| clue to damage recognition by uvrb: residues in the beta-hairpin structure prevent binding to non-damaged dna. | uvrb, the ultimate damage-recognizing component of bacterial nucleotide excision repair, contains a flexible beta-hairpin rich in hydrophobic residues. we describe the properties of uvrb mutants in which these residues have been mutated. the results show that y101 and f108 in the tip of the hairpin are important for the strand-separating activity of uvrb, supporting the model that the beta-hairpin inserts between the two dna strands during the search for dna damage. residues y95 and y96 at the b ... | 2001 | 11689453 |
| structural and mutational studies of the recognition of the arginine trna-specific major identity element, a20, by arginyl-trna synthetase. | arginyl-trna synthetase (argrs) recognizes two major identity elements of trna(arg): a20, located at the outside corner of the l-shaped trna, and c35, the second letter of the anticodon. only a few exceptional organisms, such as the yeast saccharomyces cerevisiae, lack a20 in trna(arg). in the present study, we solved the crystal structure of a typical a20-recognizing argrs from thermus thermophilus at 2.3 a resolution. the structure of the t. thermophilus argrs was found to be similar to that o ... | 2001 | 11698642 |
| brucella abortus genes identified following constitutive growth and macrophage infection. | the chronicity of brucella abortus infection in humans and animals depends on the organism's ability to escape host defenses by gaining entry and surviving inside the macrophage. although no human vaccine exists for brucella, vaccine development in other bacteria has been based on deletions of selective nutritional as well as regulatory systems. our goal is to develop a vaccine for brucella. to further this aim, we have used a green fluorescent protein (gfp) reporter system to identify constitut ... | 2001 | 11705955 |
| nog2p, a putative gtpase associated with pre-60s subunits and required for late 60s maturation steps. | eukaryotic ribosome maturation depends on a set of well ordered processing steps. here we describe the functional characterization of yeast nog2p (ynr053cp), a highly conserved nuclear protein. nog2p contains a putative gtp-binding site, which is essential in vivo. kinetic and steady-state measurements of the levels of pre-rrnas in nog2p-depleted cells showed a defect in 5.8s and 25s maturation and a concomitant increase in the levels of both 27sb(s) and 7s(s) precursors. we found nog2p physical ... | 2001 | 11707418 |
| crystal structure of thermostable dna photolyase: pyrimidine-dimer recognition mechanism. | dna photolyase is a pyrimidine-dimer repair enzyme that uses visible light. photolyase generally contains two chromophore cofactors. one is a catalytic cofactor directly contributing to the repair of a pyrimidine-dimer. the other is a light-harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor. photolyases are classified according to their second cofactor into either a folate- or deazaflavin-type. the native structures of both types of photolyases have a ... | 2001 | 11707580 |
| the hunt for living gold. the search for organisms in extreme environments yields useful enzymes for industry. | | 2001 | 11713183 |
| saturation mutagenesis of 5s rrna in saccharomyces cerevisiae. | rrnas are the central players in the reactions catalyzed by ribosomes, and the individual rrnas are actively involved in different ribosome functions. our previous demonstration that yeast 5s rrna mutants (called mof9) can impact translational reading frame maintenance showed an unexpected function for this ubiquitous biomolecule. at the time, however, the highly repetitive nature of the genes encoding rrnas precluded more detailed genetic and molecular analyses. a new genetic system allows all ... | 2001 | 11713264 |
| overexpression, purification and characterization of recj protein from thermus thermophilus hb8 and its core domain. | a recj homolog was cloned from the extremely thermophilic bacterium thermus themophilus hb8. it encodes a 527 amino acid protein that has 33% identity to escherichia coli recj protein and includes the characteristic motifs conserved among recj homologs. although t.thermophilus recj protein (ttrecj) was expressed as an inclusion body, it was purified in soluble form through denaturation with urea and subsequent refolding steps. limited proteolysis showed that ttrecj has a protease-resistant core ... | 2001 | 11713311 |
