Publications

structural origins of amino acid selection without editing by cysteinyl-trna synthetase.	cysteinyl-trna synthetase (cysrs) is highly specific for synthesis of cysteinyl adenylate, yet does not possess the amino acid editing activity characteristic of many other trna synthetases. to elucidate how cysrs is able to distinguish cysteine from non-cognate amino acids, crystal structures of the escherichia coli enzyme were determined in apo and cysteine-bound states. the structures reveal that the substrate cysteine thiolate forms a single direct interaction with a zinc ion bound at the ba ...	2002	12032090
importance of compartment formation for a self-encoding system.	a self-encoding system designed to have strict "compartition" of the molecules, i.e., to contain only a single molecule of dna in each compartment, was established, and its evolutionary fate was analyzed. the system comprised the thermus thermophilus dna polymerase gene as the informational molecule and its protein product replicating the gene as the functional molecule. imposing strict compartition allows the self-encoding system to last up to at least the tenth generation, whereas the system c ...	2002	12032314
evidence for strong selective constraint acting on the nucleotide composition of 16s ribosomal rna genes.	previous studies have shown that the guanine plus cytosine (g+c) content of ribosomal rnas (rrnas) is highly correlated with bacterial growth temperatures. this correlation is strongest in the double-stranded stem regions of the rrna, a fact that can be explained by selection for increased structural stability at high growth temperatures. in this study, we examined the single-stranded regions of 16s rrnas. we reasoned that, since these regions of the molecule are subject to less structural const ...	2002	12034839
transfer rna determinants for translational editing by escherichia coli valyl-trna synthetase.	valyl-trna synthetase (valrs) has difficulty differentiating valine from structurally similar non-cognate amino acids, most prominently threonine. to minimize errors in aminoacylation and translation the enzyme catalyzes a proofreading (editing) reaction that is dependent on the presence of cognate trna(val). editing occurs at a site functionally distinct from the aminoacylation site of valrs and previous results have shown that the 3'-terminus of trna(val) is recognized differently at the two s ...	2002	12034843
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
a membrane-bound archaeal lon protease displays atp-independent proteolytic activity towards unfolded proteins and atp-dependent activity for folded proteins.	in contrast to the eucaryal 26s proteasome and the bacterial atp-dependent proteases, little is known about the energy-dependent proteolysis in members of the third domain, archae. we cloned a gene homologous to atp-dependent lon protease from a hyperthermophilic archaeon and observed the unique properties of the archaeal lon. lon from thermococcus kodakaraensis kod1 (lon(tk)) is a 70-kda protein with an n-terminal atpase domain belonging to the aaa(+) superfamily and a c-terminal protease domai ...	2002	12057965
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
crystal structure of the lactococcus lactis formamidopyrimidine-dna glycosylase bound to an abasic site analogue-containing dna.	the formamidopyrimidine-dna glycosylase (fpg, mutm) is a bifunctional base excision repair enzyme (dna glycosylase/ap lyase) that removes a wide range of oxidized purines, such as 8-oxoguanine and imidazole ring-opened purines, from oxidatively damaged dna. the structure of a non-covalent complex between the lactoccocus lactis fpg and a 1,3-propanediol (pr) abasic site analogue-containing dna has been solved. through an asymmetric interaction along the damaged strand and the intercalation of the ...	2002	12065399
a novel uracil-dna glycosylase with broad substrate specificity and an unusual active site.	uracil-dna glycosylases (udgs) catalyse the removal of uracil by flipping it out of the double helix into their binding pockets, where the glycosidic bond is hydrolysed by a water molecule activated by a polar amino acid. interestingly, the four known udg families differ in their active site make-up. the activating residues in ung and smug enzymes are aspartates, thermostable udgs resemble ung-type enzymes, but carry glutamate rather than aspartate residues in their active sites, and the less ac ...	2002	12065430
resistance to quinupristin-dalfopristin due to mutation of l22 ribosomal protein in staphylococcus aureus.	the mechanism of resistance to the streptogramin antibiotics quinupristin and dalfopristin was studied in a staphylococcus aureus clinical isolate selected under quinupristin-dalfopristin therapy, in four derivatives of s. aureus rn4220 selected in vitro, and in a mutant selected in a model of rabbit aortic endocarditis. for all strains the mics of erythromycin, quinupristin, and quinupristin-dalfopristin were higher than those for the parental strains but the mics of dalfopristin and lincomycin ...	2002	12069975
immunization of rhesus macaques with a dna prime/modified vaccinia virus ankara boost regimen induces broad simian immunodeficiency virus (siv)-specific t-cell responses and reduces initial viral replication but does not prevent disease progression following challenge with pathogenic sivmac239.	producing a prophylactic vaccine for human immunodeficiency virus (hiv) has proven to be a challenge. most biological isolates of hiv are difficult to neutralize, so that conventional subunit-based antibody-inducing vaccines are unlikely to be very effective. in the rhesus macaque model, some protection was afforded by dna/recombinant viral vector vaccines. however, these studies used as the challenge virus shiv-89.6p, which is neutralizable, making it difficult to determine whether the observed ...	2002	12072518
novel dna-binding proteins in the cyanobacterium anabaena sp. strain pcc 7120.	as an approach towards elucidation of the biochemical regulation of the progression of heterocyst differentiation in anabaena sp. strain pcc 7120, we have identified proteins that bind to a 150-bp sequence upstream from hepc, a gene that plays a role in the synthesis of heterocyst envelope polysaccharide. such proteins were purified in four steps from extracts of vegetative cells of anabaena sp. two of these proteins (abp1 and abp2) are encoded by neighboring genes in the anabaena sp. chromosome ...	2002	12081965
