaks in double-stranded dna. despite their occurrence in all organisms, dna ligases show a wide diversity of amino acid sequences, molecular sizes and properties. the enzymes fall into two groups based on their cofactor specificity, those requiring nad(+) for activity and those requiring atp. the eukaryotic, viral and archael bacteri ...	2000	11058099
escherichia coli tehb requires s-adenosylmethionine as a cofactor to mediate tellurite resistance.	the escherichia coli chromosomal determinant for tellurite resistance consists of two genes (teha and tehb) which, when expressed on a multicopy plasmid, confer resistance to k(2)teo(3) at 128 microg/ml, compared to the mic of 2 microg/ml for the wild type. tehb is a cytoplasmic protein which possesses three conserved motifs (i, ii, and iii) found in s-adenosyl-l-methionine (sam)-dependent non-nucleic acid methyltransferases. replacement of the conserved aspartate residue in motif i by asparagin ...	2000	11053398
a dna ligase from a hyperthermophilic archaeon with unique cofactor specificity.	a gene encoding dna ligase (lig(tk)) from a hyperthermophilic archaeon, thermococcus kodakaraensis kod1, has been cloned and sequenced, and its protein product has been characterized. lig(tk) consists of 1,686 bp, corresponding to a polypeptide of 562 amino acids with a predicted molecular mass of 64,079 da. sequence comparison with previously reported dna ligases and the presence of conserved motifs suggested that lig(tk) was an atp-dependent dna ligase. phylogenetic analysis indicated that lig ...	2000	11053387
analysis of the levels of conservation of the j domain among the various types of dnaj-like proteins.	dnaj-like proteins are defined by the presence of an approximately 73 amino acid region termed the j domain. this region bears similarity to the initial 73 amino acids of the escherichia coli protein dnaj. although the structures of the j domains of e coli dnaj and human heat shock protein 40 have been solved using nuclear magnetic resonance, no detailed analysis of the amino acid conservation among the j domains of the various dnaj-like proteins has yet been attempted. a multiple alignment of 2 ...	2000	11048657
escherichia coli dna polymerase iii tau- and gamma-subunit conserved residues required for activity in vivo and in vitro.	the escherichia coli dna polymerase iii tau and gamma subunits are single-strand dna-dependent atpases (the latter requires the delta and delta' subunits for significant atpase activity) involved in loading processivity clamp beta. they are homologous to clamp-loading proteins of many organisms from phages to humans. alignment of 27 prokaryotic tau/gamma homologs and 1 eukaryotic tau/gamma homolog has refined the sequences of nine previously defined identity and functional motifs. mutational ana ...	2000	11029431
two-dimensional gel electrophoresis analyses of ph-dependent protein expression in facultatively alkaliphilic bacillus pseudofirmus of4 lead to characterization of an s-layer protein with a role in alkaliphily.	the large majority of proteins of alkaliphilic bacillus pseudofirmus of4 grown at ph 7.5 and 10.5, as studied by two-dimensional gel electrophoresis analyses, did not exhibit significant ph-dependent variation. a new surface layer protein (slpa) was identified in these studies. although the prominence of some apparent breakdown products of slpa in gels from ph 10.5-grown cells led to discovery of the alkaliphile s-layer, the largest and major slpa forms were present in large amounts in gels from ...	2000	11029415
tissue-specific and developmental pattern of expression of the rice sps1 gene.	sucrose-phosphate synthase (sps) is one of the key regulatory enzymes in carbon assimilation and partitioning in plants. sps plays a central role in the production of sucrose in photosynthetic cells and in the conversion of starch or fatty acids into sucrose in germinating seeds. to explore the mechanisms that regulate the tissue-specific and developmental distribution of sps, the expression pattern of rice (oryza sativa) sps1 (genbank accession no. u33175) was examined by in situ reverse transc ...	2000	11027714
elongation of repetitive dna by dna polymerase from a hyperthermophilic bacterium thermus thermophilus.	short repetitive dna sequences are believed to be one of the primordial genetic elements that served as a source of complex large dna found in the genome of modern organisms. however, the mechanism of its expansion (increase in repeat number) during the course of evolution is unclear. we demonstrate that the dna polymerase of the hyperthermophilic bacterium thermus thermophilus can elongate oligodna with several tandem repeats to very long dna in vitro. for instance, 48mer repetitive oligodna (t ...	2000	11024180
evaluation of the abbott lcx hiv-1 rna quantitative, a new assay for quantitative determination of human immunodeficiency virus type 1 rna.	a new quantitative reverse transcription (rt)-pcr assay for human immunodeficiency virus type 1 (hiv-1) rna (abbott lcx hiv rna quantitative assay) has been compared with the organon nuclisens assay on 521 retrospective samples obtained from hiv-1-positive patients monitored during highly active antiretroviral therapy, 79 of whom were assayed also by the chiron quantiplex 3.0 system and on characterized panels. the lcx system showed a moderate correlation (r = 0.795) and gave higher results than ...	2000	11015428
the escherichia coli heat shock protein clpb restores acquired thermotolerance to a cyanobacterial clpb deletion mutant.	in both prokaryotes and eukaryotes, the heat shock protein clpb functions as a molecular chaperone and plays a key role in resisting high temperature stress. clpb is important for the development of thermotolerance in yeast and cyanobacteria but apparently not in escherichia coli. we undertook a complementation study to investigate whether the clpb protein from e coli (ecclpb) differs functionally from its cyanobacterial counterpart in the unicellular cyanobacterium synechococcus sp. pcc 7942. t ...	2000	11005383
organization and expression of a thermus thermophilus arginine cluster: presence of unidentified open reading frames and absence of a shine-dalgarno sequence.	a group of genes regulated by arginine was found clustered in the order argf-orf1-argc-argj-orf4 between other, as yet uncharacterized, open reading frames (orfs). transcription starts were identified immediately upstream from argf and orf4. arginine repressed transcription that was initiated at argf but induced transcription of orf4. the functions of orf1 and orf4 are unknown, but analysis of the sequence of orf4 suggests that it is a membrane protein, possibly involved in transport of arginine ...	2000	11004195
