Publications

protein synthesis in escherichia coli with mischarged trna.	two types of aspartyl-trna synthetase exist: the discriminating enzyme (d-asprs) forms only asp-trna(asp), while the nondiscriminating one (nd-asprs) also synthesizes asp-trna(asn), a required intermediate in protein synthesis in many organisms (but not in escherichia coli). on the basis of the e. coli trpa34 missense mutant transformed with heterologous nd-asps genes, we developed a system with which to measure the in vivo formation of asp-trna(asn) and its acceptance by elongation factor ef-tu ...	2003	12775689
nmr structure of the active conformation of the varkud satellite ribozyme cleavage site.	substrate cleavage by the neurospora varkud satellite (vs) ribozyme involves a structural change in the stem-loop i substrate from an inactive to an active conformation. we have determined the nmr solution structure of a mutant stem-loop i that mimics the active conformation of the cleavage site internal loop. this structure shares many similarities, but also significant differences, with the previously determined structures of the inactive internal loop. the active internal loop displays differ ...	2003	12782785
functional asymmetry in the lysyl-trna synthetase explored by molecular dynamics, free energy calculations and experiment.	charging of transfer-rna with cognate amino acid is accomplished by the aminoacyl-trna synthetases, and proceeds through an aminoacyl adenylate intermediate. the lysyl-trna synthetase has evolved an active site that specifically binds lysine and atp. previous molecular dynamics simulations of the heat-inducible escherichia coli lysyl-trna synthetase, lysu, have revealed differences in the binding of atp and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme ...	2003	12787471
the bacterium thermus thermophilus, like hyperthermophilic archaea, uses a two-step pathway for the synthesis of mannosylglycerate.	the biosynthetic pathway for the synthesis of the compatible solute alpha-mannosylglycerate (mg) in the thermophilic bacterium thermus thermophilus hb27 was identified based on the activities of recombinant mannosyl-3-phosphoglycerate synthase (mpgs) (ec 2.4.1.217) and mannosyl-3-phosphoglycerate phosphatase (mpgp) (ec 3.1.3.70). the sequences of homologous genes from the archaeon pyrococcus horikoshii were used to identify mpgs and mpgp genes in t. thermophilus hb27 genome. both genes were sepa ...	2003	12788726
quantitation of human immunodeficiency virus type 1 in breast milk.	the distribution and stability of human immunodeficiency virus type 1 (hiv-1) in breast milk (bm) components remain largely unknown. inhibitory effects, if any, of bm on hiv rna and dna pcr amplification are poorly understood. we have addressed these issues by using virus-spiked bm samples from hiv-negative women. bm samples from hiv-negative women were spiked with hiv-1 virions or cells containing a single integrated copy of hiv dna (8e5/lav). after incubation under different experimental condi ...	2003	12791866
a snorna that guides the two most conserved pseudouridine modifications within rrna confers a growth advantage in yeast.	ribosomal rnas contain a number of modified nucleotides. the most abundant nucleotide modifications found within rrnas fall into two types: 2'-o-ribose methylations and pseudouridylations. in eukaryotes, small nucleolar guide rnas, the snornas that are the rna components of the snornps, specify the position of these modifications. the 2'-o-ribose methylations and pseudouridylations are guided by the box c/d and box h/aca snornas, respectively. the role of these modifications in rrna remains poor ...	2003	12810910
viridans group streptococci are donors in horizontal transfer of topoisomerase iv genes to streptococcus pneumoniae.	a total of 46 ciprofloxacin-resistant (cip(r)) streptococcus pneumoniae strains were isolated from 1991 to 2001 at the hospital of bellvitge. five of these strains showed unexpectedly high rates of nucleotide variations in the quinolone resistance-determining regions (qrdrs) of their parc, pare, and gyra genes. the nucleotide sequence of the full-length parc, pare, and gyra genes of one of these isolates revealed a mosaic structure compatible with an interspecific recombination origin. southern ...	2003	12821449
dissection of the triple tryptophan electron transfer chain in escherichia coli dna photolyase: trp382 is the primary donor in photoactivation.	in escherichia coli photolyase, excitation of the fad cofactor in its semireduced radical state (fadh) induces an electron transfer over approximately 15 a from tryptophan w306 to the flavin. it has been suggested that two additional tryptophans are involved in an electron transfer chain fadh <-- w382 <-- w359 <-- w306. to test this hypothesis, we have mutated w382 into redox inert phenylalanine. ultrafast transient absorption studies showed that, in wt photolyase, excited fadh* decayed with a ...	2003	12835419
contribution of structural genomics to understanding the biology of escherichia coli.		2003	12837772
determinants of the src homology domain 3-like fold.	in eukaryotes, the src homology domain 3 (sh3) is a very important motif in signal transduction. sh3 domains recognize poly-proline-rich peptides and are involved in protein-protein interactions. until now, the existence of sh3 domains has not been demonstrated in prokaryotes. however, the structure of the c-terminal domain of dtxr clearly shows that the fold of this domain is very similar to that of the sh3 domain. in addition, there is evidence that the c-terminal domain of dtxr binds to poly- ...	2003	12837782
crystal structures of the quinone oxidoreductase from thermus thermophilus hb8 and its complex with nadph: implication for nadph and substrate recognition.	the crystal structures of the zeta-crystalline-like soluble quinone oxidoreductase from thermus thermophilus hb8 (qor(tt)) and of its complex with nadph have been determined at 2.3- and 2.8-a resolutions, respectively. qor(tt) is composed of two domains, and its overall fold is similar to the folds of escherichia coli quinone oxidoreductase (qor(ec)) and horse liver alcohol dehydrogenase. qor(tt) forms a homodimer in the crystal by interaction of the betaf-strands in domain ii, forming a large b ...	2003	12837796
structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium thermus nonproteolyticus hg102.	the three-dimensional structure of a thermostable beta-glycosidase (gly(tn)) from the thermophilic eubacterium thermus nonproteolyticus hg102 was determined at a resolution of 2.4 a. the core of the structure adopts the (betaalpha)(8) barrel fold. the sequence alignments and the positions of the two glu residues in the active center indicate that gly(tn) belongs to the glycosyl hydrolases of retaining family 1. we have analyzed the structural features of gly(tn) related to the thermostability an ...	2003	12837801
