Publications

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
s-layer proteins.		2000	10648507
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
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
two c or not two c: recurrent disruption of zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins.	ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. in prokaryotes, the genes for most ribosomal proteins are clustered in several highly conserved operons, which ensures efficient co-regulation of their expression. duplications of ribosomal-protein genes are infrequent, and given their coordinated expression and functioning, it is generally assumed that ribosomal-protein genes are unlikely to undergo horizontal transfer. howe ...	2001	11574053
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
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
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
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
characterization of a heme-dependent catalase from methanobrevibacter arboriphilus.	recently it was reported that methanogens of the genus methanobrevibacter exhibit catalase activity. this was surprising, since methanobrevibacter species belong to the order methanobacteriales, which are known not to contain cytochromes and to lack the ability to synthesize heme. we report here that methanobrevibacter arboriphilus strains az and dh1 contained catalase activity only when the growth medium was supplemented with hemin. the heme catalase was purified and characterized, and the enco ...	2001	11425719
natural transformation in mesophilic and thermophilic bacteria: identification and characterization of novel, closely related competence genes in acinetobacter sp. strain bd413 and thermus thermophilus hb27.	the mesophile acinetobacter sp. strain bd413 and the extreme thermophile thermus thermophilus hb27 display high frequencies of natural transformation. in this study we identified and characterized a novel competence gene in acinetobacter sp. strain bd413, coma, whose product displays significant similarities to the competence proteins coma and comec in neisseria and bacillus species. transcription of coma correlated with growth phase-dependent transcriptional regulation of the recently identifie ...	2001	11425734
molecular characterization of desulfovibrio gigas neelaredoxin, a protein involved in oxygen detoxification in anaerobes.	desulfovibrio gigas neelaredoxin is an iron-containing protein of 15 kda, having a single iron site with a his(4)cys coordination. neelaredoxins and homologous proteins are widespread in anaerobic prokaryotes and have superoxide-scavenging activity. to further understand its role in anaerobes, its genomic organization and expression in d. gigas were studied and its ability to complement escherichia coli superoxide dismutase deletion mutant was assessed. in d. gigas, neelaredoxin is transcribed a ...	2001	11443075
rad54 protein stimulates the postsynaptic phase of rad51 protein-mediated dna strand exchange.	rad54 and rad51 are important proteins for the repair of double-stranded dna breaks by homologous recombination in eukaryotes. as previously shown, rad51 protein forms nucleoprotein filaments on single-stranded dna, and rad54 protein directly interacts with such filaments to enhance synapsis, the homologous pairing with a double-stranded dna partner. here we demonstrate that saccharomyces cerevisiae rad54 protein has an additional role in the postsynaptic phase of dna strand exchange by stimulat ...	2001	11459988
high stability of a ferredoxin from the hyperthermophilic archaeon a. ambivalens: involvement of electrostatic interactions and cofactors.	the ferredoxin from the thermophilic archaeon acidianus ambivalens is a small monomeric seven-iron protein with a thermal midpoint (t(m)) of 122 degrees c (ph 7). to gain insight into the basis of its thermostability, we have characterized unfolding reactions induced chemically and thermally at various phs. thermal unfolding of this ferredoxin, in the presence of various guanidine hydrochloride (guhcl) concentrations, yields a linear correlation between unfolding enthalpies (deltah[t(m)]) and t( ...	2001	11468351
assessment, by transcription-mediated amplification, of virologic response in patients with chronic hepatitis c virus treated with peginterferon alpha-2a.	transcription-mediated amplification (tma) is an isothermal, autocatalytic target amplification method which has the potential to detect less than 50 hepatitis c virus (hcv) rna copies/ml (10 iu/ml). the tma assay was used to assess the presence of residual hcv rna in plasma from patients treated with polyethylene glycol-modified interferon alpha-2a (peginterferon alpha-2a) who showed a virologic relapse after the end of therapy. stored end-of-treatment and end-of-follow-up plasma samples from 1 ...	2001	11474002
the kink-turn: a new rna secondary structure motif.	analysis of the haloarcula marismortui large ribosomal subunit has revealed a common rna structure that we call the kink-turn, or k-turn. the six k-turns in h.marismortui 23s rrna superimpose with an r.m.s.d. of 1.7 a. there are two k-turns in the structure of thermus thermophilus 16s rrna, and the structures of u4 snrna and l30e mrna fragments form k-turns. the structure has a kink in the phosphodiester backbone that causes a sharp turn in the rna helix. its asymmetric internal loop is flanked ...	2001	11483524