transcriptional regulation of the cpr gene cluster in ortho-chlorophenol-respiring desulfitobacterium dehalogenans.	to characterize the expression and possible regulation of reductive dehalogenation in halorespiring bacteria, a 11.5-kb genomic fragment containing the o-chlorophenol reductive dehalogenase-encoding cprba genes of the gram-positive bacterium desulfitobacterium dehalogenans was subjected to detailed molecular characterization. sequence analysis revealed the presence of eight designated genes with the order cprtkzebacd and with the same polarity except for cprt. the deduced cprc and cprk gene prod ...	2000	11004165
uv-induced crosslinks in the 16s rrnas of escherichia coli, bacillus subtilis and thermus aquaticus and their implications for ribosome structure and photochemistry.	sixteen long-range crosslinks are induced in escherichia coli 16s rrna by far-uv irradiation. crosslinking patterns in two other organisms, bacillus subtilis and thermus aquaticus, were investigated to determine if the number and location of crosslinks in e.coli occur because of unusually photoreactive nucleotides at particular locations in the rrna sequence. thirteen long-range crosslinks in b.subtilis and 15 long-range crosslinks in t.aquaticus were detected by gel electrophoresis and 10 cross ...	2000	11000271
physical and functional interaction between the eukaryotic orthologs of prokaryotic translation initiation factors if1 and if2.	to initiate protein synthesis, a ribosome with bound initiator methionyl-trna must be assembled at the start codon of an mrna. this process requires the coordinated activities of three translation initiation factors (if) in prokaryotes and at least 12 translation initiation factors in eukaryotes (eif). the factors eif1a and eif5b from eukaryotes show extensive amino acid sequence similarity to the factors if1 and if2 from prokaryotes. by a combination of two-hybrid, coimmunoprecipitation, and in ...	2000	10982835
structure and activity of clpb from escherichia coli. role of the amino-and -carboxyl-terminal domains.	clpb is a member of a protein-disaggregating multi-chaperone system in escherichia coli. the mechanism of protein-folding reactions mediated by clpb is currently unknown, and the functional role of different sequence regions in clpb is under discussion. we have expressed and purified the full-length clpb and three truncated variants with the n-terminal, c-terminal, and a double n- and c-terminal deletion. we studied the protein concentration-dependent and atp-induced oligomerization of clpb, cas ...	2000	10982797
search and discovery strategies for biotechnology: the paradigm shift.	profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. the advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. in this ...	2000	10974127
crystal structure of a eukaryote/archaeon-like protyl-trna synthetase and its complex with trnapro(cgg).	prolyl-trna synthetase (prors) is a class iia synthetase that, according to sequence analysis, occurs in different organisms with one of two quite distinct structural architectures: prokaryote-like and eukaryote/archaeon-like. the primary sequence of prors from the hypothermophilic eubacterium thermus thermophilus (prorstt) shows that this enzyme is surprisingly eukaryote/archaeon-like. we describe its crystal structure at 2.43 angstom resolution, which reveals a feature that is unique among cla ...	2000	10970866
bacterial slh domain proteins are non-covalently anchored to the cell surface via a conserved mechanism involving wall polysaccharide pyruvylation.	several bacterial proteins are non-covalently anchored to the cell surface via an s-layer homology (slh) domain. previous studies have suggested that this cell surface display mechanism involves a non-covalent interaction between the slh domain and peptidoglycan-associated polymers. here we report the characterization of a two-gene operon, csaab, for cell surface anchoring, in bacillus anthracis. its distal open reading frame (csab) is required for the retention of slh-containing proteins on the ...	2000	10970841
thermostable chitosanase from bacillus sp. strain ck4: cloning and expression of the gene and characterization of the enzyme.	a thermostable chitosanase gene from the environmental isolate bacillus sp. strain ck4, which was identified on the basis of phylogenetic analysis of the 16s rrna gene sequence and phenotypic analysis, was cloned, and its complete dna sequence was determined. the thermostable chitosanase gene was composed of an 822-bp open reading frame which encodes a protein of 242 amino acids and a signal peptide corresponding to a 30-kda enzyme. the deduced amino acid sequence of the chitosanase from bacillu ...	2000	10966383
genetic analysis of an incomplete muts gene from pseudomonas putida.	we genetically characterized the pseudomonas putida muts gene and found that it encodes a smaller muts protein than do the genes of other bacteria. this gene is able to function in the muts mutants of escherichia coli and bacillus subtilis. a p. putida muts mutant has a mutation frequency 1,000-fold greater than that of the wild-type strain.	2000	10960118
a hydrogen peroxide-forming nadh oxidase that functions as an alkyl hydroperoxide reductase in amphibacillus xylanus.	the amphibacillus xylanus nadh oxidase, which catalyzes the reduction of oxygen to hydrogen peroxide with beta-nadh, can also reduce hydrogen peroxide to water in the presence of free flavin adenine dinucleotide (fad) or the small disulfide-containing salmonella enterica ahpc protein. the enzyme has two disulfide bonds, cys128-cys131 and cys337-cys340, which can act as redox centers in addition to the enzyme-bound fad (k. ohnishi, y. niimura, m. hidaka, h. masaki, h. suzuki, t. uozumi, and t. ni ...	2000	10960086
designed protein tetramer zipped together with a hydrophobic alzheimer homology: a structural clue to amyloid assembly.	limited solubility and precipitation of amyloidogenic sequences such as the alzheimer peptide (beta-ap) are major obstacles to a molecular understanding of protein fibrillation and deposition processes. here we have circumvented the solubility problem by stepwise engineering a beta-ap homology into a soluble scaffold, the monomeric protein s6. the s6 construct with the highest beta-ap homology crystallizes as a tetramer that is linked by the beta-ap residues forming intermolecular antiparallel b ...	2000	10944185