detecting protein-protein interactions in the intact cell of bacillus subtilis (atcc 6633).	the salt bridge, paired group-specific reagent cyanogen (ethanedinitrile; c(2)n(2)) converts naturally occurring pairs of functional groups into covalently linked products. cyanogen readily permeates cell walls and membranes. when the paired groups are shared between associated proteins, isolation of the covalently linked proteins allows their identity to be assigned. examination of organisms of known genome sequence permits identification of the linked proteins by mass spectrometric techniques ...	2003	12837803
pilin-like proteins in the extremely thermophilic bacterium thermus thermophilus hb27: implication in competence for natural transformation and links to type iv pilus biogenesis.	the extreme thermophile thermus thermophilus hb27 exhibits high frequencies of natural transformation. although we recently reported identification of the first competence genes in thermus, the molecular basis of dna uptake is unknown. a pilus-like structure is assumed to be involved. twelve genes encoding prepilin-like proteins were identified in three loci in the genome of t. thermophilus. mutational analyses, described in this paper, revealed that one locus, which contains four genes that enc ...	2003	12839734
a modified saccharomyces cerevisiae strain that consumes l-arabinose and produces ethanol.	metabolic engineering is a powerful method to improve, redirect, or generate new metabolic reactions or whole pathways in microorganisms. here we describe the engineering of a saccharomyces cerevisiae strain able to utilize the pentose sugar l-arabinose for growth and to ferment it to ethanol. expanding the substrate fermentation range of s. cerevisiae to include pentoses is important for the utilization of this yeast in economically feasible biomass-to-ethanol fermentation processes. after over ...	2003	12839792
development of antibiotic-overproducing strains by site-directed mutagenesis of the rpsl gene in streptomyces lividans.	certain rpsl (which encodes the ribosomal protein s12) mutations that confer resistance to streptomycin markedly activate the production of antibiotics in streptomyces spp. these rpsl mutations are known to be located in the two conserved regions within the s12 protein. to understand the roles of these two regions in the activation of silent genes, we used site-directed mutagenesis to generate eight novel mutations in addition to an already known (k88e) mutation that is capable of activating ant ...	2003	12839808
molecular phylogenetic exploration of bacterial diversity in a bakreshwar (india) hot spring and culture of shewanella-related thermophiles.	the bacterial diversity of a hot spring in bakreshwar, india, was investigated by a culture-independent approach. 16s ribosomal dna clones derived from the sediment samples were found to be associated with gamma-proteobacteria, cyanobacteria, and green nonsulfur and low-gc gram-positive bacteria. the first of the above phylotypes cobranches with shewanella, a well-known iron reducer. this phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing mic ...	2003	12839826
direct observation of protonation reactions during the catalytic cycle of cytochrome c oxidase.	cytochrome c oxidase, the terminal protein in the respiratory chain, converts oxygen into water and helps generate the electrochemical gradient used in the synthesis of atp. the catalytic action of cytochrome c oxidase involves electron transfer, proton transfer, and o2 reduction. these events trigger specific molecular changes at the active site, which, in turn, influence changes throughout the protein, including alterations of amino acid side chain orientations, hydrogen bond patterns, and pro ...	2003	12851460
x-ray crystal structures of the wt and a hyper-accurate ribosome from escherichia coli.	protein biosynthesis on the ribosome requires accurate reading of the genetic code in mrna. two conformational rearrangements in the small ribosomal subunit, a closing of the head and body around the incoming trna and an rna helical switch near the mrna decoding site, have been proposed to select for complementary base-pairing between mrna codons and trna anticodons. we determined x-ray crystal structures of the wt and a hyper-accurate variant of the escherichia coli ribosome at resolutions of 1 ...	2003	12853578
a new thermus sp. class-iis enzyme sub-family: isolation of a 'twin' endonuclease tspdti with a novel specificity 5'-atgaa(n(11/9))-3', related to tspgwi, taqii and tth111ii.	the tspdti restriction endonuclease, which shows a novel recognition specificity 5'-atgaa(n(11/9))-3', was isolated from thermus sp. dt. tspdti appears to be a 'twin' of restriction endonuclease tspgwi from thermus sp. gw, as we have previously reported. tspgwi was isolated from the same location as tspdti, it recognizes a related sequence 5'-acgga(n(11/9))-3' and has conserved cleavage positions. both enzymes resemble two other class-iis endonucleases from thermus sp.: taqii and tth111ii. n-ter ...	2003	12853651
ribosomal localization of translation initiation factor if2.	bacterial translation initiation factor if2 is a gtp-binding protein that catalyzes binding of initiator fmet-trna in the ribosomal p site. the topographical localization of if2 on the ribosomal subunits, a prerequisite for understanding the mechanism of initiation complex formation, has remained elusive. here, we present a model for the positioning of if2 in the 70s initiation complex as determined by cleavage of rrna by the chemical nucleases cu(ii):1,10-orthophenanthroline and fe(ii):edta tet ...	2003	12869707
when contemporary aminoacyl-trna synthetases invent their cognate amino acid metabolism.	faithful protein synthesis relies on a family of essential enzymes called aminoacyl-trna synthetases, assembled in a piecewise fashion. analysis of the completed archaeal genomes reveals that all archaea that possess asparaginyl-trna synthetase (asnrs) also display a second orf encoding an asnrs truncated from its anticodon binding-domain (asnrs2). we show herein that pyrococcus abyssi asnrs2, in contrast to asnrs, does not sustain asparaginyl-trnaasn synthesis but is instead capable of converti ...	2003	12874385
identification of protein biochemical functions by similarity search using the molecular surface database ef-site.	the identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. we have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database ef-site (electrostati ...	2003	12876308
crystal structure of the conserved protein tt1542 from thermus thermophilus hb8.	the tt1542 protein from thermus thermophilus hb8 is annotated as a conserved hypothetical protein, and belongs to the duf158 family in the pfam database. a blast search revealed that homologs of tt1542 are present in a wide range of organisms. the tt1542 homologs in eukaryotes, pig-l in mammals, and gpi12 in yeast and protozoa, have n-acetylglucosaminylphosphatidylinositol (glcnac-pi) de-n-acetylase activity. although most of the homologs in prokaryotes are hypothetical and have no known functio ...	2003	12876312
dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.	combining structural data for the ribosome from x-ray crystallography and cryo-electron microscopy with dynamic models based on elastic network normal mode analysis, an atomically detailed picture of functionally important structural rearrangements that occur during translocation is elucidated. the dynamic model provides a near-atomic description of the ratchet-like rearrangement of the 70s ribosome seen in cryo-electron microscopy, and permits the identification of bridging interactions that ei ...	2003	12878726
a novel is element, is621, of the is110/is492 family transposes to a specific site in repetitive extragenic palindromic sequences in escherichia coli.	an escherichia coli strain, ecor28, was found to have insertions of an identical sequence (1,279 bp in length) at 10 loci in its genome. this insertion sequence (named is621) has one large open reading frame encoding a putative protein that is 326 amino acids in length. a computer-aided homology search using the dna sequence as the query revealed that is621 was homologous to the piv genes, encoding pilin gene invertase (piv). a homology search using the amino acid sequence of the putative protei ...	2003	12897009
temperature-dependent hypermutational phenotype in reca mutants of thermus thermophilus hb27.	the reca gene from thermus thermophilus hb27 was cloned and engineered to obtain insertion (reca::kat) and deletion (deltareca) derivatives. transcription of reca in this extreme thermophile was induced by mitomycin c, leading to the synthesis of a monocistronic mrna. this dna damage-mediated induction was dependent on the integrity of reca. in addition to uv sensitivity, the reca mutants of t. thermophilus showed severe pleiotropic defects, ranging from irregular nucleoid condensation and segre ...	2003	12897010
directed evolution of thermus maltogenic amylase toward enhanced thermal resistance.	the thermostability of maltogenic amylase from thermus sp. strain im6501 (thma) was improved greatly by random mutagenesis using dna shuffling. four rounds of dna shuffling and subsequent recombination of the mutations produced the highly thermostable mutant enzyme thma-dm, which had a total of seven individual mutations. the seven amino acid substitutions in thma-dm were identified as r26q, s169n, i333v, m375t, a398v, q411l, and p453l. the optimal reaction temperature of the recombinant enzyme ...	2003	12902281
is the in situ accessibility of the 16s rrna of escherichia coli for cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30s ribosomal subunit?	systematic studies on the hybridization of fluorescently labeled, rrna-targeted oligonucleotides have shown strong variations in in situ accessibility. reliable predictions of target site accessibility would contribute to more-rational design of probes for the identification of individual microbial cells in their natural environments. during the past 3 years, numerous studies of the higher-order structure of the ribosome have advanced our understanding of its spatial conformation. these studies ...	2003	12902289
comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins.	zinc is an important component of many proteins, but in large concentrations it is poisonous to the cell. thus its transport is regulated by zinc repressors zur of proteobacteria and gram-positive bacteria from the bacillus group and adcr of bacteria from the streptococcus group. comparative computational analysis allowed us to identify binding signals of zur repressors gaaatgttatantataacatttc for gamma-proteobacteria, gtaatgtaataacattac for the agrobacterium group, gatatgttataacatatc for the rh ...	2003	12904577
glutathione synthetase homologs encode alpha-l-glutamate ligases for methanogenic coenzyme f420 and tetrahydrosarcinapterin biosyntheses.	proteins in the atp-grasp superfamily of amide bond-forming ligases have evolved to function in a number of unrelated biosynthetic pathways. previously identified homologs encoding glutathione synthetase, d-alanine:d-alanine ligase and the bacterial ribosomal protein s6:glutamate ligase have been vertically inherited within certain organismal lineages. although members of this specificity-diverse superfamily share a common reaction mechanism, the nonoverlapping set of amino acid and peptide subs ...	2003	12909715
analysis of the dna joining repertoire of chlorella virus dna ligase and a new crystal structure of the ligase-adenylate intermediate.	chlorella virus dna ligase is the smallest eukaryotic atp-dependent dna ligase known; it suffices for yeast cell growth in lieu of the essential yeast dna ligase cdc9. the chlorella virus ligase-adenylate intermediate has an intrinsic nick sensing function and its dna footprint extends 8-9 nt on the 3'-hydroxyl (3'-oh) side of the nick and 11-12 nt on the 5'-phosphate (5'-po4) side. here we establish the minimal length requirements for ligatable 3'-oh and 5'-po4 strands at the nick (6 nt) and de ...	2003	12930960
mutations in rpobc suppress the defects of a sinorhizobium meliloti rela mutant.	the nitrogen-fixing symbiosis between sinorhizobium meliloti and medicago sativa requires complex physiological adaptation by both partners. one method by which bacteria coordinately control physiological adaptation is the stringent response, which is triggered by the presence of the nucleotide guanosine tetraphosphate (ppgpp). ppgpp, produced by the rela enzyme, is thought to bind to and alter the ability of rna polymerase (rnap) to initiate and elongate transcription and affect the affinity of ...	2003	12949113
inference of protein function and protein linkages in mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach.	the genome of mycobacterium tuberculosis was analyzed using recently developed computational approaches to infer protein function and protein linkages. we evaluated and employed a method to infer genes likely to belong to the same operon, as judged by the nucleotide distance between genes in the same genomic orientation, and combined this method with those of the rosetta stone, phylogenetic profile and conserved gene neighbor computational methods for the inference of protein function.	2003	12952538
characterization of microbial communities in gas industry pipelines.	culture-independent techniques, denaturing gradient gel electrophoresis (dgge) analysis, and random cloning of 16s rrna gene sequences amplified from community dna were used to determine the diversity of microbial communities in gas industry pipelines. samples obtained from natural gas pipelines were used directly for dna extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. the variable v2-v3 (average siz ...	2003	12957923
