Publications

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
aminoglycosides: perspectives on mechanisms of action and resistance and strategies to counter resistance.		2000	11083623
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
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
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
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
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
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
vima gene downstream of reca is involved in virulence modulation in porphyromonas gingivalis w83.	a 0.9-kb open reading frame encoding a unique 32-kda protein was identified downstream of the reca gene of porphyromonas gingivalis. reverse transcription-pcr and northern blot analysis showed that both the reca gene and this open reading frame are part of the same transcriptional unit. this cloned fragment was insertionally inactivated using the ermf-ermam antibiotic resistance cassette to create a defective mutant by allelic exchange. when plated on brucella blood agar, the mutant strain, desi ...	2001	11119521
aminoacyl-trna synthetases database.	aminoacyl-trna synthetases (aarss) are at the center of the question of the origin of life. they constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. aarss arose early in evolution and are believed to be a group of ancient proteins. they are responsible for attaching amino acid residues to their cognate trna molecules, which is the first step in the protein synthesis. the role they play in a living cell is essential for the precise decip ...	2001	11125115
molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins.	phylogenetic analysis of tetracycline resistance genes encoding the ribosomal protection proteins (rpps) revealed the monophyletic origin of these genes. the most deeply branching class, exemplified by tet and otra, consisted of genes from the antibiotic-producing organisms streptomyces rimosus and streptomyces lividans. with a high degree of confidence, the corresponding genes of the other seven classes (tet m, tet s, tet o, tet w, tet q, tet t, and tetb p) formed phylogenetically distinct sepa ...	2001	11133424
ihfa gene of the bacterium myxococcus xanthus and its role in activation of carotenoid genes by blue light.	myxococcus xanthus responds to blue light by producing carotenoids. several regulatory genes are known that participate in the light action mechanism, which leads to the transcriptional activation of the carotenoid genes. we had already reported the isolation of a carotenoid-less, tn5-induced strain (mr508), whose mutant site was unlinked to the indicated regulatory genes. here, we show that omegamr508::tn5 affects all known light-inducible promoters in different ways. it blocks the activation o ...	2001	11133949
gene cluster of rhodothermus marinus high-potential iron-sulfur protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases.	the respiratory chain of the thermohalophilic bacterium rhodothermus marinus contains an oxygen reductase, which uses hipip (high potential iron-sulfur protein) as an electron donor. the structural genes encoding the four subunits of this hipip:oxygen oxidoreductase were cloned and sequenced. the genes for subunits ii, i, iii, and iv (named rcoxa to rcoxd) are found in this order and seemed to be organized in an operon of at least five genes with a terminator structure a few nucleotides downstre ...	2001	11133964
identification of the outer membrane porin of thermus thermophilus hb8: the channel-forming complex has an unusually high molecular mass and an extremely large single-channel conductance.	the outer membrane of the thermophilic bacterium thermus thermophilus was isolated using sucrose step gradient centrifugation. its detergent extracts contained an ion-permeable channel with an extremely high single-channel conductance of 20 ns in 1 m kcl. the channel protein was purified by preparative sodium dodecyl sulfate (sds)-polyacylamide gel electrophoresis. it has a high molecular mass of 185 kda, and its channel-forming ability resists boiling in sds for 10 min.	2001	11133980
a subunit of human nuclear rnase p has atpase activity.	human nuclear rnase p purified from hela cells has atpase activity. this activity is associated with one of the protein subunits of the enzyme, rpp20. thus, human nuclear rnase p, which contains several proteins and one essential rna, has at least one other enzymatic activity in addition to cleavage of phosphoester bonds in rna. the amino acid sequence of rpp20 has a signature motif found in an atpase-containing subunit of a family of protein complexes (abc transporters) that mediate a variety o ...	2001	11149958