identification of enzymes homologous to isocitrate dehydrogenase that are involved in coenzyme b and leucine biosynthesis in methanoarchaea.	two putative methanococcus jannaschii isocitrate dehydrogenase genes, mj1596 and mj0720, were cloned and overexpressed in escherichia coli, and their gene products were tested for the ability to catalyze the nad- and nadp-dependent oxidative decarboxylation of dl-threo-3-isopropylmalic acid, threo-isocitrate, erythro-isocitrate, and homologs of threo-isocitrate. neither enzyme was found to use any of the isomers of isocitrate as a substrate. the protein product of the mj1596 gene, designated aks ...	2000	10940051
tarp: a nuclear protein expressed in prostate and breast cancer cells derived from an alternate reading frame of the t cell receptor gamma chain locus.	previously, we identified the expression of a prostate-specific form of t cell receptor gamma chain (tcrgamma) mrna in the human prostate and demonstrated that it originates from epithelial cells and not from infiltrating t lymphocytes. here, we show that this prostate-specific transcript is also expressed in three breast cancer cell lines and breast cancer tissues. analysis of the cdna sequence predicts that this transcript can encode two protein products of 7 and 13 kda, and in vitro translati ...	2000	10931945
visualization of trna movements on the escherichia coli 70s ribosome during the elongation cycle.	three-dimensional cryomaps have been reconstructed for trna-ribosome complexes in pre- and posttranslocational states at 17-a resolution. the positions of trnas in the a and p sites in the pretranslocational complexes and in the p and e sites in the posttranslocational complexes have been determined. of these, the p-site trna position is the same as seen earlier in the initiation-like fmet-trna(f)(met)-ribosome complex, where it was visualized with high accuracy. now, the positions of the a- and ...	2000	10931859
crystal structure of a repair enzyme of oxidatively damaged dna, mutm (fpg), from an extreme thermophile, thermus thermophilus hb8.	the mutm [formamidopyrimidine dna glycosylase (fpg)] protein is a trifunctional dna base excision repair enzyme that removes a wide range of oxidatively damaged bases (n-glycosylase activity) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (ap lyase activity). the crystal structure of mutm from an extreme thermophile, thermus thermophilus hb8, was determined at 1.9 a resolution with multiwavelength anomalous diffraction phasing using the intrinsic ...	2000	10921868
anaerobic xylose fermentation by recombinant saccharomyces cerevisiae carrying xyl1, xyl2, and xks1 in mineral medium chemostat cultures.	for ethanol production from lignocellulose, the fermentation of xylose is an economic necessity. saccharomyces cerevisiae has been metabolically engineered with a xylose-utilizing pathway. however, the high ethanol yield and productivity seen with glucose have not yet been achieved. to quantitatively analyze metabolic fluxes in recombinant s. cerevisiae during metabolism of xylose-glucose mixtures, we constructed a stable xylose-utilizing recombinant strain, tmb 3001. the xyl1 and xyl2 genes fro ...	2000	10919795
sequencing, cloning, and high-level expression of the pfp gene, encoding a pp(i)-dependent phosphofructokinase from the extremely thermophilic eubacterium dictyoglomus thermophilum.	the sequencing, cloning, and expression of the pfp gene from dictyoglomus thermophilum, which consists of 1,041 bp and encodes a pyrophosphate-dependent phosphofructokinase, are described. a phylogenetic analysis indicates that the enzyme is closely related to the pyrophosphate-dependent enzyme from thermoproteus tenax. the recombinant and native enzymes share a high degree of similarity for most properties examined.	2000	10913106
a carboxy-terminal 16-amino-acid region of sigma(38) of escherichia coli is important for transcription under high-salt conditions and sigma activities in vivo.	sigma(38) (or sigma(s), the rpos gene product) is a sigma subunit of rna polymerase in escherichia coli and directs transcription from a number of stationary-phase promoters as well as osmotically inducible promoters. in this study, we analyzed the function of the carboxy-terminal 16-amino-acid region of sigma(38) (residues 315 to 330), which is well conserved among the rpos gene products of enteric bacterial species. truncation of this region was shown to result in the loss of sigma activity in ...	2000	10913098
common fold in helix-hairpin-helix proteins.	helix-hairpin-helix (hhh) is a widespread motif involved in non-sequence-specific dna binding. the majority of hhh motifs function as dna-binding modules, however, some of them are used to mediate protein-protein interactions or have acquired enzymatic activity by incorporating catalytic residues (dna glycosylases). from sequence and structural analysis of hhh-containing proteins we conclude that most hhh motifs are integrated as a part of a five-helical domain, termed (hhh)(2) domain here. it t ...	2000	10908318
arginines 29 and 59 of elongation factor g are important for gtp hydrolysis or translocation on the ribosome.	gtp hydrolysis by elongation factor g (ef-g) is essential for the translocation step in protein elongation. the low intrinsic gtpase activity of ef-g is strongly stimulated by the ribosome. here we show that a conserved arginine, r29, of escherichia coli ef-g is crucial for gtp hydrolysis on the ribosome, but not for gtp binding or ribosome interaction, suggesting that it may be directly involved in catalysis. another conserved arginine, r59, which is homologous to the catalytic arginine of g(al ...	2000	10880458
crystal structure of cystalysin from treponema denticola: a pyridoxal 5'-phosphate-dependent protein acting as a haemolytic enzyme.	cystalysin is a c(beta)-s(gamma) lyase from the oral pathogen treponema denticola catabolyzing l-cysteine to produce pyruvate, ammonia and h(2)s. with its ability to induce cell lysis, cystalysin represents a new class of pyridoxal 5'-phosphate (plp)-dependent virulence factors. the crystal structure of cystalysin was solved at 1.9 a resolution and revealed a folding and quaternary arrangement similar to aminotransferases. based on the active site architecture, a detailed catalytic mechanism is ...	2000	10880431