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
the identification of spermine binding sites in 16s rrna allows interpretation of the spermine effect on ribosomal 30s subunit functions.	a photoreactive analogue of spermine, n1-azidobenzamidino (aba)-spermine, was covalently attached after irradiation to escherichia coli 30s ribosomal subunits or naked 16s rrna. by means of rnase h digestion and primer extension, the cross-linking sites of aba-spermine in naked 16s rrna were characterised and compared with those identified in 30s subunits. the 5' domain, the internal and terminal loops of helix h24, as well as the upper part of helix h44 in naked 16s rrna, were found to be prefe ...	2002	12087167
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
molecular characterization of the s-layer gene, sbpa, of bacillus sphaericus ccm 2177 and production of a functional s-layer fusion protein with the ability to recrystallize in a defined orientation while presenting the fused allergen.	the nucleotide sequence encoding the crystalline bacterial cell surface (s-layer) protein sbpa of bacillus sphaericus ccm 2177 was determined by a pcr-based technique using four overlapping fragments. the entire sbpa sequence indicated one open reading frame of 3,804 bp encoding a protein of 1,268 amino acids with a theoretical molecular mass of 132,062 da and a calculated isoelectric point of 4.69. the n-terminal part of sbpa, which is involved in anchoring the s-layer subunits via a distinct t ...	2002	12089001
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
stress-inducible protein 1 is a cell surface ligand for cellular prion that triggers neuroprotection.	prions are composed of an isoform of a normal sialoglycoprotein called prp(c), whose physiological role has been under investigation, with focus on the screening for ligands. our group described a membrane 66 kda prp(c)-binding protein with the aid of antibodies against a peptide deduced by complementary hydropathy. using these antibodies in western blots from two-dimensional protein gels followed by sequencing the specific spot, we have now identified the molecule as stress-inducible protein 1 ...	2002	12093732
the unique tuf2 gene from the kirromycin producer streptomyces ramocissimus encodes a minor and kirromycin-sensitive elongation factor tu.	streptomyces ramocissimus, the producer of elongation factor tu (ef-tu)-targeted antibiotic kirromycin, contains three divergent tuf-like genes, with tuf1 encoding regular kirromycin-sensitive ef-tu1; the functions of tuf2 and tuf3 are unknown. analysis of the tuf gene organization in nine producers of kirromycin-type antibiotics revealed that they all contain homologues of tuf1 and sometimes of tuf3 but that tuf2 was found in s. ramocissimus only. the tuf2-flanking regions were sequenced, and t ...	2002	12107139
genomic and functional analyses of sxt, an integrating antibiotic resistance gene transfer element derived from vibrio cholerae.	sxt is representative of a family of conjugative-transposon-like mobile genetic elements that encode multiple antibiotic resistance genes. in recent years, sxt-related conjugative, self-transmissible integrating elements have become widespread in asian vibrio cholerae. we have determined the 100-kb dna sequence of sxt. this element appears to be a chimera composed of transposon-associated antibiotic resistance genes linked to a variety of plasmid- and phage-related genes, as well as to many gene ...	2002	12107144
mutant analysis shows that alanine racemases from pseudomonas aeruginosa and escherichia coli are dimeric.	alanine racemases are ubiquitous prokaryotic enzymes providing the essential peptidoglycan precursor d-alanine. we present evidence that the enzymes from pseudomonas aeruginosa and escherichia coli function exclusively as homodimers. moreover, we demonstrate that expression of a k35a y235a double mutation of dadx in e. coli suppresses bacterial growth in a dominant negative fashion.	2002	12107154
class i tyrosyl-trna synthetase has a class ii mode of cognate trna recognition.	bacterial tyrosyl-trna synthetases (tyrrs) possess a flexibly linked c-terminal domain of approximately 80 residues, which has hitherto been disordered in crystal structures of the enzyme. we have determined the structure of thermus thermophilus tyrrs at 2.0 a resolution in a crystal form in which the c-terminal domain is ordered, and confirm that the fold is similar to part of the c-terminal domain of ribosomal protein s4. we have also determined the structure at 2.9 a resolution of the complex ...	2002	12110594
pcr-based ordered genomic libraries: a new approach to drug target identification for streptococcus pneumoniae.	described here are the development and validation of a novel approach to identify genes encoding drug targets in streptococcus pneumoniae. the method relies on the use of an ordered genomic library composed of pcr amplicons that were generated under error-prone conditions so as to introduce random mutations into the dna. since some of the mutations occur in drug target-encoding genes and subsequently affect the binding of the drug to its respective cellular target, amplicons containing drug targ ...	2002	12121925
regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.	the riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. a model for regulation based on formation of alternative rna structures involving the rfn elements is suggested. in gram-positive bacteria including actinomycetes, thermotoga, thermus and deinococcus, the riboflavin metabolism and transport genes are predicted to be regulated by transcriptional attenuation, whereas in most gram-negative bacteria, the riboflavin biosynthesis ...	2002	12136096
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
functional annotation of class i lysyl-trna synthetase phylogeny indicates a limited role for gene transfer.	functional and comparative genomic studies have previously shown that the essential protein lysyl-trna synthetase (lysrs) exists in two unrelated forms. most prokaryotes and all eukaryotes contain a class ii lysrs, whereas most archaea and a few bacteria contain a less common class i lysrs. in bacteria the class i lysrs is only found in the alpha-proteobacteria and a scattering of other groups, including the spirochetes, while the class i protein is by far the most common form of lysrs in archae ...	2002	12142429
biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil.	isolated soil dna from an oak-hornbeam forest close to cologne, germany, was suitable for pcr amplification of gene segments coding for the 16s rrna and nitrogenase reductase (nifh), nitrous oxide reductase (nosz), cytochrome cd(1)-containing nitrite reductase (nirs), and cu-containing nitrite reductase (nirk) of denitrification. for each gene segment, diverse pcr products were characterized by cloning and sequencing. none of the 16s rrna gene sequences was identical to any deposited in the data ...	2002	12147477
experimental evaluation of topological parameters determining protein-folding rates.	recent work suggests that structural topology plays a key role in determining protein-folding rates and pathways. the refolding rates of small proteins that fold without intermediates are found to correlate with simple structural parameters such as relative contact order, long-range order, or the fraction of short-range contacts. to test and evaluate the role of structural topology experimentally, a set of circular permutants of the ribosomal protein s6 from thermus thermophilus was analyzed. de ...	2002	12149462
the methanobacterium thermoautotrophicum mcm protein can form heptameric rings.	mini-chromosome maintenance (mcm) proteins form a conserved family found in all eukaryotes and are essential for dna replication. they exist as heteromultimeric complexes containing as many as six different proteins. these complexes are believed to be the replicative helicases, functioning as hexameric rings at replication forks. in most archaea a single mcm protein exists. the protein from methanobacterium thermoautotrophicum (mtmcm) has been reported to assemble into a large complex consistent ...	2002	12151340
human small intestinal mucosa harbours a small population of cytolytically active cd8+ alphabeta t lymphocytes.	intraepithelial lymphocytes (iel) in normal human small intestine exhibit cytotoxicity. this study was undertaken to characterize the effector cells and their mode of action. freshly isolated jejunal iel and lamina propria lymphocytes (lpl), as well as iel and lpl depleted of cd4+, cd8+ and t-cell receptor (tcr)-gammadelta+ cells were used as effector cells in anti-cd3-mediated redirected cytotoxicity against a murine fcgammar-expressing cell line. effector cell frequencies were estimated by eff ...	2002	12153510
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
16s rrna mutation-mediated tetracycline resistance in helicobacter pylori.	most helicobacter pylori strains are susceptible to tetracycline, an antibiotic commonly used for the eradication of h. pylori. however, an increase in incidence of tetracycline resistance in h. pylori has recently been reported. here the mechanism of tetracycline resistance of the first dutch tetracycline-resistant (tet(r)) h. pylori isolate (strain 181) is investigated. twelve genes were selected from the genome sequences of h. pylori strains 26695 and j99 as potential candidate genes, based o ...	2002	12183259
structural insights into peptide bond formation.	the large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-rna fragments of trna. we have refined at 3-a resolution the structures of both a and p site substrate and product analogues, as well as an intermediate analogue, bound to the haloarcula marismortui 50s ribosomal subunit. a p site substrate, cca-phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the p site. the cca portions of thes ...	2002	12185246
crystal structures of transcription factor nusg in light of its nucleic acid- and protein-binding activities.	microbial transcription modulator nusg interacts with rna polymerase and termination factor rho, displaying striking functional homology to eukaryotic spt5. the protein is also a translational regulator. we have determined crystal structures of aquifex aeolicus nusg showing a modular design: an n-terminal rnp-like domain, a c-terminal element with a kow sequence motif and a species-specific immunoglobulin-like fold. the structures reveal bona fide nucleic acid binding sites, and nucleic acid bin ...	2002	12198166
albidovulum inexpectatum gen. nov., sp. nov., a nonphotosynthetic and slightly thermophilic bacterium from a marine hot spring that is very closely related to members of the photosynthetic genus rhodovulum.	several bacterial isolates, with an optimum growth temperature of about 50 degrees c, were recovered from the marine hot spring at ferraria on the island of são miguel in the azores. the geothermal water emerged from a porous lava flow and rapidly cooled in contact with seawater except at low tide. the bacterial species represented by strains frr-10(t) and frr-11 was nonpigmented, strictly aerobic, and organotrophic. several genes, bchz, pufb, pufa, pufl, or pufm, encoding the photosynthetic rea ...	2002	12200275
novel domains and orthologues of eukaryotic transcription elongation factors.	the passage of rna polymerase ii across eukaryotic genes is impeded by the nucleosome, an octamer of histones h2a, h2b, h3 and h4 dimers. more than a dozen factors in the yeast saccharomyces cerevisiae are known to facilitate transcription elongation through chromatin. in order to better understand the evolution and function of these factors, their sequences have been compared with known protein, est and dna sequences. elongator subcomplex components elp4p and elp6p are shown to be homologues of ...	2002	12202748
site-directed mutagenesis of conserved charged amino acid residues in clpb from escherichia coli.	clpb is a member of a multichaperone system in escherichia coli (with dnak, dnaj, and grpe) that reactivates strongly aggregated proteins. the sequence of clpb contains two atp-binding domains, each containing walker consensus motifs. the n- and c-terminal sequence regions of clpb do not contain known functional motifs. in this study, we performed site-directed mutagenesis of selected charged residues within the walker a motifs (lys212 and lys611) and the c-terminal region of clpb (asp797, arg81 ...	2002	12220194
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