molecular analysis of echovirus 13 isolates and aseptic meningitis, spain.	echovirus 13 (ev13), considered rare, was reported worldwide in 2000, mostly related to aseptic meningitis outbreaks. in spain, 135 ev13 isolates were identified. the genetic relationships between 64 representative strains from spain and other reported isolates from the united states, germany, italy, japan, and sweden were described by analyzing the partial sequence of the major capsid protein (vp1) gene. the strains from spain were clearly identified as ev13 (79.5% similarity with the ev13 refe ...	2003	12967490
single-nucleotide polymorphism genotyping on optical thin-film biosensor chips.	single-nucleotide polymorphisms (snps) constitute the bulk of human genetic variation and provide excellent markers to identify genetic factors contributing to complex disease susceptibility. a rapid, sensitive, and inexpensive assay is important for large-scale snp scoring. here we report the development of a multiplex snp detection system using silicon chips coated to create a thin-film optical biosensor. allele-discriminating, aldehyde-labeled oligonucleotides are arrayed and covalently attac ...	2003	12975525
the extended loops of ribosomal proteins l4 and l22 are not required for ribosome assembly or l4-mediated autogenous control.	ribosomal proteins l4 and l22 both have a globular domain that sits on the surface of the large ribosomal subunit and an extended loop that penetrates its core. the tips of both loops contribute to the lining of the peptide exit tunnel and have been implicated in a gating mechanism that might regulate the exit of nascent peptides. also, the extensions of l4 and l22 contact multiple domains of 23s rrna, suggesting they might facilitate rrna folding during ribosome assembly. to learn more about th ...	2003	13130133
a noncognate aminoacyl-trna synthetase that may resolve a missing link in protein evolution.	efforts to delineate the advent of many enzymes essential to protein translation are often limited by the fact that the modern genetic code evolved before divergence of the tree of life. glutaminyl-trna synthetase (glnrs) is one noteworthy exception to the universality of the translation apparatus. in eukaryotes and some bacteria, this enzyme is essential for the biosynthesis of gln-trnagln, an obligate intermediate in translation. glnrs is absent, however, in archaea, and most bacteria, organel ...	2003	13679580
role of residual structure in the unfolded state of a thermophilic protein.	ribonucleases h from the thermophilic bacterium thermus thermophilus and the mesophile escherichia coli demonstrate a dramatic and surprising difference in their change in heat capacity upon unfolding (deltacp degrees ). the lower deltacp degrees of the thermophilic protein directly contributes to its higher thermal denaturation temperature (tm). we propose that this deltacp degrees difference originates from residual structure in the unfolded state of the thermophilic protein; we verify this hy ...	2003	14504401
genetic characterization of optochin-susceptible viridans group streptococci.	two clinical isolates of viridans group streptococci (vs) with different degrees of susceptibility to optochin (opt), i.e., fully opt-susceptible (opt(s)) vs strain 1162/99 (for which the mic was equal to that for streptococcus pneumoniae, 0.75 micro g/ml) and intermediate opt(s) vs strain 1174/97 (mic, 6 micro g/ml) were studied. besides being opt susceptible, they showed characteristics typical of vs, such as bile insolubility; lack of reaction with pneumococcal capsular antibodies; and lack o ...	2003	14506029
osmotic adaptation of thermus thermophilus rq-1: lesson from a mutant deficient in synthesis of trehalose.	strains of thermus thermophilus accumulate primarily trehalose and smaller amounts of mannosylglycerate in response to salt stress in yeast extract-containing media (o. c. nunes, c. m. manaia, m. s. da costa, and h. santos, appl. environ. microbiol. 61:2351-2357, 1995). a 2.4-kbp dna fragment from t. thermophilus strain rq-1 carrying otsa (encoding trehalose-phosphate synthase [tps]), otsb (encoding trehalose-phosphate phosphatase [tpp]), and a short sequence of the 5' end of tres (trehalose syn ...	2003	14526004
atp-bound conformation of topoisomerase iv: a possible target for quinolones in streptococcus pneumoniae.	topoisomerase iv, a c(2)e(2) tetramer, is involved in the topological changes of dna during replication. this enzyme is the target of antibacterial compounds, such as the coumarins, which target the atp binding site in the pare subunit, and the quinolones, which bind, outside the active site, to the quinolone resistance-determining region (qrdr). after site-directed and random mutagenesis, we found some mutations in the atp binding site of pare near the dimeric interface and outside the qrdr tha ...	2003	14526026
the ribosome and yidc. new insights into the biogenesis of escherichia coli inner membrane proteins.	in the bacterium escherichia coli, inner membrane proteins (imps) are generally targeted through the signal recognition particle pathway to the sec translocon, which is capable of both linear transport into the periplasm and lateral transport into the lipid bilayer. lateral transport seems to be assisted by the imp yidc. in this article, we discuss recent observations that point to a key role for the ribosome in imp targeting and to the diverse roles of yidc in imp assembly.	2003	14528263
structures of deacylated trna mimics bound to the e site of the large ribosomal subunit.	during translation, trnas cycle through three binding sites on the ribosome: the a, the p, and the e sites. we have determined the structures of complexes between the haloarcula marismortui large ribosomal subunit and two different e site substrates: a deacylated trna acceptor stem minihelix and a cca-acceptor end. both of these trna mimics contain analogs of adenosine 76, the component responsible for a large proportion of e site binding affinity. they bind in the center of the loop-extension o ...	2003	14561884
the saccharomyces cerevisiae u2 snrna:pseudouridine-synthase pus7p is a novel multisite-multisubstrate rna:psi-synthase also acting on trnas.	the saccharomyces cerevisiae pus7 protein was recently characterized as a novel rna:pseudouridine (psi)-synthase acting at position 35 in u2 snrna. however, u2 snrna was the only potential substrate tested for this enzyme. in this work, we demonstrated that although pus7p is responsible for the formation of only one of the six psi residues present in yeast usnrnas, it catalyzes u to psi conversion at position 13 in cytoplasmic trnas and at position 35 in pre-trna(tyr). sites of rna modification ...	2003	14561887
microbial community structure in midgut and hindgut of the humus-feeding larva of pachnoda ephippiata (coleoptera: scarabaeidae).	the guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. in a companion paper (t. lemke, u. stingl, m. egert, m. w. friedrich, and a. brune, appl. environ. microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and ...	2003	14602626