| importance of the conserved nucleotides around the trna-like structure of escherichia coli transfer-messenger rna for protein tagging. | a bacterial rna functioning as both trna and mrna, transfer-messenger rna (tmrna) rescues stalled ribosomes and clears the cell of incomplete polypeptides. for function, escherichia coli tmrna requires an elaborate interplay between a trna-like structure and an internal mrna domain that are connected by a 295 nt long compact secondary structure. the trna-like structure is surrounded by 16 unpaired nt, including 10 residues that are >95% conserved among the known 140 tmrna sequences. all these re ... | 2001 | 11713316 |
| behavior of dna fibers stretched by precise meniscus motion control. | a modified dna combing method, which can precisely locate straightened dna fibers on a substrate, has been developed. precise motion control of a dna solution droplet on hydrophobic surfaces has allowed detailed analyses of dna straightening behavior. our method provides a technique for consistently straightening lambda phage dna on a trace of droplet motion, though the straightened dnas had several variations in their alignments. the dependence of the straightened dna frequency upon motion rate ... | 2001 | 11713329 |
| structure and dynamics of translation initiation factor aif-1a from the archaeon methanococcus jannaschii determined by nmr spectroscopy. | translation initiation factor 1a (aif-1a) from the archaeon methanococcus jannaschii was expressed in escherichia coli, purified, and characterized in terms of its structure and dynamics using multidimensional nmr methods. the protein was found to be a member of the ob-fold family of rna-associated proteins, containing a barrel of five beta-strands, a feature that is shared with the homologous eukaryotic translation initiation factor 1a (eif-1a), as well as the prokaryotic translation initiation ... | 2001 | 11714910 |
| h(2)o(2)-forming nadh oxidase with diaphorase (cytochrome) activity from archaeoglobus fulgidus. | an enzyme exhibiting nadh oxidase (diaphorase) activity was isolated from the hyperthermophilic sulfate-reducing anaerobe archaeoglobus fulgidus. n-terminal sequence of the protein indicates that it is coded for by open reading frame af0395 in the a. fulgidus genome. the gene af0395 was cloned and its product was purified from escherichia coli. like the native nadh oxidase (noxa2), the recombinant noxa2 (rnoxa2) has an apparent molecular mass of 47 kda, requires flavin adenine dinucleotide for a ... | 2001 | 11717257 |
| novel posttranslational activation of the lys2-encoded alpha-aminoadipate reductase for biosynthesis of lysine and site-directed mutational analysis of conserved amino acid residues in the activation domain of candida albicans. | the alpha-aminoadipate pathway for lysine biosynthesis is present only in fungi. the alpha-aminoadipate reductase (aar) of this pathway catalyzes the conversion of alpha-aminoadipic acid to alpha-aminoadipic-delta-semialdehyde by a complex mechanism involving two gene products, lys2p and lys5p. the lys2 and lys5 genes encode, respectively, a 155-kda inactive aar and a 30-kda phosphopantetheinyl transferase (pptase) which transfers a phosphopantetheinyl group from coenzyme a (coa) to lys2p for th ... | 2001 | 11717270 |
| adp-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea. | phosphofructokinase (pfk) is a key enzyme of the glycolytic pathway in all domains of life. two related pfks, atp-dependent and pp(i)-dependent pfk, have been distinguished in bacteria and eucarya, as well as in some archaea. hyperthermophilic archaea of the order thermococcales, including pyrococcus and thermococcus spp., have recently been demonstrated to possess a unique adp-dependent pfk (adp-pfk) that appears to be phylogenetically distinct. here, we report the presence of adp-pfks in glyco ... | 2001 | 11717273 |
| different physiological roles of atp- and pp(i)-dependent phosphofructokinase isoenzymes in the methylotrophic actinomycete amycolatopsis methanolica. | cells of the actinomycete amycolatopsis methanolica grown on glucose possess only a single, exclusively pp(i)-dependent phosphofructokinase (pp(i)-pfk) (a. m. c. r. alves, g. j. w. euverink, h. j. hektor, j. van der vlag, w. vrijbloed, d.h.a. hondmann, j. visser, and l. dijkhuizen, j. bacteriol. 176:6827-6835, 1994). when this methylotrophic bacterium is grown on one-carbon (c(1)) compounds (e.g., methanol), an atp-dependent phosphofructokinase (atp-pfk) activity is specifically induced, complet ... | 2001 | 11717283 |