primary structure of a novel subunit in ba3-cytochrome oxidase from thermus thermophilus.	the bax-type cytochrome c oxidase from thermus thermophilus is known as a two subunit enzyme. deduced from the crystal structure of this enzyme, we discovered the presence of an additional transmembrane helix "subunit iia" spanning the membrane. the hydrophobic n-terminally blocked protein was isolated in high yield using high-performance liquid chromatography. its complete amino acid sequence was determined by a combination of automated edman degradation of both the deformylated and the cyanoge ...	2000	11152118
integrity of thermus thermophilus cytochrome c552 synthesized by escherichia coli cells expressing the host-specific cytochrome c maturation genes, ccmabcdefgh: biochemical, spectral, and structural characterization of the recombinant protein.	we describe the design of escherichia coli cells that synthesize a structurally perfect, recombinant cytochrome c from the thermus thermophilus cytochrome c552 gene. key features are (1) construction of a plasmid-borne, chimeric cyca gene encoding an escherichia coli-compatible, n-terminal signal sequence (metlysileseriletyralathrleu alaalaleuserleualaleuproalaglyala) followed by the amino acid sequence of mature thermus cytochrome c552; and (2) coexpression of the chimeric cyca gene with plasmi ...	2000	11152119
hepatitis c virus 3'x region interacts with human ribosomal proteins.	to identify proteins that can bind the 3' untranslated region (utr) of hepatitis c virus (hcv) we screened human cdna libraries using the saccharomyces cerevisiae three-hybrid system. screening with an rna sequence derived from the 3'-terminal 98 nucleotides (3'x region) of an infectious clone of hcv (h77c) yielded clones of human ribosomal proteins l22, l3, s3, and ml3, a mitochondrial homologue of l3. we performed preliminary characterization of the binding between the 3'x region and these pro ...	2001	11152508
development of a reverse transcription-pcr-dna enzyme immunoassay for detection of "norwalk-like" viruses and hepatitis a virus in stool and shellfish.	outbreaks of food- and waterborne gastroenteritis are being increasingly reported throughout the world. the analysis of environmental samples by newer diagnostic techniques such as reverse transcription-pcr (rt-pcr) amplification of nucleic acid has begun to identify human enteric viruses (predominantly "norwalk-like" viruses [nlvs]) as the cause of many of these outbreaks. to streamline nlv detection from environmental samples such as shellfish, we have developed an rt-pcr-oligoprobe amplificat ...	2001	11157239
the crystal structure of the ttcsaa protein: an export-related chaperone from thermus thermophilus.	the csaa protein was first characterized in bacillus subtilis as a molecular chaperone with export-related activities. here we report the 2.0 angstrom-resolution crystal structure of the thermus thermophilus csaa protein, designated ttcsaa. atomic structure and experiments in solution revealed a homodimer as the functional unit. the structure of the ttcsaa monomer is reminiscent of the well known oligonucleotide-binding fold, with the addition of extensions at the n- and c-termini that form an e ...	2001	11157762
structure of the emapii domain of human aminoacyl-trna synthetase complex reveals evolutionary dimer mimicry.	the emapii (endothelial monocyte-activating polypeptide ii) domain is a trna-binding domain associated with several aminoacyl-trna synthetases, which becomes an independent domain with inflammatory cytokine activity upon apoptotic cleavage from the p43 component of the multisynthetase complex. it comprises a domain that is highly homologous to bacterial trna-binding proteins (trbp), followed by an extra domain without homology to known proteins. trbps, which may represent ancient trna chaperones ...	2001	11157763
cloning of the soda gene from corynebacterium melassecola and role of superoxide dismutase in cellular viability.	the soda gene encoding the corynebacterium melassecola manganese-cofactored superoxide dismutase (sod) has been cloned in escherichia coli and sequenced. the gene is transcribed monocistronically; the predicted polypeptide is 200 amino acids long and associates in a homotetrameric, manganese-dependent form, able to complement an sod-deficient e. coli mutant. a second open reading frame, coding for a putative 217-amino-acid protein with high homology to peptide methionine sulfoxide reductases fro ...	2001	11157941
multiple regulatory mechanisms act on the 5' untranslated region of the s-layer gene from thermus thermophilus hb8.	the role of the 5' untranslated region (5'utr) of the s-layer gene from thermus thermophilus was analyzed through the isolation of delta 5'utr mutants. in these mutants the half-life of spla mrna was strongly reduced and slpa transcription was no longer subjected to growth phase-dependent repression. overproduction and detachment of the external envelopes of the mutants were observed in stationary phase.	2001	11157968