analysis, characterization, and loci of the tuf genes in lactobacillus and bifidobacterium species and their direct application for species identification.	we analyzed the tuf gene, encoding elongation factor tu, from 33 strains representing 17 lactobacillus species and 8 bifidobacterium species. the tuf sequences were aligned and used to infer phylogenesis among species of lactobacilli and bifidobacteria. we demonstrated that the synonymous substitution affecting this gene renders elongation factor tu a reliable molecular clock for investigating evolutionary distances of lactobacilli and bifidobacteria. in fact, the phylogeny generated by these tu ...	2003	14602655
comparative analysis of editosome proteins in trypanosomatids.	detailed comparisons of 16 editosome proteins from trypanosoma brucei, trypanosoma cruzi and leishmania major identified protein motifs associated with catalysis and protein or nucleic acid interactions that suggest their functions in rna editing. five related proteins with rnase iii-like motifs also contain a u1-like zinc finger and either dsrbm or pumilio motifs. these proteins may provide the endoribonuclease function in editing. two other related proteins, at least one of which is associated ...	2003	14602897
enhancement of dna, cdna synthesis and fidelity at high temperatures by a dimeric single-stranded dna-binding protein.	bacterial single-stranded dna-binding proteins (ssbs) are required for dna replication and repair. we have over-expressed and purified the native form and two his-tagged fusions of the ssb from thermus thermophilus (tthssb). the three proteins were found as dimers in solution. they bound in vitro to single-stranded dna specifically over a temperature range of 4-80 degrees c, and the wild-type protein could withstand incubation at 94 degrees c for 2 min. addition of tthssb to pcr halved the elong ...	2003	14602905
j protein cochaperone of the mitochondrial inner membrane required for protein import into the mitochondrial matrix.	the major hsp70 of the mitochondrial matrix (ssc1 in yeast) is critically important for the translocation of proteins from the cytosol, across the mitochondrial inner membrane, and into the matrix. tim44, a peripheral inner membrane protein with limited sequence similarity to the j domain of j-type cochaperones, tethers ssc1 to the import channel. here we report that, unlike a j protein, tim44 does not stimulate the atpase activity of ssc1, nor does it affect the stimulation by either a known mi ...	2003	14605210
coevolution of an aminoacyl-trna synthetase with its trna substrates.	glutamyl-trna synthetases (glurss) occur in two types, the discriminating and the nondiscriminating enzymes. they differ in their choice of substrates and use either trnaglu or both trnaglu and trnagln. although most organisms encode only one glurs, a number of bacteria encode two different glurs proteins; yet, the trna specificity of these enzymes and the reason for such gene duplications are unknown. a database search revealed duplicated glurs genes in >20 bacterial species, suggesting that th ...	2003	14615592
products transcribed from rearranged rrn genes of escherichia coli can assemble to form functional ribosomes.	to examine the flexibility of rrna operons with respect to fundamental organization, transcription, processing, and assembly of ribosomes, operon variations were introduced by a plasmid into an escherichia coli strain that has deletions of all chromosomal copies of rrna genes. in the reconstructed operons, a salmonella intervening sequence (ivs) from 23s helix 45 was introduced into the e. coli 23s gene at the same position. three different constructs of the e. coli 16s gene were then placed who ...	2003	14617656
quantification of alternatively spliced fgfr2 rnas using the rna invasive cleavage assay.	the regulated splicing of fibroblast growth factor receptor-2 (fgfr2) transcripts leads to tissue-specific expression of distinct receptor isoforms. these isoforms contain two different versions of the ligand binding ig-like domain iii, which are encoded by exon iiib or exon iiic. the mutually exclusive use of exon iiib and exon iiic can be recapitulated in tissue culture using dt3 and at3 rat prostate carcinoma cells. we used this well-characterized system to evaluate the precision and accuracy ...	2003	14624010
solution nmr structure of the 30s ribosomal protein s28e from pyrococcus horikoshii.	we report nmr assignments and solution structure of the 71-residue 30s ribosomal protein s28e from the archaean pyrococcus horikoshii, target jr19 of the northeast structural genomics consortium. the structure, determined rapidly with the aid of automated backbone resonance assignment (autoassign) and automated structure determination (autostructure) software, is characterized by a four-stranded beta-sheet with a classic greek-key topology and an oligonucleotide/oligosaccharide beta-barrel (ob) ...	2003	14627742
an archaebacteria-derived glutamyl-trna synthetase and trna pair for unnatural amino acid mutagenesis of proteins in escherichia coli.	the addition of novel amino acids to the genetic code of escherichia coli involves the generation of an aminoacyl-trna synthetase and trna pair that is 'orthogonal', meaning that it functions independently of the synthetases and trnas endogenous to e.coli. the amino acid specificity of the orthogonal synthetase is then modified to charge the corresponding orthogonal trna with an unnatural amino acid that is subsequently incorporated into a polypeptide in response to a nonsense or missense codon. ...	2003	14627803
regulation of lysine biosynthesis and transport genes in bacteria: yet another rna riboswitch?	comparative analysis of genes, operons and regulatory elements was applied to the lysine biosynthetic pathway in available bacterial genomes. we report identification of a lysine-specific rna element, named the lys element, in the regulatory regions of bacterial genes involved in biosynthesis and transport of lysine. similarly to the previously described rna regulatory elements for three vitamins (riboflavin, thiamin and cobalamin), purine and methionine regulons, this regulatory rna structure i ...	2003	14627808
ribosomal proteins rps0 and rps21 of saccharomyces cerevisiae have overlapping functions in the maturation of the 3' end of 18s rrna.	the rps0 proteins of saccharomyces cerevisiae are components of the 40s ribosomal subunit required for maturation of the 3' end of 18s rrna. drosophila and human homologs of the rps0 proteins physically interact with rps21 proteins, and decreased expression of both proteins in drosophila impairs control of cellular proliferation in hematopoietic organs during larval development. here, we characterize the yeast rps21a/b genes and show that strains where both genes are disrupted are not viable. re ...	2003	14627813