| complex i and its involvement in redox homeostasis and carbon and nitrogen metabolism in rhodobacter capsulatus. | a transposon mutant of rhodobacter capsulatus, strain mal7, that was incapable of photoautotrophic and chemoautotrophic growth and could not grow photoheterotrophically in the absence of an exogenous electron acceptor was isolated. the phenotype of strain mal7 suggested that the mutation was in some gene(s) not previously shown to be involved in co(2) fixation control. the site of transposition in strain mal7 was identified and shown to be in the gene nuof, which encodes one of the 14 subunits f ... | 2001 | 11717288 |
| cysteinyl-trna synthetase is not essential for viability of the archaeon methanococcus maripaludis. | the methanogenic archaea methanocaldococcus jannaschii and methanothermobacter thermautotrophicus contain a dual-specificity prolyl-trna synthetase (procysrs) that accurately forms both prolyl-trna (pro-trna) and cysteinyl-trna (cys-trna) suitable for in vivo translation. this intriguing enzyme may even perform its dual role in organisms that possess a canonical single-specificity cysteinyl-trna synthetase (cysrs), raising the question as to whether this latter aminoacyl-trna synthetase is indee ... | 2001 | 11717392 |
| recognizing the d-loop of transfer rnas. | | 2001 | 11717415 |
| degradation of xylan to d-xylose by recombinant saccharomyces cerevisiae coexpressing the aspergillus niger beta-xylosidase (xlnd) and the trichoderma reesei xylanase ii (xyn2) genes. | the beta-xylosidase-encoding xlnd gene of aspergillus niger 90196 was amplified by the pcr technique from first-strand cdna synthesized on mrna isolated from the fungus. the nucleotide sequence of the cdna fragment was verified to contain a 2,412-bp open reading frame that encodes a 804-amino-acid propeptide. the 778-amino-acid mature protein, with a putative molecular mass of 85.1 kda, was fused in frame with the saccharomyces cerevisiae mating factor alpha1 signal peptide (mfalpha1(s)) to ensu ... | 2001 | 11722900 |
| deletion of the gre3 aldose reductase gene and its influence on xylose metabolism in recombinant strains of saccharomyces cerevisiae expressing the xyla and xks1 genes. | saccharomyces cerevisiae ferments hexoses efficiently but is unable to ferment xylose. when the bacterial enzyme xylose isomerase (xi) from thermus thermophilus was produced in s. cerevisiae, xylose utilization and ethanol formation were demonstrated. in addition, xylitol and acetate were formed. an unspecific aldose reductase (ar) capable of reducing xylose to xylitol has been identified in s. cerevisiae. the gre3 gene, encoding the ar enzyme, was deleted in s. cerevisiae cen.pk2-1c, yielding y ... | 2001 | 11722921 |
| v-shaped structure of glutamyl-trna reductase, the first enzyme of trna-dependent tetrapyrrole biosynthesis. | processes vital to life such as respiration and photosynthesis critically depend on the availability of tetrapyrroles including hemes and chlorophylls. trna-dependent catalysis generally is associated with protein biosynthesis. an exception is the reduction of glutamyl-trna to glutamate-1-semialdehyde by the enzyme glutamyl-trna reductase. this reaction is the indispensable initiating step of tetrapyrrole biosynthesis in plants and most prokaryotes. the crystal structure of glutamyl-trna reducta ... | 2001 | 11726494 |
| diversity of ribosomal mutations conferring resistance to macrolides, clindamycin, streptogramin, and telithromycin in streptococcus pneumoniae. | mechanisms of resistance were studied in 22 macrolide-resistant mutants selected in vitro from 5 parental strains of macrolide-susceptible streptococcus pneumoniae by serial passage in various macrolides (t. a. davies, b. e. dewasse, m. r. jacobs, and p. c. appelbaum, antimicrob. agents chemother., 44:414-417, 2000). portions of genes encoding ribosomal proteins l22 and l4 and 23s rrna (domains ii and v) were amplified by pcr and analyzed by single-strand conformational polymorphism analysis to ... | 2002 | 11751122 |