chloroplast ribosomal protein s7 of chlamydomonas binds to chloroplast mrna leader sequences and may be involved in translation initiation.	certain mutations isolated in the 5' untranslated region (5'utr) of the chloroplast rps7 gene in chlamydomonas reduce expression of reporter genes. second site suppressors in this 5'utr sequence restore reporter expression. 5'utr sequences with the original mutations fail to bind a 20-kd protein, one of five proteins that bind to leaders of several chloroplast genes. however, 5'utrs from suppressed mutants restore binding to this protein but do not bind a 47-kd protein present on the wild type a ...	2001	11158540
role of the tat ransport system in nitrous oxide reductase translocation and cytochrome cd1 biosynthesis in pseudomonas stutzeri.	by transforming n2o to n2, the multicopper enzyme nitrous oxide reductase provides a periplasmic electron sink for a respiratory chain that is part of denitrification. the signal sequence of the enzyme carries the heptameric twin-arginine consensus motif characteristic of the tat pathway. we have identified tat genes of pseudomonas stutzeri and functionally analyzed the unlinked tatc and tate loci. a tatc mutant retained n2o reductase in the cytoplasm in the unprocessed form and lacking the meta ...	2001	11160097
new host-vector system for thermus spp. based on the malate dehydrogenase gene.	a thermus thermophilus hb27 strain was constructed in which the malate dehydrogenase (mdh) gene was deleted. the deltamdh colonies are recognized by a small-colony phenotype. wild-type phenotype is restored by transformation with thermus plasmids or integration vector containing an intact mdh gene. the wild-type phenotype provides a positive selection tool for the introduction of plasmid dna into thermus spp., and because mdh levels can be readily quantified, this host-vector system is a conveni ...	2001	11160114
kh domain: one motif, two folds.	the k homology (kh) module is a widespread rna-binding motif that has been detected by sequence similarity searches in such proteins as heterogeneous nuclear ribonucleoprotein k (hnrnp k) and ribosomal protein s3. analysis of spatial structures of kh domains in hnrnp k and s3 reveals that they are topologically dissimilar and thus belong to different protein folds. thus kh motif proteins provide a rare example of protein domains that share significant sequence similarity in the motif regions but ...	2001	11160884
characterization of rnase p from thermotoga maritima.	the protein subunit of rnase p from a thermophilic bacterium, thermotoga maritima, was overexpressed in and purified from escherichia coli. the cloned protein was reconstituted with the rna subunit transcribed in vitro. the temperature optimum of the holoenzyme is near 50 degrees c, with no enzymatic activity at 65 degrees c or above. this finding is in sharp contrast to the optimal growth temperature of t.maritima, which is near 80 degrees c. however, in heterologous reconstitution experiments ...	2001	11160919
crystal structure of the holliday junction migration motor protein ruvb from thermus thermophilus hb8.	we report here the crystal structure of the ruvb motor protein from thermus thermophilus hb8, which drives branch migration of the holliday junction during homologous recombination. ruvb has a crescent-like architecture consisting of three consecutive domains, the first two of which are involved in atp binding and hydrolysis. dna is likely to interact with a large basic cleft, which encompasses the atp-binding pocket and domain boundaries, whereas the junction-recognition protein ruva may bind a ...	2001	11171970
connection between poly-beta-hydroxybutyrate biosynthesis and growth on c(1) and c(2) compounds in the methylotroph methylobacterium extorquens am1.	several dna regions containing genes involved in poly-beta-hydroxybutyrate (phb) biosynthesis and degradation and also in fatty acid degradation were identified from genomic sequence data and have been characterized in the serine cycle facultative methylotroph methylobacterium extorquens am1. genes involved in phb biosynthesis include those encoding beta-ketothiolase (phaa), nadph-linked acetoacetyl coenzyme a (acetyl-coa) reductase (phab), and phb synthase (phac). phaa and phab are closely link ...	2001	11208803
experimental evolution of enzyme temperature activity profile: selection in vivo and characterization of low-temperature-adapted mutants of pyrococcus furiosus ornithine carbamoyltransferase.	we have obtained mutants of pyrococcus furiosus ornithine carbamoyltransferase active at low temperatures by selecting for complementation of an appropriate yeast mutant after in vivo mutagenesis. the mutants were double ones, still complementing at 15 degrees c, a temperature already in the psychrophilic range. their kinetic analysis is reported.	2001	11208811