influence of sulfide and temperature on species composition and community structure of hot spring microbial mats.	in solfataric fields in southwestern iceland, neutral and sulfide-rich hot springs are characterized by thick bacterial mats at 60 to 80 degrees c that are white or yellow from precipitated sulfur (sulfur mats). in low-sulfide hot springs in the same area, grey or pink streamers are formed at 80 to 90 degrees c, and a chloroflexus mat is formed at 65 to 70 degrees c. we have studied the microbial diversity of one sulfur mat (high-sulfide) hot spring and one chloroflexus mat (low-sulfide) hot spr ...	2000	10877776
importance of discriminator base stacking interactions: molecular dynamics analysis of a73 microhelix(ala) variants.	transfer of alanine from escherichia coli alanyl-trna synthetase (alars) to rna minihelices that mimic the amino acid acceptor stem of trna(ala) has been shown, by analysis of variant minihelix aminoacylation activities, to involve a transition state sensitive to changes in the 'discriminator' base at position 73. solution nmr has indicated that this single-stranded nucleotide is predominantly stacked onto g1 of the first base pair of the alanine acceptor stem helix. we report the activity of a ...	2000	10871402
characterization of an atp-dependent dna ligase from the thermophilic archaeon methanobacterium thermoautotrophicum.	we report the production, purification and characterization of a dna ligase encoded by the thermophilic archaeon methanobacterium thermoautotrophicum. the 561 amino acid mth: ligase catalyzed strand-joining on a singly nicked dna in the presence of a divalent cation (magnesium, manganese or cobalt) and atp (k(m) 1.1 microm). datp can substitute for atp, but ctp, gtp, utp and nad(+) cannot. mth: ligase activity is thermophilic in vitro, with optimal nick-joining at 60 degrees c. mutational analys ...	2000	10871342
peptide deformylase in staphylococcus aureus: resistance to inhibition is mediated by mutations in the formyltransferase gene.	peptide deformylase, a bacterial enzyme, represents a novel target for antibiotic discovery. two deformylase homologs, defa and defb, were identified in staphylococcus aureus. the defa homolog, located upstream of the transformylase gene, was identified by genomic analysis and was cloned from chromosomal dna by pcr. a distinct homolog, defb, was cloned from an s. aureus genomic library by complementation of the arabinose-dependent phenotype of a p(bad)-def escherichia coli strain grown under ara ...	2000	10858337
the location of protein s8 and surrounding elements of 16s rrna in the 70s ribosome from combined use of directed hydroxyl radical probing and x-ray crystallography.	ribosomal protein s8, which is essential for the assembly of the central domain of 16s rrna, is one of the most thoroughly studied rna-binding proteins. to map its surrounding rna in the ribosome, we carried out directed hydroxyl radical probing of 16s rrna using fe(ii) tethered to nine different positions on the surface of protein s8 in 70s ribosomes. hydroxyl radical-induced cleavage was observed near the classical s8-binding site in the 620 stem, and flanking the other s8-footprinted regions ...	2000	10836793
three-dimensional cryo-electron microscopy localization of ef2 in the saccharomyces cerevisiae 80s ribosome at 17.5 a resolution.	using a sordarin derivative, an antifungal drug, it was possible to determine the structure of a eukaryotic ribosome small middle dotef2 complex at 17.5 a resolution by three-dimensional (3d) cryo-electron microscopy. ef2 is directly visible in the 3d map and the overall arrangement of the complex from saccharomyces cerevisiae corresponds to that previously seen in escherichia coli. however, pronounced differences were found in two prominent regions. first, in the yeast system the interaction be ...	2000	10835368
performance of the cobas amplicor hcv monitor test, version 2.0, an automated reverse transcription-pcr quantitative system for hepatitis c virus load determination.	a clinical evaluation of an automated quantitative pcr assay, the cobas amplicor hcv monitor test, version 2.0 (v2.0), was carried out to assess the performance of this test in comparison with that of the previous, manual version, the amplicor hcv monitor test, and with that of nested pcr. serial dilutions of serum samples infected with genotype 1b, 2a, or 3, as well as synthetic rna transcripts and serum samples derived from 87 patients with chronic hepatitis c and infected with genotype 1a, 1b ...	2000	10834978
the 2 a crystal structure of leucyl-trna synthetase and its complex with a leucyl-adenylate analogue.	leucyl-, isoleucyl- and valyl-trna synthetases are closely related large monomeric class i synthetases. each contains a homologous insertion domain of approximately 200 residues, which is thought to permit them to hydrolyse ('edit') cognate trna that has been mischarged with a chemically similar but non-cognate amino acid. we describe the first crystal structure of a leucyl-trna synthetase, from the hyperthermophile thermus thermophilus, at 2.0 a resolution. the overall architecture is similar t ...	2000	10811626
conversion of a c type cytochrome to a b type that spontaneously forms in vitro from apo protein and heme: implications for c type cytochrome biogenesis and folding.	cytochrome c(552) from hydrogenobacter thermophilus, a thermophilic bacterium, has been converted into a b type cytochrome, after mutagenesis of both heme-binding cysteines to alanine and expression in the cytoplasm of escherichia coli. the b type variant is less stable, with the guanidine hydrochloride unfolding midpoint occurring at a concentration 2 m lower than for the wild-type protein. the reduction potential is 75 mv lower than that of the recombinant wild-type protein. the heme can be re ...	2000	10792037
thermostabilization of proteins by diglycerol phosphate, a new compatible solute from the hyperthermophile archaeoglobus fulgidus.	diglycerol phosphate accumulates under salt stress in the archaeon archaeoglobus fulgidus (l. o. martins, r. huber, h. huber, k. o. stetter, m. s. da costa, and h. santos, appl. environ. microbiol. 63:896-902, 1997). this solute was purified after extraction from the cell biomass. in addition, the optically active and the optically inactive (racemic) forms of the compound were synthesized, and the ability of the solute to act as a protecting agent against heating was tested on several proteins d ...	2000	10788369