identification of a streptolysin s-associated gene cluster and its role in the pathogenesis of streptococcus iniae disease.	streptococcus iniae causes meningoencephalitis and death in cultured fish species and soft-tissue infection in humans. we recently reported that s. iniae is responsible for local tissue necrosis and bacteremia in a murine subcutaneous infection model. the ability to cause bacteremia in this model is associated with a genetic profile unique to strains responsible for disease in fish and humans (j. d. fuller, d. j. bast, v. nizet, d. e. low, and j. c. s. de azavedo, infect. immun. 69:1994-2000, 20 ...	2002	12228303
coordinated methyl and rna binding is required for heterochromatin localization of mammalian hp1alpha.	in mammalian cells, as in schizosaccharomyces pombe and drosophila, hp1 proteins bind histone h3 tails methylated on lysine 9 (k9). however, whereas k9-methylated h3 histones are distributed throughout the nucleus, hp1 proteins are enriched in pericentromeric heterochromatin. this observation suggests that the methyl-binding property of hp1 may not be sufficient for its heterochromatin targeting. we show that the association of hp1alpha with pericentromeric heterochromatin depends not only on it ...	2002	12231507
correlations between shine-dalgarno sequences and gene features such as predicted expression levels and operon structures.	this work assesses relationships for 30 complete prokaryotic genomes between the presence of the shine-dalgarno (sd) sequence and other gene features, including expression levels, type of start codon, and distance between successive genes. a significant positive correlation of the presence of an sd sequence and the predicted expression level of a gene based on codon usage biases was ascertained, such that predicted highly expressed genes are more likely to possess a strong sd sequence than avera ...	2002	12270832
functional expression of enterobacterial o-polysaccharide biosynthesis enzymes in bacillus subtilis.	the expression of heterologous bacterial glycosyltransferases is of interest for potential application in the emerging field of carbohydrate engineering in gram-positive organisms. to assess the feasibility of using enzymes from gram-negative bacteria, the functional expression of the genes wbap (formerly rfbp), weca (formerly rfe), and wbbo (formerly rfbf) from enterobacterial lipopolysaccharide o-polysaccharide biosynthesis pathways was examined in bacillus subtilis. wbap and weca are initiati ...	2002	12324313
having it both ways: transcription factors that bind dna and rna.	multifunctional proteins challenge the conventional 'one protein-one function' paradigm. here we note apparent multifunctional proteins with nucleic acid partners, tabulating eight examples. we then focus on eight additional cases of transcription factors that bind double-stranded dna with sequence specificity, but that also appear to lead alternative lives as rna-binding proteins. exemplified by the prototypic xenopus tfiiia protein, and more recently by mammalian p53, this list of transcriptio ...	2002	12364590
conservation of the biotin regulon and the bira regulatory signal in eubacteria and archaea.	biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. the strict control of biotin biosynthesis in escherichia coli is mediated by the bifunctional bira protein, which acts both as a biotin-protein ligase and as a transcriptional repressor of the biotin operon. little is known about regulation of biotin biosynthesis in other bacteria. using comparative genomics and phylogenetic analysis, we describe the biotin biosynthetic pathway and the bira r ...	2002	12368242
interaction of avilamycin with ribosomes and resistance caused by mutations in 23s rrna.	the antibiotic growth promoter avilamycin inhibits protein synthesis by binding to bacterial ribosomes. here the binding site is further characterized on escherichia coli ribosomes. the drug interacts with domain v of 23s rrna, giving a chemical footprint at nucleotides a2482 and a2534. selection of avilamycin-resistant halobacterium halobium cells revealed mutations in helix 89 of 23s rrna. furthermore, mutations in helices 89 and 91, which have previously been shown to confer resistance to eve ...	2002	12384333
highly conserved modified nucleosides influence mg2+-dependent trna folding.	transfer rna structure involves complex folding interactions of the tpsic domain with the d domain. however, the role of the highly conserved nucleoside modifications in the tpsic domain, rt54, psi55 and m5c49, in tertiary folding is not understood. to determine whether these modified nucleosides have a role in trna folding, the association of variously modified yeast trna(phe) t-half molecules (nucleosides 40-72) with the corresponding unmodified d-half molecule (nucleosides 1-30) was detected ...	2002	12409466
proteomic characterization of the small subunit of chlamydomonas reinhardtii chloroplast ribosome: identification of a novel s1 domain-containing protein and unusually large orthologs of bacterial s2, s3, and s5.	to understand how chloroplast mrnas are translated into functional proteins, a detailed understanding of all of the components of chloroplast translation is needed. to this end, we performed a proteomic analysis of the plastid ribosomal proteins in the small subunit of the chloroplast ribosome from the green alga chlamydomonas reinhardtii. twenty proteins were identified, including orthologs of escherichia coli s1, s2, s3, s4, s5, s6, s7, s9, s10, s12, s13, s14, s15, s16, s17, s18, s19, s20, and ...	2002	12417713
crystal structure of a human aminoacyl-trna synthetase cytokine.	the 20 aminoacyl-trna synthetases catalyze the first step of protein synthesis and establish the rules of the genetic code through aminoacylation reactions. biological fragments of two human enzymes, tyrosyl-trna synthetase (tyrrs) and tryptophanyl-trna synthetase, connect protein synthesis to cell-signaling pathways including angiogenesis. alternative splicing or proteolysis produces these fragments. the proangiogenic n-terminal fragment mini-tyrrs has il-8-like cytokine activity that, like oth ...	2002	12427973