occurrence of transsulfuration in synthesis of l-homocysteine in an extremely thermophilic bacterium, thermus thermophilus hb8.	a cell extract of an extremely thermophilic bacterium, thermus thermophilus hb8, cultured in a synthetic medium catalyzed cystathionine gamma-synthesis with o-acetyl-l-homoserine and l-cysteine as substrates but not beta-synthesis with dl-homocysteine and l-serine (or o-acetyl-l-serine). the amounts of synthesized enzymes metabolizing sulfur-containing amino acids were estimated by determining their catalytic activities in cell extracts. the syntheses of cystathionine beta-lyase (ec 4.4.1.8) and ...	2001	11222609
crystal structure of the lrp-like transcriptional regulator from the archaeon pyrococcus furiosus.	the lrpa protein from the hyperthermophilic archaeon pyrococcus furiosus belongs to the lrp/asnc family of transcriptional regulatory proteins, of which the escherichia coli leucine-responsive regulatory protein is the archetype. its crystal structure has been determined at 2.9 a resolution and is the first for a member of the lrp/asnc family, as well as one of the first for a transcriptional regulator from a hyperthermophile. the structure consists of an n-terminal domain containing a helix-tur ...	2001	11230123
hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.	enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees c), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. these enzymes share the same catalytic mechanisms with their mesophilic counterparts. when cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, ind ...	2001	11238984
genome of the extremely radiation-resistant bacterium deinococcus radiodurans viewed from the perspective of comparative genomics.	the bacterium deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, uv radiation, oxidizing agents, and electrophilic mutagens. d. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. these characte ...	2001	11238985
crystal structure of hiv-1 reverse transcriptase in complex with a polypurine tract rna:dna.	we have determined the 3.0 a resolution structure of wild-type hiv-1 reverse transcriptase in complex with an rna:dna oligonucleotide whose sequence includes a purine-rich segment from the hiv-1 genome called the polypurine tract (ppt). the ppt is resistant to ribonuclease h (rnase h) cleavage and is used as a primer for second dna strand synthesis. the 'rnase h primer grip', consisting of amino acids that interact with the dna primer strand, may contribute to rnase h catalysis and cleavage spec ...	2001	11250910
prediction of structural domains of tap reveals details of its interaction with p15 and nucleoporins.	vertebrate tap is a nuclear mrna export factor homologous to yeast mex67p. the middle domain of tap binds directly to p15, a protein related to the nuclear transport factor 2 (ntf2), whereas its c-terminal domain interacts with various nucleoporins, the components of the nuclear pore complex (npc). here, we report that the middle domain of tap is also similar to ntf2, as well as to regions in ras-gap sh3 domain binding protein (g3bp) and some plant protein kinases. based on the known three-dimen ...	2000	11256625
peptide deformylase as an antibacterial drug target: assays for detection of its inhibition in escherichia coli cell homogenates and intact cells.	an assay was developed to determine the activity of peptide deformylase (pdf) inhibitors under conditions as close as possible to the physiological situation. the assay principle is the detection of n-terminal [35s]methionine labeling of a protein that contains no internal methionine. if pdf is active, the deformylation of the methionine renders the peptide a substrate for methionine aminopeptidase, resulting in the removal of the n-terminal methionine label. in the presence of a pdf inhibitor, ...	2001	11257015
peptide deformylase as an antibacterial drug target: target validation and resistance development.	new inhibitors of peptide deformylase (pdf) which are very potent against the isolated enzyme and show a certain degree of antibacterial activity have recently been synthesized by our group. several lines of experimental evidence indicate that these inhibitors indeed interfere with the target enzyme in the bacterial cell. (i) the inhibition of escherichia coli growth could be counteracted by overexpression of pdf from different organisms, including e. coli, streptococcus pneumoniae, and haemophi ...	2001	11257016
a new era for the rna world. conference: rna 2000.		2000	11258477
enhancing the catalytic repertoire of nucleic acids: a systematic study of linker length and rigidity.	the incorporation of potentially catalytic groups in dna is of interest for the in vitro selection of novel deoxyribozymes. a series of 10 c5-modified analogues of 2'-deoxyuridine triphosphate have been synthesised that possess side chains of differing flexibility and bearing a primary amino or imidazole functionality. for each series of nucleotide analogues differing degrees of flexibility of the c5 side chain was achieved through the use of alkynyl, alkenyl and alkyl moieties. the imidazole fu ...	2001	11266559