| complete polar lipid composition of thermoplasma acidophilum ho-62 determined by high-performance liquid chromatography with evaporative light-scattering detection. | polar ether lipids of thermoplasma acidophilum ho-62 were purified by high-performance liquid chromatography with an evaporative light-scattering detector. structures of purified lipids were investigated by capillary gas chromatography, mass spectrometry, and nuclear magnetic resonance. three types of ether lipids were found: phospholipids, glycolipids, and phosphoglycolipids. the two phospholipids had glycerophosphate as the phosphoester moiety. the seven glycolipids had different combinations ... | 2002 | 11751835 |
| cloning, sequencing, and expression of the cold-inducible hutu gene from the antarctic psychrotrophic bacterium pseudomonas syringae. | a promoter-fusion study with a tn 5-based promoter probe vector had earlier found that the hutu gene which encodes the enzyme urocanase for the histidine utilization pathway is upregulated at a lower temperature (4 degrees c) in the antarctic psychrotrophic bacterium pseudomonas syringae. to examine the characteristics of the urocanase gene and its promoter elements from the psychrotroph, the complete hutu and its upstream region from p. syringae were cloned, sequenced, and analyzed in the prese ... | 2002 | 11772602 |
| simultaneous detection of measles virus, rubella virus, and parvovirus b19 by using multiplex pcr. | we describe here a multiplex reverse transcription-pcr (rtmnpcr) assay designed to detect and differentiate measles virus, rubella virus, and parvovirus b19. serial dilution experiments with vaccine strains that compared cell culture isolation of measles in b95 cells and rubella in rk13 cells showed sensitivity rates of 0.004 50% tissue culture infective dose (tcid(50)) for measles virus and 0.04 tcid(50) for rubella virus. this rtmnpcr can detect as few as 10 molecules for measles virus and rub ... | 2002 | 11773102 |
| cooperative kinetics of both hsp104 atpase domains and interdomain communication revealed by aaa sensor-1 mutants. | aaa proteins share a conserved active site for atp hydrolysis and regulate many cellular processes. aaa proteins are oligomeric and often have multiple atpase domains per monomer, which is suggestive of complex allosteric kinetics of atp hydrolysis. here, using wild-type hsp104 in the hexameric state, we demonstrate that its two aaa modules (nbd1 and nbd2) have very different catalytic activities, but each displays cooperative kinetics of hydrolysis. using mutations in the aaa sensor-1 motif of ... | 2002 | 11782421 |
| blocking site-to-site translocation of a misactivated amino acid by mutation of a class i trna synthetase. | the genetic code is established by the aminoacylation reactions of trna synthetases. its accuracy depends on editing reactions that prevent amino acids from being assigned to incorrect codons. a group of class i synthetases share a common insertion that encodes a distinct site for editing that is about 30 a from the active site. both misactivated aminoacyl adenylates and mischarged amino acids attached to trna are translocated to this site, which, in turn, is divided into subsites--one for the a ... | 2002 | 11782529 |
| contributions of folding cores to the thermostabilities of two ribonucleases h. | to investigate the contribution of the folding cores to the thermodynamic stability of rnases h, we used rational design to create two chimeras composed of parts of a thermophilic and a mesophilic rnase h. each chimera combines the folding core from one parent protein and the remaining parts of the other. both chimeras form active, well-folded rnases h. stability curves, based on cd-monitored chemical denaturations, show that the chimera with the thermophilic core is more stable, has a higher mi ... | 2002 | 11790848 |
| cell-surface-anchoring role of n-terminal surface layer homology domains of clostridium cellulovorans enge. | enge, coding for endoglucanase e, one of the three major subunits of the clostridium cellulovorans cellulosome, has been cloned and sequenced (y. tamaru and r. h. doi, j. bacteriol. 181:3270-3276, 1999). the n-terminal-half region of enge possesses three repeated surface layer homology (slh) domains, which are homologous to those of some bacterial s-layer proteins. also, the c-terminal-half region consists of a catalytic domain of glycosyl hydrolase family 5 and a duplicated sequence (dockerin) ... | 2002 | 11807046 |