emergence of tetracycline resistance in helicobacter pylori: multiple mutational changes in 16s ribosomal dna and other genetic loci.	tetracycline is useful in combination therapies against the gastric pathogen helicobacter pylori. we found 6 tetracycline-resistant (tet(r)) strains among 159 clinical isolates (from el salvador, lithuania, and india) and obtained the following four results: (i) 5 of 6 tet(r) isolates contained one or two nucleotide substitutions in one part of the primary tetracycline binding site in 16s rrna (aga(965-967) [escherichia coli coordinates] changed to gga, agc, gua, or ggc [lowercase letters are us ...	2002	12435699
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
identification and characterization of novel surface proteins in lactobacillus johnsonii and lactobacillus gasseri.	we have identified and sequenced the genes encoding the aggregation-promoting factor (apf) protein from six different strains of lactobacillus johnsonii and lactobacillus gasseri. both species harbor two apf genes, apf1 and apf2, which are in the same orientation and encode proteins of 257 to 326 amino acids. multiple alignments of the deduced amino acid sequences of these apf genes demonstrate a very strong sequence conservation of all of the genes with the exception of their central regions. n ...	2002	12450842
discontinuous and non-discontinuous subgenomic rna transcription in a nidovirus.	arteri-, corona-, toro- and roniviruses are evolutionarily related positive-strand rna viruses, united in the order nidovirales. the best studied nidoviruses, the corona- and arteriviruses, employ a unique transcription mechanism, which involves discontinuous rna synthesis, a process resembling similarity-assisted copy-choice rna recombination. during infection, multiple subgenomic (sg) mrnas are transcribed from a mirror set of sg negative-strand rna templates. the sg mrnas all possess a short ...	2002	12456663
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
elucidation of structure-function relationships in the protein subunit of bacterial rnase p using a genetic complementation approach.	rnase p is a ribonucleoprotein involved in trna biosynthesis in all living organisms. bacterial rnase p is comprised of a catalytic rna subunit and a lone protein cofactor which plays a supporting, albeit essential, role in the trna processing reaction in vivo. in this study, we have searched various databases to identify homologs of the protein subunit of rnase p from diverse bacteria and used an alignment of their primary sequences to determine the most highly conserved residues, and thereby e ...	2002	12466529
an inserted region of leucyl-trna synthetase plays a critical role in group i intron splicing.	yeast mitochondrial leucyl-trna synthetase (leurs) binds to the bi4 intron and collaborates with the bi4 maturase to aid excision of the group i intron. deletion analysis isolated the inserted leurs cp1 domain as a critical factor in the protein's splicing activity. protein fragments comprised of just the leurs cp1 region rescued complementation of a yeast strain that expressed a splicing-defective leurs. three-hybrid analysis determined that these cp1-containing leurs fragments, ranging from 21 ...	2002	12486008
deep trefoil knot implicated in rna binding found in an archaebacterial protein.		2003	12486711
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
in vivo selection of spectinomycin-binding rnas.	the folding of even short rna molecules in a random library can produce a huge number of possible macromolecular structures. using this principle, we have designed selections to seek non-coding rna transcripts capable of interfering with specific macromolecules such as transcription factors in living bacterial cells. here we show that such selections can uncover an unexpected class of rnas. in the present case, we report short rna transcripts whose expression confers bacterial resistance to the ...	2002	12490711
characterization of the interaction between the nucleotide exchange factor ef-ts from nematode mitochondria and elongation factor tu.	caenorhabditis elegans mitochondria have two elongation factor (ef)-tu species, denoted ef-tu1 and ef-tu2. recombinant nematode ef-ts purified from escherichia coli bound both of these molecules and also stimulated the translational activity of ef-tu, indicating that the nematode ef-ts homolog is a functional ef-ts protein of mitochondria. complexes formed by the interaction of nematode ef-ts with ef-tu1 and ef-tu2 could be detected by native gel electrophoresis and purified by gel filtration. a ...	2002	12490713
structure of the topoisomerase vi-b subunit: implications for type ii topoisomerase mechanism and evolution.	type iia and type iib topoisomerases each possess the ability to pass one dna duplex through another in an atp-dependent manner. the role of atp in the strand passage reaction is poorly understood, particularly for the type iib (topoisomerase vi) family. we have solved the structure of the atp-binding subunit of topoisomerase vi (topovi-b) in two states: an unliganded monomer and a nucleotide-bound dimer. we find that topovi-b is highly structurally homologous to the entire 40-43 kda atpase regi ...	2003	12505993
role of ctc from listeria monocytogenes in osmotolerance.	listeria monocytogenes is a food-borne pathogen with the ability to grow under conditions of high osmolarity. in a previous study, we reported the identification of 12 proteins showing high induction after salt stress. one of these proteins is highly similar to the general stress protein ctc of bacillus subtilis. in this study, induction of ctc after salt stress was confirmed at the transcriptional level by using rna slot blot experiments. to explore the role of the ctc gene product in resistanc ...	2003	12513990
detailed analysis of rna-protein interactions within the bacterial ribosomal protein l5/5s rrna complex.	the crystal structure of ribosomal protein l5 from thermus thermophilus complexed with a 34-nt fragment comprising helix iii and loop c of escherichia coli 5s rrna has been determined at 2.5 a resolution. the protein specifically interacts with the bulged nucleotides at the top of loop c of 5s rrna. the rrna and protein contact surfaces are strongly stabilized by intramolecular interactions. charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two ...	2002	12515387
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
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