transcript cleavage factors grea and greb act as transient catalytic components of rna polymerase.	prokaryotic transcription elongation factors grea and greb stimulate intrinsic nucleolytic activity of rna polymerase (rnap). the proposed biological role of gre-induced rna hydrolysis includes transcription proofreading, suppression of transcriptional pausing and arrest, and facilitation of rnap transition from transcription initiation to transcription elongation. using an array of biochemical and molecular genetic methods, we mapped the interaction interface between gre and rnap and identified ...	2003	14633991
effect of g-1 on histidine trna microhelix conformation.	histidine trnas (trna(his)) are unique in that they possess an extra 5'-base (g-1) not found in other trnas. deletion of g-1 results in at least a 250-fold reduction in the rate of histidine charging in vitro. to better understand the role of the g-1 nucleotide in defining the structure of trna(his), and to correlate structure with cognate amino acid charging, nmr and molecular dynamics (md) studies were performed on the wild-type and a deltag-1 mutant escherichia coli histidine trna acceptor st ...	2003	14654706
crystal structures that suggest late development of genetic code components for differentiating aromatic side chains.	early forms of the genetic code likely generated "statistical" proteins, with similar side chains occupying the same sequence positions at different ratios. in this scenario, groups of related side chains were treated by aminoacyl-trna synthetases as a single molecular species until a discrimination mechanism developed that could separate them. the aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. a crystal structure of human tryptophanyl-trna s ...	2003	14671330
structure of mth11/mth rpp29, an essential protein subunit of archaeal and eukaryotic rnase p.	we have determined the solution structure of mth11 (mth rpp29), an essential subunit of the rnase p enzyme from the archaebacterium methanothermobacter thermoautotrophicus (mth). rnase p is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of trnas in all three domains of life. in eubacteria, this enzyme is made up of two subunits: a large rna ( approximately 120 kda) responsible for mediating catalysis, and a small protein cofactor ...	2003	14673079
on the evolution of structure in aminoacyl-trna synthetases.	the aminoacyl-trna synthetases are one of the major protein components in the translation machinery. these essential proteins are found in all forms of life and are responsible for charging their cognate trnas with the correct amino acid. the evolution of the trna synthetases is of fundamental importance with respect to the nature of the biological cell and the transition from an rna world to the modern world dominated by protein-enzymes. we present a structure-based phylogeny of the aminoacyl-t ...	2003	14665676
molecular basis of bacterial outer membrane permeability revisited.	gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. this review summarizes the development in the field since ...	2003	14665678
evolutionary connection between the catalytic subunits of dna-dependent rna polymerases and eukaryotic rna-dependent rna polymerases and the origin of rna polymerases.	the eukaryotic rna-dependent rna polymerase (rdrp) is involved in the amplification of regulatory micrornas during post-transcriptional gene silencing. this enzyme is highly conserved in most eukaryotes but is missing in archaea and bacteria. no evolutionary relationship between rdrp and other polymerases has been reported so far, hence the origin of this eukaryote-specific polymerase remains a mystery.	2003	12553882
extremophiles 2002.		2003	12813059
nucleic acid recognition by ob-fold proteins.	the ob-fold domain is a compact structural motif frequently used for nucleic acid recognition. structural comparison of all ob-fold/nucleic acid complexes solved to date confirms the low degree of sequence similarity among members of this family while highlighting several structural sequence determinants common to most of these ob-folds. loops connecting the secondary structural elements in the ob-fold core are extremely variable in length and in functional detail. however, certain features of l ...	2003	12598368
toward an understanding of the structural basis of translation.	the recently solved x-ray crystal structures of the ribosome have provided opportunities for studying the molecular basis of translation with a variety of methods including cryo-electron microscopy - where maps give the first glimpses of ribosomal evolution - and fluorescence spectroscopy techniques.	2003	14659007
position of eukaryotic initiation factor eif1 on the 40s ribosomal subunit determined by directed hydroxyl radical probing.	eukaryotic initiation factor (eif) eif1 maintains the fidelity of initiation codon selection by enabling 43s complexes to reject codon-anticodon mismatches, to recognize the initiation codon context, and to discriminate against establishing a codon-anticodon interaction with augs located <8 nt from the 5'-end of mrna. to understand how eif1 plays its discriminatory role, we determined its position on the 40s ribosomal subunit using directed hydroxyl radical cleavage. the cleavage of 18s rrna in ...	2003	14600024
solvation change and ion release during aminoacylation by aminoacyl-trna synthetases.	discrimination between cognate and non-cognate trnas by aminoacyl-trna synthetases occurs at several steps of the aminoacylation pathway. we have measured changes of solvation and counter-ion distribution at various steps of the aminoacylation pathway of glutamyl- and glutaminyl-trna synthetases. the decrease in the association constant with increasing kcl concentration is relatively small for cognate trna binding when compared to known dna-protein interactions. the electro-neutral nature of the ...	2003	14530451
over-expression of interleukin 10 in mucosal t cells of patients with active ulcerative colitis.	ulcerative colitis (uc), a chronic inflammatory bowel disease, exhibits pronounced increase of t lymphocytes in the inflamed mucosa. to understand the role of intestinal t lymphocytes in the pathogenesis of uc their cytokine production in the mucosa was analysed. intestinal t lymphocytes of uc, crohn's disease and control patients were analysed for cytokine mrna levels by real-time quantitative reverse transcription-polymerase chain reaction (rt-pcr) directly after isolation without in vitro sti ...	2003	12974765
biochemical characterization of the kink-turn rna motif.	rna, which acts as a medium for transmitting genetic information, plays a variety of roles in a cell. as with proteins, elucidation of the three- dimensional (3d) structures of rnas is important for understanding their various roles. determination of the atomic structures of crystallized ribosome has enabled the identification of previously unknown rna structural motifs. the kink-turn (k-turn or ga) motif, which causes a sharp bend in an rna double helix, was identified as one of these structura ...	2003	14500816