functional and evolutionary relationship between arginine biosynthesis and prokaryotic lysine biosynthesis through alpha-aminoadipate.	our previous studies revealed that lysine is synthesized through alpha-aminoadipate in an extremely thermophilic bacterium, thermus thermophilus hb27. sequence analysis of a gene cluster involved in the lysine biosynthesis of this microorganism suggested that the conversion from alpha-aminoadipate to lysine proceeds in a way similar to that of arginine biosynthesis. in the present study, we cloned an argd homolog of t. thermophilus hb27 which was not included in the previously cloned lysine bios ...	2001	11489859
peplomycin, a bleomycin derivative, induces myofibroblasts in pulmonary fibrosis.	to analyse the mechanism by which a bleomycin derivative, peplomycin (plm) induces pulmonary fibrosis, we investigated differentiation of rat pulmonary fibroblasts to myofibroblasts (mf). in intraperitoneally plm (5 mg/kg/day)-injected rats, the peripheries of lungs adjacent to the pleura revealed advanced fibrosis with a small number of alpha-smooth muscle actin (alpha-sma)-positive mf, which ultrastructurally possessed abundant microfilaments and cellular organelles. in the fibrotic tissue, th ...	2001	11493347
resistance of streptococcus pneumoniae to deformylase inhibitors is due to mutations in defb.	resistance to peptide deformylase inhibitors in escherichia coli or staphylococcus aureus is due to inactivation of transformylase activity. knockout experiments in streptococcus pneumoniae r6x indicate that the transformylase (fmt) and deformylase (defb) genes are essential and that a def paralog (defa) is not. actinonin-resistant mutants of s. pneumoniae atcc 49619 harbor mutations in defb but not in fmt. reintroduction of the mutated defb gene into wild-type s. pneumoniae r6x recreates the re ...	2001	11502510
high-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification.	single nucleotide polymorphisms (snps) are the foundation of powerful complex trait and pharmacogenomic analyses. the availability of large snp databases, however, has emphasized a need for inexpensive snp genotyping methods of commensurate simplicity, robustness, and scalability. we describe a solution-based, microtiter plate method for snp genotyping of human genomic dna. the method is based upon allele discrimination by ligation of open circle probes followed by rolling circle amplification o ...	2001	11511324
hybrid protein between ribosomal protein s16 and rimm of escherichia coli retains the ribosome maturation function of both proteins.	the rimm protein in escherichia coli is associated with free 30s ribosomal subunits but not with 70s ribosomes and is important for efficient maturation of the 30s subunits. a mutant lacking rimm shows a sevenfold-reduced growth rate and a reduced translational efficiency. here we show that a double alanine-for-tyrosine substitution in rimm prevents it from associating with the 30s subunits and reduces the growth rate of e. coli approximately threefold. several faster-growing derivatives of the ...	2001	11514519
recombinational transfer of 100-kilobase genomic dna to plasmid in bacillus subtilis 168.	transformation of bacillus subtilis by a plasmid requires a circular multimeric form. in contrast, linearized plasmids can be circularized only when homologous sequences are present in the host genome. a recombinational transfer system was constructed with this intrinsic b. subtilis recombinational repair pathway. the vector, pgets103, a derivative of the theta-type replicating plasmid ptb19 of thermophilic bacillus, had the full length of escherichia coli plasmid pbr322. a multimeric form of pg ...	2001	11514534
a conformational change in the ribosomal peptidyl transferase center upon active/inactive transition.	the ribosome is a dynamic particle that undergoes many structural changes during translation. we show through chemical probing with dimethyl sulfate (dms) that conformational changes occur at several nucleotides in the peptidyl transferase center upon alterations in ph, temperature, and monovalent ion concentration, consistent with observations made by elson and coworkers over 30 years ago. moreover, we have found that the ph-dependent dms reactivity of a2451 in the center of the 23s rrna peptid ...	2001	11517305
production of recombinant alpha-galactosidases in thermus thermophilus.	a thermus thermophilus selector strain for production of thermostable and thermoactive alpha-galactosidase was constructed. for this purpose, the native alpha-galactosidase gene (agat) of t. thermophilus th125 was inactivated to prevent background activity. in our first attempt, insertional mutagenesis of agat by using a cassette carrying a kanamycin resistance gene led to bacterial inability to utilize melibiose (alpha-galactoside) and galactose as sole carbohydrate sources due to a polar effec ...	2001	11526023