uptake and antifungal activity of oligonucleotides in candida albicans.	candida albicans is a significant cause of disease in immunocompromised humans. because the number of people infected by fungal pathogens is increasing, strategies are being developed to target rnas in fungi. this work shows that oligonucleotides can serve as therapeutics against c. albicans. in particular, oligonucleotides are taken up from cell culture medium in an energy-dependent process. after uptake, oligonucleotides, including rna, remain mostly intact after 12 h in culture. for culture c ...	2003	12552085
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
atp binding by glutamyl-trna synthetase is switched to the productive mode by trna binding.	aminoacyl-trna synthetases catalyze the formation of an aminoacyl-amp from an amino acid and atp, prior to the aminoacyl transfer to trna. a subset of aminoacyl-trna synthetases, including glutamyl-trna synthetase (glurs), have a regulation mechanism to avoid aminoacyl-amp formation in the absence of trna. in this study, we determined the crystal structure of the 'non-productive' complex of thermus thermophilus glurs, atp and l-glutamate, together with those of the glurs.atp, glurs.trna.atp and ...	2003	12554668
the crystal structure of a 26-nucleotide rna containing a hook-turn.	a crystal structure has been obtained for a 26-nucleotide rna that contains the loop e sequence from chromatium minutissimum. rather than having a loop e-like conformation, it consists of an a-form helix that splits into two separate strands following a sheared a-g base pair. the backbone of the strand containing the g of the a-g pair makes a turn of almost 180 degrees in the space of two nucleotides, and then interacts with the minor groove of the helix from which it originates. similar structu ...	2003	12554875
mechanism of molecular interactions for trna(val) recognition by valyl-trna synthetase.	the molecular interactions between valyl-trna synthetase (valrs) and trna(val), with the c34-a35-c36 anticodon, from thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. in the valrs-bound structure of trna(val), the successive a35-c36 residues (the major identity elements) of trna(val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of valrs. hydrogen bonds are formed between valrs and a35-c36 of trna(val) in a ...	2003	12554880
the deoxyxylulose phosphate pathway of isoprenoid biosynthesis: studies on the mechanisms of the reactions catalyzed by ispg and isph protein.	earlier in vivo studies have shown that the sequential action of the ispg and isph proteins is essential for the reductive transformation of 2c-methyl-d-erythritol 2,4-cyclodiphosphate into dimethylallyl diphosphate and isopentenyl diphosphate via 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate. a recombinant fusion protein comprising maltose binding protein and ispg protein domains was purified from a recombinant escherichia coli strain. the purified protein failed to transform 2c-methyl-d-eryth ...	2003	12571359
the structural basis of cysteine aminoacylation of trnapro by prolyl-trna synthetases.	cysteinyl-trna synthetase is an essential enzyme required for protein synthesis. genes encoding this protein have not been identified in methanocaldococcus jannaschii, methanothermobacter thermautotrophicus, or methanopyrus kandleri. it has previously been proposed that the prolyl-trna synthetase (prors) enzymes in these organisms recognize either proline or cysteine and can aminoacylate their cognate trnas through a dual-specificity mechanism. we report five crystal structures at resolutions be ...	2003	12578991
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
evidence for rotation of v1-atpase.	v(o)v(1)-atpase is responsible for acidification of eukaryotic intracellular compartments and atp synthesis of archaea and some eubacteria. from the similarity to f(o)f(1)-atp synthase, v(o)v(1)-atpase has been assumed to be a rotary motor, but to date there are no experimental data to support this. here we visualized the rotation of single molecules of v(1)-atpase, a catalytic subcomplex of v(o)v(1)-atpase. v(1)-atpase from thermus thermophilus was immobilized onto a glass surface, and a bead w ...	2003	12598655
orientation and interactions of an essential tryptophan (trp-38) in the capsid subunit of pf3 filamentous virus.	the filamentous bacteriophage pf3 consists of a covalently closed dna single strand of 5833 nucleotides sheathed by approximately 2500 copies of a 44-residue capsid subunit. the capsid subunit contains a single tryptophan residue (trp-38), which is located within the basic c-terminal sequence (-rwikaqff) and is essential for virion assembly in vivo. polarized raman microspectroscopy has been employed to determine the orientation of the trp-38 side chain in the native virus structure. the polariz ...	2003	12609899
genetic diversity: frameshift mechanisms alter coding of a gene (epstein-barr virus lf3 gene) that contains multiple 102-base-pair direct sequence repeats.	frameshift mutations provide recognized mechanisms for changing the coding potential of an organism. here, multiple frameshifts are identified in repetitive sequences within an epstein-barr virus unspliced early gene, lf3, which is associated with the viral replicative cycle and also transcriptionally expressed in many virally associated tumors. on the dna strand encoding lf3, there are three open reading frames, only one of which contains an initiation codon. most (>95%) of the gene consists of ...	2003	12612089
the feci extracytoplasmic-function sigma factor of escherichia coli interacts with the beta' subunit of rna polymerase.	transcription of the ferric citrate transport system of escherichia coli k-12 is mediated by the extracytoplasmic-function (ecf) sigma factor feci, which is activated by ferric citrate in the growth medium. by using a bacterial two-hybrid system, it was shown in vivo that feci binds to the beta' subunit of rna polymerase. the inactive mutant protein feci(k155e) displayed reduced binding to beta', and small deletions along the entire feci protein led to total impairment of beta' binding. in vitro ...	2003	12618442
the rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.	the rhomboid family of polytopic membrane proteins shows a level of evolutionary conservation unique among membrane proteins. they are present in nearly all the sequenced genomes of archaea, bacteria and eukaryotes, with the exception of several species with small genomes. on the basis of experimental studies with the developmental regulator rhomboid from drosophila and the aara protein from the bacterium providencia stuartii, the rhomboids are thought to be intramembrane serine proteases whose ...	2003	12620104