detection of infectious cryptosporidium parvum oocysts in mussels (mytilus galloprovincialis) and cockles (cerastoderma edule).	infective cryptosporidium parvum oocysts were detected in mussels (mytilus galloprovincialis) and cockles (cerastoderma edule) from a shellfish-producing region (gallaecia, northwest spain, bounded by the atlantic ocean) that accounts for the majority of european shellfish production. shellfish were collected from bay sites with different degrees of organic pollution. shellfish harboring c. parvum oocysts were recovered only from areas located near the mouths of rivers with a high density of gra ...	2000	10788352
structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus.	cytochrome c oxidase is a respiratory enzyme catalysing the energy-conserving reduction of molecular oxygen to water. the crystal structure of the ba(3)-cytochrome c oxidase from thermus thermophilus has been determined to 2.4 a resolution using multiple anomalous dispersion (mad) phasing and led to the discovery of a novel subunit iia. a structure-based sequence alignment of this phylogenetically very distant oxidase with the other structurally known cytochrome oxidases leads to the identificat ...	2000	10775261
generation of dominant selectable markers for resistance to pseudomonic acid by cloning and mutagenesis of the iles gene from the archaeon methanosarcina barkeri fusaro.	currently, only one selectable marker is available for genetic studies in the archaeal genus methanosarcina. here we report the generation of selectable markers that encode resistance to pseudomonic acid (pa(r)) in methanosarcina species by mutagenesis of the isoleucyl-trna synthetase gene (iles) from methanosarcina barkeri fusaro. the m. barkeri iles gene was obtained by screening of a genomic library for hybridization to a pcr fragment. the complete 3,787-bp dna sequence surrounding and includ ...	2000	10762266
genome plasticity among related ++lactococcus strains: identification of genetic events associated with macrorestriction polymorphisms.	the genomic diversity of nine strains of the lactococcus lactis subsp. cremoris (ncdo712, ncdo505, ncdo2031, ncdo763, mms36, c2, lm0230, lm2301, and mg1363) was studied by macrorestriction enzyme analysis using pulsed-field gel electrophoresis. these strains were considered adequate for the investigation of genomic plasticity because they have been described as belonging to the same genetic lineage. comparison of apai and smai genome fingerprints of each strain revealed the presence of several m ...	2000	10762249
a hierarchy of rna subdomains in assembly of the central domain of the 30 s ribosomal subunit.	beginning with the framework that has been developed for the assembly of the 30 s ribosomal subunit, we have identified a series of rnas that are minimal binding sites for proteins s15, s6, s18, and s11 in the central domain from thermus thermophilus. the minimal binding rna for proteins s15, s6, and s18 consists of helix 22 and three-way junctions at both ends composed of portions of helices 20, 21, and 23. addition of the remaining portion of helix 23 to this construct results in the minimal s ...	2000	10744024
expression of a heterologous glutamate dehydrogenase gene in lactococcus lactis highly improves the conversion of amino acids to aroma compounds.	the first step of amino acid degradation in lactococci is a transamination, which requires an alpha-keto acid as the amino group acceptor. we have previously shown that the level of available alpha-keto acid in semihard cheese is the first limiting factor for conversion of amino acids to aroma compounds, since aroma formation is greatly enhanced by adding alpha-ketoglutarate to cheese curd. in this study we introduced a heterologous catabolic glutamate dehydrogenase (gdh) gene into lactococcus l ...	2000	10742211
two nitrate/nitrite transporters are encoded within the mobilizable plasmid for nitrate respiration of thermus thermophilus hb8.	thermus thermophilus hb8 can grow anaerobically by using a membrane-bound nitrate reductase to catalyze the reduction of nitrate as a final electron acceptor in respiration. in contrast to other denitrifiers, the nitrite produced does not continue the reduction pathway but accumulates in the growth medium after its active extrusion from the cell. we describe the presence of two genes, nark1 and nark2, downstream of the nitrate reductase-encoding gene cluster (nar) that code for two homologues to ...	2000	10735860
one tube mutation detection using sensitive fluorescent dyeing of muts protected dna.	a novel, universal method for mutation detection utilising the ability of muts protein to recognise dna incomplementarities is proposed. the examined and reference dna fragments are pcr amplified. the pcr products are purified, mixed, heated and cooled to form heteroduplexes. in the case of mutation the heteroduplex dna containing mismatch is protected against exonuclease digestion by muts, while the dna without mismatches is degraded. the protection effect is visualised by the direct addition o ...	2000	10734213
a missense mutation in the nuclear gene coding for the mitochondrial aspartyl-trna synthetase suppresses a mitochondrial trna(asp) mutation.	the nuclear suppressor allele nsm3 in strain ff1210-6c/170-e22 (e22), which suppresses a mutation of the yeast mitochondrial trna(asp)gene in saccharomyces cerevisiae, was cloned and identified. to isolate the nsm3 allele, a genomic dna library using the vector yep13 was constructed from strain e22. nine yep13 recombinant plasmids were isolated and shown to suppress the mutation in the mitochondrial trna(asp)gene. these nine plasmids carry a common 4. 5-kb chromosomal dna fragment which contains ...	2000	10710420
aminoacyl-trna synthetases, the genetic code, and the evolutionary process.	the aminoacyl-trna synthetases (aarss) and their relationship to the genetic code are examined from the evolutionary perspective. despite a loose correlation between codon assignments and aars evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. nevertheless, the aarss are very informative about the evolutionary process. examination of the phylogenetic trees for each of the aarss reveals the following. ...	2000	10704480
metabolic engineering of saccharomyces cerevisiae.	comprehensive knowledge regarding saccharomyces cerevisiae has accumulated over time, and today s. cerevisiae serves as a widley used biotechnological production organism as well as a eukaryotic model system. the high transformation efficiency, in addition to the availability of the complete yeast genome sequence, has facilitated genetic manipulation of this microorganism, and new approaches are constantly being taken to metabolicially engineer this organism in order to suit specific needs. in t ...	2000	10704473