xylulokinase overexpression in two strains of saccharomyces cerevisiae also expressing xylose reductase and xylitol dehydrogenase and its effect on fermentation of xylose and lignocellulosic hydrolysate.	fermentation of the pentose sugar xylose to ethanol in lignocellulosic biomass would make bioethanol production economically more competitive. saccharomyces cerevisiae, an efficient ethanol producer, can utilize xylose only when expressing the heterologous genes xyl1 (xylose reductase) and xyl2 (xylitol dehydrogenase). xylose reductase and xylitol dehydrogenase convert xylose to its isomer xylulose. the gene xks1 encodes the xylulose-phosphorylating enzyme xylulokinase. in this study, we determi ...	2001	11526030
the structure of an asprs-trna(asp) complex reveals a trna-dependent control mechanism.	the 2.6 a resolution crystal structure of an inactive complex between yeast trna(asp) and escherichia coli aspartyl-trna synthetase reveals the molecular details of a trna-induced mechanism that controls the specificity of the reaction. the dimer is asymmetric, with only one of the two bound trnas entering the active site cleft of its subunit. however, the flipping loop, which controls the proper positioning of the amino acid substrate, acts as a lid and prevents the correct positioning of the t ...	2001	11566892
multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes.	a large fragment of the dissimilatory sulfite reductase genes (dsrab) was pcr amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. in addition, the sequence of the dsrab gene homologs of the sulfite reducer desulfitobacterium dehalogenans was determined. in contrast to previous reports, comparative analysis of all available dsrab sequences produced a tree topology partially inconsistent with the corresponding 16s rrna phylogen ...	2001	11567003
characterization of a highly thermostable alkaline phosphatase from the euryarchaeon pyrococcus abyssi.	this work reports the first isolation and characterization of an alkaline phosphatase (ap) from a hyperthermophilic archaeon. an ap gene from pyrococcus abyssi, a euryarchaeon isolated from a deep-sea hydrothermal vent, was cloned and the enzyme expressed in escherichia coli. analysis of the sequence showed conservation of the active site and structural elements of the e. coli ap. the recombinant ap was purified and characterized. monomeric and homodimeric active forms were detected, with a mono ...	2001	11571149
mutations in the listerial prob gene leading to proline overproduction: effects on salt tolerance and murine infection.	the observed sensitivity of listeria monocytogenes to the toxic proline analogue l-azetidine-2-carboxylic acid (az) suggested that proline synthesis in listeria may be regulated by feedback inhibition of gamma-glutamyl kinase (gk), the first enzyme of the proline biosynthesis pathway, encoded by the prob gene. taking advantage of the epicurian coli mutator strain xl1-red, we performed random mutagenesis of the recently described proba operon and generated three independent mutations in the liste ...	2001	11571156
screening of active lyssavirus infection in wild bat populations by viral rna detection on oropharyngeal swabs.	brain analysis cannot be used for the investigation of active lyssavirus infection in healthy bats because most bat species are protected by conservation directives. consequently, serology remains the only tool for performing virological studies on natural bat populations; however, the presence of antibodies merely reflects past exposure to the virus and is not a valid marker of active infection. this work describes a new nested reverse transcription (rt)-pcr technique specifically designed for ...	2001	11574590
visualization of protein s1 within the 30s ribosomal subunit and its interaction with messenger rna.	s1 is the largest ribosomal protein, present in the small subunit of the bacterial ribosome. it has a pivotal role in stabilizing the mrna on the ribosome. thus far, s1 has eluded structural determination. we have identified the s1 protein mass in the cryo-electron microscopic map of the escherichia coli ribosome by comparing the map with a recent x-ray crystallographic structure of the 30s subunit, which lacks s1. according to our finding, s1 is located at the junction of head, platform, and ma ...	2001	11593008
characterization of a brucella species 25-kilobase dna fragment deleted from brucella abortus reveals a large gene cluster related to the synthesis of a polysaccharide.	in the present study we completed the nucleotide sequence of a brucella melitensis 16m dna fragment deleted from b. abortus that accounts for 25,064 bp and show that the other brucella spp. contain the entire 25-kb dna fragment. two short direct repeats of four nucleotides, detected in the b. melitensis 16m dna flanking both sides of the fragment deleted from b. abortus, might have been involved in the deletion formation by a strand slippage mechanism during replication. in addition to omp31, co ...	2001	11598046
sequence analysis of four shigella boydii o-antigen loci: implication for escherichia coli and shigella relationships.	shigella strains are in reality clones of escherichia coli and are believed to have emerged relatively recently (g. m. pupo, r. lan, and p. r. reeves, proc. natl. acad. sci. usa 97:10567-10572, 2000). there are 33 o-antigen forms in these shigella clones, of which 12 are identical to o antigens of other e. coli strains. we sequenced o-antigen gene clusters from shigella boydii serotypes 4, 5, 6, and 9 and also studied the o53- and o79-antigen gene clusters of e. coli, encoding o antigens identic ...	2001	11598067