in situ accessibility of small-subunit rrna of members of the domains bacteria, archaea, and eucarya to cy3-labeled oligonucleotide probes.	low accessibility of the rrna is together with cell wall impermeability and low cellular ribosome content a frequent reason for failure of whole-cell fluorescence hybridization with fluorescently labeled oligonucleotide probes. in this study we compare accessibility data for the 16s rrna of escherichia coli (gamma proteobacteria, bacteria) with the phylogenetically distantly related organisms pirellula sp. strain 1 (planctomycetes, bacteria) and metallosphaera sedula (crenarchaeota, archaea) and ...	2003	12620867
characterization of a novel thermostable o-acetylserine sulfhydrylase from aeropyrum pernix k1.	an o-acetylserine sulfhydrylase (oass) from the hyperthermophilic archaeon aeropyrum pernix k1, which shares the pyridoxal 5'-phosphate binding motif with both oass and cystathionine beta-synthase (cbs), was cloned and expressed by using escherichia coli rosetta(de3). the purified protein was a dimer and contained pyridoxal 5'-phosphate. it was shown to be an enzyme with cbs activity as well as oass activity in vitro. the enzyme retained 90% of its activity after a 6-h incubation at 100 degrees ...	2003	12644499
antagonistic signals within the cox2 mrna coding sequence control its translation in saccharomyces cerevisiae mitochondria.	translation of the mitochondrially coded cox2 mrna within the organelle in yeast produces the precursor of cox2p (pre-cox2p), which is processed and assembled into cytochrome c oxidase. the mrna sequence of the first 14 cox2 codons, specifying the pre-cox2p leader peptide, was previously shown to contain a positively acting element required for translation of a mitochondrial reporter gene, arg8(m), fused to the 91st codon of cox2. here we show that three relatively short sequences within the cox ...	2003	12649494
the yeast eif3 subunits tif32/a, nip1/c, and eif5 make critical connections with the 40s ribosome in vivo.	initiation factor 3 (eif3) forms a multifactor complex (mfc) with eif1, eif2, and eif5 that stimulates met-trna(i)(met) binding to 40s ribosomes and promotes scanning or aug recognition. we have previously characterized mfc subcomplexes produced in vivo from affinity-tagged eif3 subunits lacking discrete binding domains for other mfc components. here we asked whether these subcomplexes can bind to 40s ribosomes in vivo. we found that the n- and c-terminal domains of nip1/eif3c, the n- and c-term ...	2003	12651896
high-efficiency generation of antibiotic-resistant strains of streptococcus pneumoniae by pcr and transformation.	we designed a method by which to generate antibiotic-resistant strains of streptococcus pneumoniae at frequencies 4 orders of magnitude greater than the spontaneous mutation rate. the method is based on the natural ability of this organism to be genetically transformed with pcr products carrying sequences homologous to its chromosome. the genes encoding the targets of ciprofloxacin (parc, encoding the parc subunit of dna topoisomerase iv), rifampin (rpob, encoding the beta subunit of rna polymer ...	2003	12654655
non-discriminating and discriminating aspartyl-trna synthetases differ in the anticodon-binding domain.	in most organisms, trna aminoacylation is ensured by 20 aminoacyl-trna synthetases (aarss). in eubacteria, however, synthetases can be duplicated as in thermus thermophilus, which contains two distinct asprss. while asprs-1 is specific, asprs-2 is non-discriminating and aspartylates trna(asp) and trna(asn). the structure at 2.3 a resolution of asprs-2, the first of a non-discriminating synthetase, was solved. it differs from that of asprs-1 but has resemblance to that of discriminating and archa ...	2003	12660169
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
phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core.	the examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. we developed a method for aseptically sampling a sediment-containing portion of a greenland ice core that had remained at -9 degrees c for over 100,000 years. epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. anaerobic enrichment cultures inoculated w ...	2003	12676695
ribosomal protein s15 represses its own translation via adaptation of an rrna-like fold within its mrna.	the 16s rrna-binding ribosomal protein s15 is a key component in the assembly of the small ribosomal subunit in bacteria. we have shown that s15 from the extreme thermophile thermus thermophilus represses the translation of its own mrna in vitro, by interacting with the leader segment of its mrna. the s15 mrna-binding site was characterized by footprinting experiments, deletion analysis and site-directed mutagenesis. s15 binding triggers a conformational rearrangement of its mrna into a fold tha ...	2003	12682022
a novel uracil-dna glycosylase family related to the helix-hairpin-helix dna glycosylase superfamily.	cytosine bases can be deaminated spontaneously to uracil, causing dna damage. uracil-dna glycosylase (udg), a ubiquitous uracil-excising enzyme found in bacteria and eukaryotes, is one of the enzymes that repair this kind of dna damage. to date, no udg-coding gene has been identified in methanococcus jannaschii, although its entire genome was deciphered. here, we have identified and characterized a novel udg from m.jannaschii designated as mjudg. it efficiently removed uracil from both single- a ...	2003	12682355
cloning and characterization of trna (m1a58) methyltransferase (trmi) from thermus thermophilus hb27, a protein required for cell growth at extreme temperatures.	n1-methyladenosine (m1a) is found at position 58 in the t-loop of many trnas. in yeast, the formation of this modified nucleoside is catalyzed by the essential trna (m1a58) methyltransferase, a tetrameric enzyme that is composed of two types of subunits (gcd14p and gcd10p). in this report we describe the cloning, expression and characterization of a gcd14p homolog from the hyperthermophilic bacterium thermus thermophilus. the purified recombinant enzyme behaves as a homotetramer of 150 kda by ge ...	2003	12682365