| tetracycline induces stabilization of mrna in bacillus subtilis. | the tet(l) gene of bacillus subtilis confers low-level tetracycline (tc) resistance. previous work examining the >20-fold-inducible expression of tet(l) by tc demonstrated a 12-fold translational induction. here we show that the other component of tet(l) induction is at the level of mrna stabilization. addition of a subinhibitory concentration of tc results in a two- to threefold increase in tet(l) mrna stability. using a plasmid-borne derivative of tet(l) with a large in-frame deletion of the c ... | 2002 | 11807047 |
| mode of dna-protein interaction between the c-terminal domain of escherichia coli rna polymerase alpha subunit and t7d promoter up element. | the c-terminal domain (ctd) downstream from residue 235 of escherichia coli rna polymerase alpha subunit is involved in recognition of the promoter up element. here we have demonstrated, by dnase i and hydroxyl radical mapping, the presence of two up element subsites on the promoter d of phage t7, each located half and one-and-a-half helix turns, respectively, upstream from the promoter -35 element. this non-typical up element retained its alphactd-binding capability when transferred into the ge ... | 2001 | 11812819 |
| a protonated base pair participating in rrna tertiary structural interactions. | in the recently published x-ray crystallographic structure for the 50s subunit of haloarcula marismortui ribosomes, residue u2546 of the 23s rrna forms a non-watson-crick base pair with u2610. the corresponding residues in the secondary structure of the escherichia coli 23s molecule are u2511 and c2575, and it follows that the latter base (c2575) should be protonated in order to form a base pair that is isostructural with its counterpart in h.marismortui. this prediction was demonstrated experim ... | 2001 | 11812838 |
| nmr structure of a ribosomal rna hairpin containing a conserved cucaa pentaloop. | the structure of a 23 nt rna sequence, rggacccgggcucaaccugggucc, was elucidated using homonuclear nmr, distance geometry and restrained molecular dynamics. this rna is analogous to residues 612-628 of the escherichia coli 16s rrna. the structure of the rna reveals the presence of a pentaloop closed by a duplex stem in typical a-form conformation. the loop does not form a u-turn motif, as previously predicted. a non-planar a.c.a triple base interaction (hydrogen bonds a13 nh6-c10 o2 and c10 n3-a1 ... | 2001 | 11812846 |
| molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium thermus thermophilus strain hb27. | thermus thermophilus hb27, an extremely thermophilic bacterium, exhibits high competence for natural transformation. to identify genes of the natural transformation machinery of t. thermophilus hb27, we performed homology searches in the partially completed t. thermophilus genomic sequence for conserved competence genes. these analyses resulted in the detection of 28 open reading frames (orfs) exhibiting significant similarities to known competence proteins of gram-negative and gram-positive bac ... | 2002 | 11823215 |
| corynebacterium glutamicum utilizes both transsulfuration and direct sulfhydrylation pathways for methionine biosynthesis. | a direct sulfhydrylation pathway for methionine biosynthesis in corynebacterium glutamicum was found. the pathway was catalyzed by mety encoding o-acetylhomoserine sulfhydrylase. the gene mety, located immediately upstream of meta, was found to encode a protein of 437 amino acids with a deduced molecular mass of 46,751 da. in accordance with dna and protein sequence data, the introduction of mety into c. glutamicum resulted in the accumulation of a 47-kda protein in the cells and a 30-fold incre ... | 2002 | 11844756 |
| structural analysis of an escherichia coli endonuclease viii covalent reaction intermediate. | endonuclease viii (nei) of escherichia coli is a dna repair enzyme that excises oxidized pyrimidines from dna. nei shares with formamidopyrimidine-dna glycosylase (fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential beta-elimination steps. however, nei differs significantly from fpg in substrate specificity. we determined the structure of nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 a re ... | 2002 | 11847126 |