crystal structure of nad(+)-dependent dna ligase: modular architecture and functional implications.	dna ligases catalyze the crucial step of joining the breaks in duplex dna during dna replication, repair and recombination, utilizing either atp or nad(+) as a cofactor. despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of dna ligase share basically the same catalytic mechanism. in this study, the crystal structure of an nad(+)-dependent dna ligase from thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwav ...	2000	10698952
evolution of arginine biosynthesis in the bacterial domain: novel gene-enzyme relationships from psychrophilic moritella strains (vibrionaceae) and evolutionary significance of n-alpha-acetyl ornithinase.	in the arginine biosynthetic pathway of the vast majority of prokaryotes, the formation of ornithine is catalyzed by an enzyme transferring the acetyl group of n-alpha-acetylornithine to glutamate (ornithine acetyltransferase [oatase]) (argj encoded). only two exceptions had been reported-the enterobacteriaceae and myxococcus xanthus (members of the gamma and delta groups of the class proteobacteria, respectively)-in which ornithine is produced from n-alpha-acetylornithine by a deacylase, acetyl ...	2000	10692366
ligation reaction specificities of an nad(+)-dependent dna ligase from the hyperthermophile aquifex aeolicus.	an nad(+)-dependent dna ligase from the hyperthermophilic bacterium aquifex aeolicus was cloned, expressed in escherichia coli and purified to homogeneity. the enzyme is most active in slightly alkaline ph conditions with either mg(2+)or mn(2+)as the metal cofactor. ca(2+)and ni(2+)mainly support formation of dna-adenylate intermediates. the catalytic cycle is characterized by a low k (cat)value of 2 min(-1)with concomitant accumulation of the dna - adenylate intermediate when mg(2+)is used as t ...	2000	10684941
modified constructs of the trna tpsic domain to probe substrate conformational requirements of m(1)a(58) and m(5)u(54) trna methyltransferases.	the tpsic stem and loop (tsl) of trna contains highly conserved nucleoside modifications, m(5)c(49), t(54), psi(55)and m(1)a(58). u(54)is methylated to m(5)u (t) by m(5)u(54)methyltransferase (rumt); a(58)is methylated to m(1)a by m(1)a(58)trna methyltransferase (ramt). rumt recognizes and methylates a minimal tsl heptadecamer and ramt has previously been reported to recognize and methylate the 3'-half of the trna molecule. we report that ramt can recognize and methylate a tsl heptadecamer. to b ...	2000	10684932
nonlinearity in genetic decoding: homologous dna replicase genes use alternatives of transcriptional slippage or translational frameshifting.	the tau and gamma subunits of dna polymerase iii are both encoded by a single gene in escherichia coli and thermus thermophilus. gamma is two-thirds the size of tau and shares virtually all its amino acid sequence with tau. e. coli and t. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between tau and gamma. both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller gamma protein. in e. coli ...	2000	10677518
effect of temperature on stability and activity of elongation factor 2 proteins from antarctic and thermophilic methanogens.	despite the presence and abundance of archaea in low-temperature environments, little information is available regarding their physiological and biochemical properties. in order to investigate the adaptation of archaeal proteins to low temperatures, we purified and characterized the elongation factor 2 (ef-2) protein from the antarctic methanogen methanococcoides burtonii, which was expressed in escherichia coli, and compared it to the recombinant ef-2 protein from a phylogenetically related the ...	2000	10671454
cyanobacterial cell walls: news from an unusual prokaryotic envelope.		2000	10671437
protein sequences conserved in prokaryotic aminoacyl-trna synthetases are important for the activity of the processivity factor of human mitochondrial dna polymerase.	previous studies have shown that the small subunit of xenopus dna polymerase gamma (pol gammab) acts as a processivity factor to stimulate the 140 kda catalytic subunit of human dna polymerase gamma. a putative human pol gammab initially identified by analysis of dna sequence had not been shown to be functional, and appeared to be an incomplete clone. in this paper, we report the cloning of full-length human and mouse pol gammab. both human and mouse pol gammab proteins were expressed in their m ...	2000	10666468
pcr-based assay to quantify human immunodeficiency virus type 1 dna in peripheral blood mononuclear cells.	an assay that quantifies the amount of human immunodeficiency virus type 1 (hiv-1) dna in peripheral blood mononuclear cells has been developed. pcr amplification of the hiv-1 dna is performed in the presence of an internal quantitation standard, and colorimetric detection of the amplified product is performed with microwell plates. the copies of hiv-1 dna are normalized to total genomic dna input. the assay has an analytical sensitivity of 10 input copies per amplification reaction and a three- ...	2000	10655358
a recurrent rna-binding domain is appended to eukaryotic aminoacyl-trna synthetases.	aminoacyl-trna synthetases of higher eukaryotes possess polypeptide extensions in contrast to their prokaryotic counterparts. these extra domains of poorly understood function are believed to be involved in protein-protein or protein-rna interactions. here we showed by gel retardation and filter binding experiments that the repeated units that build the linker region of the bifunctional glutamyl-prolyl-trna synthetase had a general rna-binding capacity. the solution structure of one of these rep ...	2000	10654942
structure and expression of the human p68 rna helicase gene.	nuclear dead box protein p68 is immunologically related to sv40 large tumour antigen and both proteins possess rna helicase activity. in this report, we describe the structural organisation of the human p68 gene and aspects of the regulation of its expression. northern blot and primer extension analyses indicate that, although its level is variable, the p68 rna helicase appears to be expressed from a single transcription start site in all tissues tested. sequence analysis revealed that the p68 p ...	2000	10648785