hydrogen peroxide-forming nadh oxidase belonging to the peroxiredoxin oxidoreductase family: existence and physiological role in bacteria.	amphibacillus xylanus and sporolactobacillus inulinus nadh oxidases belonging to the peroxiredoxin oxidoreductase family show extremely high peroxide reductase activity for hydrogen peroxide and alkyl hydroperoxides in the presence of the small disulfide redox protein, ahpc (peroxiredoxin). in order to investigate the distribution of this enzyme system in bacteria, 15 bacterial strains were selected from typical aerobic, facultatively anaerobic, and anaerobic bacteria. ahpc-linked alkyl hydroper ...	2001	11274101
rac, a stable ribosome-associated complex in yeast formed by the dnak-dnaj homologs ssz1p and zuotin.	the yeast cytosol contains multiple homologs of the dnak and dnaj chaperone family. our current understanding of which homologs functionally interact is incomplete. zuotin is a dnaj homolog bound to the yeast ribosome. we have now identified the dnak homolog ssz1p/pdr13p as zuotin's partner chaperone. zuotin and ssz1p form a ribosome-associated complex (rac) that is bound to the ribosome via the zuotin subunit. rac is unique among the eukaryotic dnak-dnaj systems, as the 1:1 complex is stable, e ...	2001	11274393
bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16s ribosomal dna sequencing.	we investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. for this investigation, we developed a composite method based on analyses of pcr amplicons containing the ribosomal intergenic spacer (ris) and its flanking partial 16s rrna gene. community percent similarity was determined on the basis of ris length polymorphism. a community succession was evident in the lagoon, indicated by a progressive community transition through seven sam ...	2001	11282606
purification and characterization of the recombinant thermus sp. strain t2 alpha-galactosidase expressed in escherichia coli.	the nucleotide sequence of the thermus sp. strain t2 dna coding for a thermostable alpha-galactosidase was determined. the deduced amino acid sequence of the enzyme predicts a polypeptide of 474 amino acids (m(r), 53,514). the observed homology between the deduced amino acid sequences of the enzyme and alpha-galactosidase from thermus brockianus was over 70%. thermus sp. strain t2 alpha-galactosidase was expressed in its active form in escherichia coli and purified. native polyacrylamide gel ele ...	2001	11282611
crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and if3.	the small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. we analyzed by x-ray crystallography the structures of three different complexes of the small ribosomal subunit of thermus thermophilus with the a-site inhibitor tetracycline, the universal initiation inhibitor edeine and the c-terminal domain of the translation initiation factor if3. the crystal structure analysis of the complex with tetracycline reveal ...	2001	11296217
rna tertiary interactions in the large ribosomal subunit: the a-minor motif.	analysis of the 2.4-a resolution crystal structure of the large ribosomal subunit from haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes rna tertiary and quaternary structures. this motif is termed the a-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at c-g base pairs, where they form hydrogen bonds with one or both of the 2' ohs of ...	2001	11296253
conservation of the binding site for the arginine repressor in all bacterial lineages.	the arginine repressor argr/ahrc is a transcription factor universally conserved in bacterial genomes. its recognition signal (the arg box), a weak palindrome, is also conserved between genomes, despite a very low degree of similarity between individual sites within a genome. thus, the arginine repressor is different from two other universal transcription factors - hrca, whose recognition signal is very strongly conserved both within and between genomes, and lexa/dinr, whose signal is strongly c ...	2001	11305941
attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer.	the bacteria colonizing geologic core sections (attached) were contrasted with those found suspended in the groundwater (unattached) by examining the microbiology of 16 depth-paired core and groundwater samples using a suite of culture-independent and culture-dependent analyses. one hundred twenty-two meters was continuously cored from a buried chalcopyrite ore hosted in a biotite-quartz-monzonite porphyry at the mineral park mine near kingman, ariz. every fourth 1.5-m core was acquired using mi ...	2001	11319087