| identification of a mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions. | tuberculosis remains a leading killer worldwide, and new approaches for its treatment and prevention are urgently needed. this effort will benefit greatly from a better understanding of gene regulation in mycobacterium tuberculosis, particularly with respect to this pathogen's response to its host environment. we examined the behavior of two promoters from the divergently transcribed m. tuberculosis genes acr/hspx/rv2031c (alpha-crystallin homolog) and rv2032/acg (acr-coregulated gene) by using ... | 2002 | 11854240 |
| trna-like recognition of group i introns by a tyrosyl-trna synthetase. | the neurospora crassa mitochondrial tyrosyl-trna synthetase (cyt-18 protein) functions in splicing group i introns by promoting the formation of the catalytically active rna structure. previous work suggested that cyt-18 recognizes a conserved trna-like structure of the group i intron catalytic core. here, directed hydroxyl-radical cleavage assays show that the nucleotide-binding fold and c-terminal domains of cyt-18 interact with the expected group i intron cognates of the aminoacyl-acceptor st ... | 2002 | 11854463 |
| polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational release factors. | the mechanism of stop codon recognition during translation has long been a puzzle. only recently has it been established that a tripeptide in the bacterial release factors (rfs) 1 and 2 serves as the "anticodon" in deciphering stop codons in mrna. however, the molecular basis of the accuracy of stop codon recognition is unknown. although specific tripeptides in the rfs are primarily responsible for selective reading of cognate stop codons, charge-flip variant rf proteins, altered at conserved gl ... | 2002 | 11854484 |
| identification and comparative analysis of the chloroplast alpha-subunit gene of dna-dependent rna polymerase from seven euglena species. | when the sequence of the euglena gracilis chloroplast genome was reported in 1993 the alpha-subunit gene (rpoa) of rna polymerase appeared to be missing, based on a comparison of all putative reading frames to the then known rpoa loci. since there has been a large increase in known rpoa sequences, the question of a euglena chloroplast rpoa gene was re-examined. a previously described unknown reading frame of 161 codons was found to be part of an rpoa gene split by a single group iii intron. this ... | 2002 | 11861918 |
| analysis of the aaa sensor-2 motif in the c-terminal atpase domain of hsp104 with a site-specific fluorescent probe of nucleotide binding. | hsp104 from saccharomyces cerevisiae is a hexameric protein with two aaa atpase domains (n- and c-terminal nucleotide-binding domains nbd1 and nbd2, respectively) per monomer. our previous analysis of the hsp104 atp hydrolysis cycle revealed that nbd1 and nbd2 have very different catalytic properties, but each shows positive cooperativity in hydrolysis. there is also communication between the two domains, in that atp hydrolysis at nbd1 depends on the nucleotide that is bound to nbd2. here, we ex ... | 2002 | 11867765 |
| transfer rna-dependent amino acid biosynthesis: an essential route to asparagine formation. | biochemical experiments and genomic sequence analysis showed that deinococcus radiodurans and thermus thermophilus do not possess asparagine synthetase (encoded by asna or asnb), the enzyme forming asparagine from aspartate. instead these organisms derive asparagine from asparaginyl-trna, which is made from aspartate in the trna-dependent transamidation pathway [becker, h. d. & kern, d. (1998) proc. natl. acad. sci. usa 95, 12832-12837; and curnow, a. w., tumbula, d. l., pelaschier, j. t., min, ... | 2002 | 11880622 |
| filamentous phage active on the gram-positive bacterium propionibacterium freudenreichii. | we present the first description of a single-stranded dna filamentous phage able to replicate in a gram-positive bacterium. phage b5 infects propionibacterium freudenreichii and has a genome consisting of 5,806 bases coding for 10 putative open reading frames. the organization of the genome is very similar to the organization of the genomes of filamentous phages active on gram-negative bacteria. the putative coat protein exhibits homology with the coat proteins of phages ph75 and pf3 active on t ... | 2002 | 11889111 |