s-layer proteins.		2000	10648507
optimised ligation of oligonucleotides by thermal ligases: comparison of thermus scotoductus and rhodothermus marinus dna ligases to other thermophilic ligases.	we describe the characterisation of four thermo-stable nad(+)-dependent dna ligases, from thermus thermophilus (tth), thermus scotoductus (ts), rhodothermus marinus (rm) and thermus aquaticus (taq), by an assay which measures ligation rate and mismatch discrimination. complete libraries of octa-, nona- and decanucleotides were used as substrates. the assay comprised the polymerisation of oligo-nucleotides initiated from a 17 base 'primer', using m13mp18 ssdna as template. polymers of ligation pr ...	2000	10637340
active site constraints in the hydrolysis reaction catalyzed by bacterial rnase p: analysis of precursor trnas with a single 3'-s-phosphorothiolate internucleotide linkage.	endonucleolytic processing of precursor trnas (ptrnas) by rnase p yields 3'-oh and 5'-phosphate termini, and at least two metal ions are thought to be essential for catalysis. to determine if the hydrolysis reaction catalyzed by bacterial rnase p (rnas) involves stabilization of the 3'-oxyanion leaving group by direct coordination to one of the catalytic metal ions, ptrna substrates with single 3'- s -phosphorothiolate linkages at the rnase p cleavage site were synthesized. with a 3'- s -phospho ...	2000	10637323
flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein l12.	protein l12, the only multicopy component of the ribosome, is presumed to be involved in the binding of translation factors, stimulating factor-dependent gtp hydrolysis. crystal structures of l12 from thermotogamaritima have been solved in two space groups by the multiple anomalous dispersion method and refined at 2.4 and 2.0 a resolution. in both crystal forms, an asymmetric unit comprises two full-length l12 molecules and two n-terminal l12 fragments that are associated in a specific, hetero-t ...	2000	10637222
functional analysis of the small component of the 4-hydroxyphenylacetate 3-monooxygenase of escherichia coli w: a prototype of a new flavin:nad(p)h reductase subfamily.	escherichia coli w uses the aromatic compound 4-hydroxyphenylacetate (4-hpa) as a sole source of carbon and energy for growth. the monooxygenase which converts 4-hpa into 3,4-dihydroxyphenylacetate, the first intermediate of the pathway, consists of two components, hpab (58.7 kda) and hpac (18.6 kda), encoded by the hpab and hpac genes, respectively, that form a single transcription unit. overproduction of the small hpac component in e. coli k-12 cells has facilitated the purification of the pro ...	2000	10633095
identification and characterization of immunoglobulin g in blood as a major inhibitor of diagnostic pcr.	a major inhibitor of diagnostic pcr in human plasma was identified and the mechanism of inhibition was characterized. human blood was divided by centrifugation into buffy coat, plasma, platelets, and erythrocytes. all these blood fractions were found to be highly inhibitory to a standardized pcr mixture containing the thermostable dna polymerase amplitaq gold. pcr inhibitors in human plasma were purified by chromatographic procedures and were characterized by a process of elimination, so that th ...	2000	10618113
the heme-copper oxidases of thermus thermophilus catalyze the reduction of nitric oxide: evolutionary implications.	we show that the heme-copper terminal oxidases of thermus thermophilus (called ba(3) and caa(3)) are able to catalyze the reduction of nitric oxide (no) to nitrous oxide (n(2)o) under reducing anaerobic conditions. the rate of no consumption and n(2)o production were found to be linearly dependent on enzyme concentration, and activity was abolished by enzyme denaturation. thus, contrary to the eukaryotic enzyme, both t. thermophilus oxidases display a no reductase activity (3.0 +/- 0.7 mol no/mo ...	1999	10611279
structural and functional analyses of the secondary cell wall polymer of bacillus sphaericus ccm 2177 that serves as an s-layer-specific anchor.	sacculi of bacillus sphaericus ccm 2177 contain a secondary cell wall polymer which was completely extracted with 48% hydrofluoric acid. nuclear magnetic resonance analysis showed that the polymer is composed of repeating units, as follows: -->3)-[4, 6-o-(1-carboxyethylidene)]( approximately 0. 5)-beta-d-manpnac-(1-->4)-beta-d-glcpnac-(1-->. the n-terminal part of the s-layer protein carrying s-layer homologous motifs recognizes this polymer as a binding site.	1999	10601228
aminoacyl-trna synthetases database y2k.	the aminoacyl-trna synthetases (aars) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from dna into protein. they catalyse the attachment of amino acids to transfer rnas and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid. currently, 818 aars primary structures have been reported from archaebacteria, eubacteria, mitochondria, chloro-plasts and eukaryotic cells. the ...	2000	10592262
tmrdb (tmrna database).	the tmrna database (tmrdb) is maintained at the university of texas health science center at tyler, texas, and is accessible on the www at url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.++ +html. a tmrdb mirror site is located on the campus of auburn university, auburn, alabama, reachable at the url http://www.ag.auburn.edu/mirror/tmrdb/. since april 1997, the tmrdb has provided sequences of tmrna (previously called 10sa rna), a molecule present in most bacteria and some organelles. this release ad ...	2000	10592214
5s ribosomal rna database y2k.	this paper presents the updated version (y2k) of the database of ribosomal 5s ribonucleic acids (5s rrna) and their genes (5s rdna), http://rose.man/poznan.pl/5sdata/index.html. this edition of the database contains 1985primary structures of 5s rrna and 5s rdna. they include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. the nucleotide sequences of the 5s rrnas or 5s rdnas are divided according to the taxonomic position of the source organisms.	2000	10592212
the small ribosomal subunit from thermus thermophilus at 4.5 a resolution: pattern fittings and the identification of a functional site.	the electron density map of the small ribosomal subunit from thermus thermophilus, constructed at 4.5 a resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal rna and proteins. unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein s13 at a position compatible with previous assignments, whereas the s ...	1999	10588692