cloning and functional characterization of an nad(+)-dependent dna ligase from staphylococcus aureus.	a staphylococcus aureus mutant conditionally defective in dna ligase was identified by isolation of complementing plasmid clones that encode the s. aureus liga gene. orthologues of the putative s. aureus nad(+)-dependent dna ligase could be identified in the genomes of bacillus stearothermophilus and other gram-positive bacteria and confirmed the presence of four conserved amino acid motifs, including motif i, kxdg with lysine 112, which is believed to be the proposed site of adenylation. dna se ...	2001	11325928
evidence against an interaction between the mrna downstream box and 16s rrna in translation initiation.	based on the complementarity of the initial coding region (downstream box [db]) of several bacterial and phage mrnas to bases 1469 to 1483 in helix 44 of 16s rrna (anti-downstream box [adb]), it has been proposed that db-adb base pairing enhances translation in a way that is similar to that of the shine-dalgarno (sd)/anti-shine-dalgarno (asd) interaction. computer modeling of helix 44 on the 30s subunit shows that the topography of the 30s ribosome does not allow a simultaneous db-adb interactio ...	2001	11344158
oxaloacetate synthesis in the methanarchaeon methanosarcina barkeri: pyruvate carboxylase genes and a putative escherichia coli-type bifunctional biotin protein ligase gene (bpl/bira) exhibit a unique organization.	evidence is presented that, in methanosarcina barkeri oxaloacetate synthesis, an essential and major co(2) fixation reaction is catalyzed by an apparent alpha(4)beta(4)-type acetyl coenzyme a-independent pyruvate carboxylase (pyc), composed of 64.2-kda biotinylated and 52.9-kda atp-binding subunits. the purified enzyme was most active at 70 degrees c, insensitive to aspartate and glutamate, mildly inhibited by alpha-ketoglutarate, and severely inhibited by atp, adp, and excess mg(2+). it showed ...	2001	11371547
the renaissance of aminoacyl-trna synthesis.	the role of trna as the adaptor in protein synthesis has held an enduring fascination for molecular biologists. over four decades of study, taking in numerous milestones in molecular biology, led to what was widely held to be a fairly complete picture of how trnas and amino acids are paired prior to protein synthesis. however, recent developments in genomics and structural biology have revealed an unexpected array of new enzymes, pathways and mechanisms involved in aminoacyl-trna synthesis. as a ...	2001	11375928
specific interaction between the ribosome recycling factor and the elongation factor g from mycobacterium tuberculosis mediates peptidyl-trna release and ribosome recycling in escherichia coli.	once the translating ribosomes reach a termination codon, the nascent polypeptide chain is released in a factor-dependent manner. however, the p-site-bound deacylated trna and the ribosomes themselves remain bound to the mrna (post-termination complex). the ribosome recycling factor (rrf) plays a vital role in dissociating this complex. here we show that the mycobacterium tuberculosis rrf (mturrf) fails to rescue escherichia coli lj14, a strain temperature-sensitive for rrf (frr(ts)). more inter ...	2001	11387230
survey and summary: the applications of universal dna base analogues.	a universal base analogue forms 'base pairs' with each of the natural dna/rna bases with little discrimination between them. a number of such analogues have been prepared and their applications as biochemical tools investigated. most of these analogues are non-hydrogen bonding, hydrophobic, aromatic 'bases' which stabilise duplex dna by stacking interactions. this review of the literature of universal bases (to 2000) details the analogues investigated, and their uses and limitations are discusse ...	2001	11410649
spontaneous erythromycin resistance mutation in a 23s rrna gene, rrla, of the extreme thermophile thermus thermophilus ib-21.	spontaneous, erythromycin-resistant mutants of thermus thermophilus ib-21 were isolated and found to carry the mutation a2058g in one of two 23s rrna operons. the heterozygosity of these mutants indicates that a2058g confers a dominant or codominant phenotype in this organism. this mutation provides a valuable tool for the genetic manipulation of the 23s rrna genes of thermus.	2001	11418580
using surface-bound rubidium ions for protein phasing.	rubidium is a monovalent metal that can be used as a counterion in protein solutions. x-ray anomalous scattering from rubidium ions bound to the protein surface was used for phasing of the crystal structure of the hsp60 apical domain from thermus thermophilus. multiple-wavelength anomalous dispersion (mad) data were collected from a crystal obtained from a solution containing 0.2 m rubidium salt. one molecule of protein (147 amino acids) binds one well ordered and one poorly ordered rb atom. pha ...	2001	11418770