glycyl trna synthetase mutations in charcot-marie-tooth disease type 2d and distal spinal muscular atrophy type v.	charcot-marie-tooth disease type 2d (cmt2d) and distal spinal muscular atrophy type v (dsma-v) are axonal peripheral neuropathies inherited in an autosomal dominant fashion. our previous genetic and physical mapping efforts localized the responsible gene(s) to a well-defined region on human chromosome 7p. here, we report the identification of four disease-associated missense mutations in the glycyl trna synthetase gene in families with cmt2d and dsma-v. this is the first example of an aminoacyl ...	2003	12690580
structure-function studies of escherichia coli rpoh (sigma32) by in vitro linker insertion mutagenesis.	the sigma factor rpoh (sigma(32)) is the key regulator of the heat shock response in escherichia coli. many structural and functional properties of the sigma factor are poorly understood. to gain further insight into rpoh regions that are either important or dispensable for its cellular activity, we generated a collection of tetrapeptide insertion variants by a recently established in vitro linker insertion mutagenesis technique. thirty-one distinct insertions were obtained, and their sigma fact ...	2003	12700252
involvement of the adc operon and manganese homeostasis in streptococcus gordonii biofilm formation.	pioneer oral bacteria, including streptococcus gordonii, initiate the formation of oral biofilms on tooth surfaces, which requires differential expression of genes that recognize unique environmental cues. an s. gordonii::tn917-lac biofilm-defective mutant was isolated by using an in vitro biofilm formation assay. subsequent inverse pcr and sequence analyses identified the transposon insertion to be near the 3' end of an open reading frame (orf) encoding a protein homologous to a streptococcus p ...	2003	12700268
role of 16s rrna helix 44 in ribosomal resistance to hygromycin b.	hygromycin b is an aminoglycoside antibiotic active against prokaryotic and eukaryotic ribosomes. ribosomal alterations in bacteria conferring resistance to hygromycin b have not been described, prompting us to use a single rrna allelic derivative of the gram-positive bacterium mycobacterium smegmatis for investigation of the molecular mechanisms involved in ribosomal resistance to hygromycin b in eubacteria. resistance mutations were found to localize exclusively in 16s rrna. the mutations obse ...	2003	12709313
the versatile thymine dna-glycosylase: a comparative characterization of the human, drosophila and fission yeast orthologs.	human thymine-dna glycosylase (tdg) is well known to excise thymine and uracil from g.t and g.u mismatches, respectively, and was therefore proposed to play a central role in the cellular defense against genetic mutation through spontaneous deamination of 5-methylcytosine and cytosine. in this study, we characterized two newly discovered orthologs of tdg, the drosophila melanogaster thd1p and the schizosaccharomyces pombe thp1p proteins, with an objective to address the function of this subfamil ...	2003	12711670
involvement of conserved asparagine and arginine residues from the n-terminal region in the catalytic mechanism of rat liver and trypanosoma cruzi tyrosine aminotransferases.	rat liver and trypanosoma cruzi tyrosine aminotransferases (tats) share over 40% sequence identity, but differ in their substrate specificities. to explore the molecular features related to these differences, comparative mutagenesis studies were conducted on full length t. cruzi tat and n-terminally truncated rat tat recombinant enzymes. the functionality of arg315 and arg417 in rat tat was investigated for comparison with the conserved arg292 and arg386 in aspartate and bacterial aromatic amino ...	2003	12717026
an unusual mechanism of bacterial gene expression revealed for the rnase p protein of thermus strains.	the rnase p protein gene (rnpa) completely overlaps the rpmh gene (encoding ribosomal protein l34) out of frame in the thermophilic bacterium thermus thermophilus. this results in the synthesis of an extended rnase p protein (c5) of 163 aa and, by inference, of 240 aa in the related strain thermus filiformis. start codons of rnpa and rpmh, apparently governed by the same ribosome binding site, are separated by only 4 nt, which suggests a regulatory linkage between l34 and c5 translation and, acc ...	2003	12719542
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
expanding trna recognition of a trna synthetase by a single amino acid change.	aspartyl-trna synthetase (asprs) occurs in two types: the discriminating enzyme (d-asprs) forms only asp-trna(asp), whereas the nondiscriminating enzyme (nd-asprs) also synthesizes asp-trna(asn), which is a required intermediate for protein synthesis in many organisms. we attempted to expand the trna recognition of the discriminating thermococcus kodakaraensis asprs to that of a nd-asprs by in vitro mutagenesis. an alignment of 26 archaeal asprs proteins revealed two positions (26 and 85 in the ...	2003	12730374
global expression profiling and physiological characterization of corynebacterium glutamicum grown in the presence of l-valine.	addition of l-valine (50 to 200 mm) to glucose minimal medium had no effect on the growth of wild-type corynebacterium glutamicum atcc 13032 but inhibited the growth of the derived valine production strain val1 [13032 deltailva deltapanbc(pjc1ilvbncd)] in a concentration-dependent manner. in order to explore this strain-specific valine effect, genomewide expression profiling was performed using dna microarrays, which showed that valine caused an increased ilvbn mrna level in val1 but not in the ...	2003	12732517
rna polymerase mutations that impair conversion to a termination-resistant complex by q antiterminator proteins.	bacteriophage lambda q-protein stably binds and modifies rna polymerase (rnap) to a termination-resistant form. we describe amino acid substitutions in rnap that disrupt q-mediated antitermination in vivo and in vitro. the positions of these substitutions in the modeled rnap/dna/rna ternary elongation complex, and their biochemical properties, suggest that they do not define a binding site for q in rnap, but instead act by impairing interactions among core rnap subunits and nucleic acids that ar ...	2003	12756229