stress genes and proteins in the archaea.	the field covered in this review is new; the first sequence of a gene encoding the molecular chaperone hsp70 and the first description of a chaperonin in the archaea were reported in 1991. these findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular ...	1999	10585970
cloning, overexpression, and mutagenesis of the sporobolomyces salmonicolor aku4429 gene encoding a new aldehyde reductase, which catalyzes the stereoselective reduction of ethyl 4-chloro-3-oxobutanoate to ethyl (s)-4-chloro-3-hydroxybutanoate.	we cloned and sequenced the gene encoding an nadph-dependent aldehyde reductase (arii) in sporobolomyces salmonicolor aku4429, which reduces ethyl 4-chloro-3-oxobutanoate (4-cobe) to ethyl (s)-4-chloro-3-hydroxybutanoate. the arii gene is 1,032 bp long, is interrupted by four introns, and encodes a 37,315-da polypeptide. the deduced amino acid sequence exhibited significant levels of similarity to the amino acid sequences of members of the mammalian 3beta-hydroxysteroid dehydrogenase-plant dihyd ...	1999	10583966
ligase-based detection of mononucleotide repeat sequences.	up to 15% of all colorectal cancers are considered to be replication error positive (rer(+)) and contain mutations at hundreds of thousands of microsatellite repeat sequences. recently, a number of intragenic mononucleotide repeat sequences have been demonstrated to be targets for inactivating genes in rer(+)colorectal tumors. in this study, thermostable dna ligases were tested for the ability to detect alterations in microsatellite sequences in colon tumor samples. ligation profiles on mononucl ...	1999	10572192
sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network.	a major activity of molecular chaperones is to prevent aggregation and refold misfolded proteins. however, when allowed to form, protein aggregates are refolded poorly by most chaperones. we show here that the sequential action of two escherichia coli chaperone systems, clpb and dnak-dnaj-grpe, can efficiently solubilize excess amounts of protein aggregates and refold them into active proteins. measurements of aggregate turbidity, congo red, and 4,4'-dianilino-1, 1'-binaphthyl-5,5'-disulfonic ac ...	1999	10570141
structural distribution of stability in a thermophilic enzyme.	stability parameters for individual residues in thermus thermophilus cysteine-free rnase h were determined by native state hydrogen exchange, thus providing a unique comparison of regional thermodynamics between thermophilic and mesophilic homologues. the general distribution of stability in the thermophilic protein is similar to that of its mesophilic homologue, with a proportional increase in stability for almost all residues. as a consequence, the residue-specific stabilities of the two prote ...	1999	10570131
genome sequence of the radioresistant bacterium deinococcus radiodurans r1.	the complete genome sequence of the radiation-resistant bacterium deinococcus radiodurans r1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of d. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of dna damage were ...	1999	10567266
determination of bovine rotavirus g and p serotypes in italy by pcr.	determination of the g and p serotypes of group a bovine rotaviruses from 149 samples of feces or intestinal contents collected from calves showing clinical signs of neonatal diarrhea was performed by a nested reverse transcription-pcr typing assay. the g6 serotype was the most prevalent, accounting for viruses in 55.7% of the samples; viruses of the g10 and g8 serotypes were found in 34.9 and 4.7% of the samples, respectively. the virus in one sample (0.7%) was not classified due to concomitant ...	1999	10565900
improving proteolytic cleavage at the 3a/3b site of the hepatitis a virus polyprotein impairs processing and particle formation, and the impairment can be complemented in trans by 3ab and 3abc.	the orchestrated liberation of viral proteins by 3c(pro)-mediated proteolysis is pivotal for gene expression by picornaviruses. proteolytic processing is regulated either by the amino acid sequence at the cleavage site of the substrate or by cofactors covalently or noncovalently linked to the viral proteinase. to determine the role of the amino acid sequence at cleavage sites 3a/3b and 3b/3c that are essential for the liberation of 3c(pro) from its precursors and to assess the function of the st ...	1999	10559299
specific inhibition of the eubacterial dna ligase by arylamino compounds.	all known dna ligases catalyze the formation of a phosphodiester linkage between adjacent termini in double-stranded dna via very similar mechanisms. the ligase family can, however, be divided into two classes: eubacterial ligases, which require nad(+) as a cofactor, and other ligases, from viruses, archaea, and eukaryotes, which use atp. drugs that discriminate between dna ligases from different sources may have antieubacterial activity. we now report that a group of arylamino compounds, includ ...	1999	10543760
loss of cytochrome c oxidase activity and acquisition of resistance to quinone analogs in a laccase-positive variant of azospirillum lipoferum.	laccase, a p-diphenol oxidase typical of plants and fungi, has been found recently in a proteobacterium, azospirillum lipoferum. laccase activity was detected in both a natural isolate and an in vitro-obtained phase variant that originated from the laccase-negative wild type. in this study, the electron transport systems of the laccase-positive variant and its parental laccase-negative forms were compared. during exponential (but not stationary) growth under fully aerobic (but not under microaer ...	1999	10542175
prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases.		1999	10542156
calibrating bacterial evolution.	attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal applica ...	1999	10535975
detection of human herpesvirus 6 by reverse transcription-pcr.	the role of human herpesvirus 6 (hhv-6) in disease beyond primary infection remains unclear. we have developed and validated a new reverse transcription-pcr (rt-pcr) assay for hhv-6 that can determine the presence of hhv-6 in clinical specimens and differentiate between latent and replicating virus. peripheral blood mononuclear cells from 109 children were evaluated for hhv-6 by rt-pcr, dna pcr, and viral culture. of these samples, 106 were suitable for analysis. a total of 20 samples were posit ...	1999	10523572