rna structure comparison, motif search and discovery using a reduced representation of rna conformational space.	given the wealth of new rna structures and the growing list of rna functions in biology, it is of great interest to understand the repertoire of rna folding motifs. the ability to identify new and known motifs within novel rna structures, to compare tertiary structures with one another and to quantify the characteristics of a given rna motif are major goals in the field of rna research; however, there are few systematic ways to address these issues. using a novel approach for visualizing and mat ...	2003	12907716
trna synthetase paralogs: evolutionary links in the transition from trna-dependent amino acid biosynthesis to de novo biosynthesis.		2003	12913115
pops: a fast algorithm for solvent accessible surface areas at atomic and residue level.	pops (parameter optimsed surfaces) is a new method to calculate solvent accessible surface areas, which is based on an empirically parameterisable analytical formula and fast to compute. atomic and residue areas (the latter represented by a single sphere centered on the c(alpha) atom of amino acids and at the p atom of nucleotides) have been optimised versus accurate all-atom methods. the parameterisation has been derived from a selected dataset of proteins and nucleic acids of different sizes a ...	2003	12824328
the long-range electrostatic interactions control trna-aminoacyl-trna synthetase complex formation.	in most cases aminoacyl-trna synthetases (aarss) are negatively charged, as are the trna substrates. it is apparent that there are driving forces that provide a long-range attraction between like charge aars and trna, and ensure formation of "close encounters." based on numerical solutions to the nonlinear poisson-boltzmann equation, we evaluated the electrostatic potential generated by different aarss. the 3d-isopotential surfaces calculated for different aarss at 0.01 kt/e contour level reveal ...	2003	12761395
unified two-metal mechanism of rna synthesis and degradation by rna polymerase.	in dna-dependent rna polymerases, reactions of rna synthesis and degradation are performed by the same active center (in contrast to dna polymerases in which they are separate). we propose a unified catalytic mechanism for multisubunit rna polymerases based on the analysis of its 3'-5' exonuclease reaction in the context of crystal structure. the active center involves a symmetrical pair of mg(2+) ions that switch roles in synthesis and degradation. one ion is retained permanently and the other ...	2003	12727889
atom depth as a descriptor of the protein interior.	atom depth, defined as the distance (dpx, a) of a nonhydrogen atom from its closest solvent-accessible protein neighbor, provides a simple but precise description of the protein interior. mean residue depths can be easily computed and are very sensitive to structural features. from the analysis of the average and maximum atom depths of a set of 136 protein structures, we derive a limit of approximately 200 residues for protein and protein domain size. the average and maximum atom depths in a pro ...	2003	12668463
deep trefoil knot implicated in rna binding found in an archaebacterial protein.		2003	12486711
structural classification of zinc fingers: survey and summary.	zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation and apoptosis. zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic aci ...	2003	12527760
interstice mutations that block site-to-site translocation of a misactivated amino acid bound to a class i trna synthetase.	class i aminoacyl-trna synthetases catalyze editing reactions that prevent ambiguity from entering the genetic code. misactivated amino acids are translocated in cis from the active site for aminoacylation to the center for editing, located approximately 30 a away. mutational analysis has functionally separated the two sites by creating mutations that disrupt the catalytic center for editing but not for aminoacylation and vice versa. what is not known is whether translocation per se can be disru ...	2003	12515858
molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils.	microorganisms that use nitrate as an alternative terminal electron acceptor play an important role in the global nitrogen cycle. the diversity of the nitrate-reducing community in soil and the influence of the maize roots on the structure of this community were studied. the narg gene encoding the membrane bound nitrate reductase was selected as a functional marker for the nitrate-reducing community. the use of narg is of special interest because the phylogeny of the narg gene closely reflects t ...	2002	12450836
the ribosome filter hypothesis.	a variety of posttranscriptional mechanisms affects the processing, subcellular localization, and translation of messenger rnas (mrnas). translational control appears to occur primarily at the initiation rather than the elongation stage. it has been suggested that translation is mediated largely by means of a cap-binding/scanning mechanism. on the basis of recent findings, we propose here that differential binding of particular mrnas to eukaryotic 40s ribosomal subunits before translation may al ...	2002	12221294
the non-watson-crick base pairs and their associated isostericity matrices.	rna molecules exhibit complex structures in which a large fraction of the bases engage in non-watson-crick base pairing, forming motifs that mediate long-range rna-rna interactions and create binding sites for proteins and small molecule ligands. the rapidly growing number of three-dimensional rna structures at atomic resolution requires that databases contain the annotation of such base pairs. an unambiguous and descriptive nomenclature was proposed recently in which rna base pairs were classif ...	2002	12177293
linamarase expression in cassava cultivars with roots of low- and high-cyanide content.	this paper reports the expression and localization of linamarase in roots of two cassava (manihot esculenta crantz) cultivars of low and high cyanide. two different patterns of linamarase activity were observed. in the low-cyanide type, young leaves displayed very high enzyme activity during the early plant growing stage (3 months), whereas in root peel, the activity increased progressively to reach a peak in 11-month-old plants. conversely, in the high-cyanide cultivar (hcv), root peel linamara ...	2002	12177481
bruce: a program for the detection of transfer-messenger rna genes in nucleotide sequences.	a computer program, bruce, was developed for the identification of transfer-messenger rna (tmrna) genes. the program employs heuristic algorithms to search for a trna(ala)-like secondary structure surrounding a short sequence encoding the tag peptide. in the 57 completely sequenced bacterial genomes where tmrna genes have been reported previously, bruce identified all with no false positives. in addition, bruce found 99 of the 100 tmrnas identified previously in other bacteria, red chloroplasts ...	2002	12140330
the time course of changes in mrna levels in tree shrew sclera during induced myopia and recovery.	in tree shrews, visual form deprivation produces increased axial elongation of the deprived eye and a myopic shift in refractive state. a change in scleral extensibility (creep rate) is closely associated with the change in axial elongation rate. these effects may be due to scleral tissue remodeling produced by a change in scleral gene expression. in this study, the authors investigated the time course of changes in scleral mrna levels for selected proteins during the development of form depriva ...	2002	12091398
parameter optimized surfaces (pops): analysis of key interactions and conformational changes in the ribosome.	we present a new method for the calculation of solvent accessible surface areas at the atomic and residue levels, which we call parameter optimized surfaces (pops-a and pops-r ). atomic and residue areas (the latter simulated with a single sphere centered at the c(alpha)s atom for amino acids and at the p atom for nucleotides) have been optimized versus accurate all-atoms methods. we concentrated on an analytical formula for the approximation of solvent accessibilities. the formula is simple, ea ...	2002	12087181
trilogy: discovery of sequence-structure patterns across diverse proteins.	we describe a new computer program, trilogy, for the automated discovery of sequence-structure patterns in proteins. trilogy implements a pattern discovery algorithm that begins with an exhaustive analysis of flexible three-residue patterns; a subset of these patterns are selected as seeds for an extension process in which longer patterns are identified. a key feature of the method is explicit treatment of both the sequence and structure components of these motifs: each trilogy pattern is a pair ...	2002	12084910
integration of dna ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms.	association studies using common sequence variants or single nucleotide polymorphisms (snps) may provide a powerful approach to dissect the genetic inheritance of common complex traits. such studies necessitate the development of cost-effective, high throughput technologies for scoring snps. the method described in this paper for the co-detection of both alleles of a snp in a single homogeneous reaction combines the specificity of a high fidelity dna ligation step with the power of rolling circl ...	2002	12060698
tracing the evolution of rna structure in ribosomes.	the elucidation of ribosomal structure has shown that the function of ribosomes is fundamentally confined to dynamic interactions established between the rna components of the ribosomal ensemble. these findings now enable a detailed analysis of the evolution of ribosomal rna (rrna) structure. the origin and diversification of rrna was studied here using phylogenetic tools directly at the structural level. a rooted universal tree was reconstructed from the combined secondary structures of large ( ...	2002	12034847
high affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands.	we have isolated 2'-fluoro-substituted rna aptamers that bind to streptavidin (sa) with an affinity around 7 +/- 1.8 nm, comparable with that of recently described peptide aptamers. binding to sa was not prevented by prior saturation with biotin, enabling nucleic acid aptamers to form useful ternary complexes. mutagenesis, secondary structure analysis, ribonuclease footprinting and deletion analysis provided evidence for the essential structural features of sa-binding aptamers. in order to provi ...	2002	12000850
the accessory subunit of dna polymerase gamma is essential for mitochondrial dna maintenance and development in drosophila melanogaster.	dna polymerase gamma, pol gamma, is the key replicative enzyme in animal mitochondria. the drosophila enzyme is a heterodimer comprising catalytic and accessory subunits of 125 kda and 35 kda, respectively. both subunits have been cloned and characterized in a variety of model systems, and genetic mutants of the catalytic subunit were first identified in drosophila, as chemically induced mutations that disrupt larval behavior (tamas). mutations in the gene encoding the accessory subunit have not ...	2002	11917141
5s ribosomal rna database.	ribosomal 5s rna (5s rrna) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. it is thought to enhance protein synthesis by stabilization of a ribosome structure. this paper presents the updated database of 5s rrna and their genes (5s rdna). its short characteristics are presented in the introduction. the database contains 2280 primary structures of 5s rrna and 5s rrna genes. these include 536 eu ...	2002	11752286
the european database on small subunit ribosomal rna.	the european database on ssu rrna can be consulted via the world wideweb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal rna sequences. sequences are provided in aligned format. the alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also av ...	2002	11752288
mmdb: entrez's 3d-structure database.	three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. the goal of entrez's 3d-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. to this end entrez's search engine provides three powerful features. (i) sequence and structure neighbors; one may select all sequences similar to one of ...	2002	11752307
modularity and specialization in superfamily 1 and 2 helicases.		2002	11889086
demystified... molecular pathology in oncology.	in the past 10 years, molecular biology has found major applications in pathology, particularly in oncology. this has been a field of enormous expansion, where pure science has found a place in clinical practice and is now of everyday use in any academic unit. this demystified review will discuss the techniques used in molecular pathology and then provide examples of how these can be used in oncology.	2002	12456768
perspectives on biotechnological applications of archaea.	many archaea colonize extreme environments. they include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. this review summarizes current knowledge about the biotechnolog ...	2002	15803645
comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale.	a comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains. thirty-four r-protein families are represented in all domains but 33 families are specific to archaea and eucarya, providing evidence for specialisation at an early stage of evolution between the bacterial lineage and the lineage leading to archaea and eukaryotes. with only one specific r-protein, the arch ...	2002	12490706