| the trna specificity of thermus thermophilus ef-tu. | by introducing a gac anticodon, 21 different escherichia coli trnas were misacylated with either phenylalanine or valine and assayed for their affinity to thermus thermophilus elongation factor tu (ef-tu)*gtp by using a ribonuclease protection assay. the presence of a common esterified amino acid permits the thermodynamic contribution of each trna body to the overall affinity to be evaluated. the e. coli elongator trnas exhibit a wide range of binding affinities that varied from -11.7 kcal/mol f ... | 2002 | 11891293 |
| mutations in the 16s rrna genes of helicobacter pylori mediate resistance to tetracycline. | low-cost and rescue treatments for helicobacter pylori infections involve combinations of several drugs including tetracycline. resistance to tetracycline has recently emerged in h. pylori. the 16s rrna gene sequences of two tetracycline-resistant clinical isolates (mic = 64 microg/ml) were determined and compared to the consensus h. pylori 16s rrna sequence. one isolate had four nucleotide substitutions, and the other had four substitutions and two deletions. natural transformation with the 16s ... | 2002 | 11914344 |
| reduced oxidative pentose phosphate pathway flux in recombinant xylose-utilizing saccharomyces cerevisiae strains improves the ethanol yield from xylose. | in recombinant, xylose-fermenting saccharomyces cerevisiae, about 30% of the consumed xylose is converted to xylitol. xylitol production results from a cofactor imbalance, since xylose reductase uses both nadph and nadh, while xylitol dehydrogenase uses only nad(+). in this study we increased the ethanol yield and decreased the xylitol yield by lowering the flux through the nadph-producing pentose phosphate pathway. the pentose phosphate pathway was blocked either by disruption of the gnd1 gene, ... | 2002 | 11916674 |
| use of fe(iii) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of geothermobacterium ferrireducens gen. nov., sp. nov. | it has recently been recognized that the ability to use fe(iii) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. this suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if fe(iii) is used as an electron acceptor. as part of a study of the microbial diversity of the obsidian pool area in yellowstone national park, wyo., hot sediment samples were used as the inoculum for enrichment cultures in med ... | 2002 | 11916691 |
| efficient trans-cleavage by the schistosoma mansoni smalpha1 hammerhead ribozyme in the extreme thermophile thermus thermophilus. | the catalytic hammerhead structure has been found in association with repetitive dna from several animals, including salamanders, crickets and schistosomes, and functions to process in cis the long multimer transcripts into monomer rna in vivo. the cellular role of these repetitive elements and their transcripts is unknown. moreover, none of these natural hammerheads have been shown to trans-cleave a host mrna in vivo. we analyzed the cis- and trans-cleavage properties of the hammerhead ribozyme ... | 2002 | 11917021 |
| tspgwi, a thermophilic class-iis restriction endonuclease from thermus sp., recognizes novel asymmetric sequence 5'-acgga(n11/9)-3'. | a novel prototype class-iis restriction endonuclease, tspgwi, was isolated from the thermophilic bacterium thermus sp. gw. the recognition sequence and cleavage positions have been established: tspgwi recognizes the non-palindromic 5-bp sequence 5'-acgga-3' and cleaves the dna 11 and 9 nt downstream in the top and bottom strand, respectively. in addition, an accompanying endonuclease, tspgwii, an isoschizomer of pst i, was found in thermus sp. gw cells. | 2002 | 11917039 |
| the large subunit of initiation factor aif2 is a close structural homologue of elongation factors. | the heterotrimeric factor e/aif2 plays a central role in eukaryotic/archaeal initiation of translation. by delivering the initiator methionyl-trna to the ribosome, e/aif2 ensures specificity of initiation codon selection. the three subunits of aif2 from the hyperthermophilic archaeon pyrococcus abyssi could be overproduced in escherichia coli. the beta and gamma subunits each contain a tightly bound zinc. the large gamma subunit is shown to form the structural core for trimer assembly. the cryst ... | 2002 | 11927566 |
| the solution structure of ribosomal protein l18 from thermus thermophilus reveals a conserved rna-binding fold. | we have determined the solution structure of ribosomal protein l18 from thermus thermophilus. l18 is a 12.5 kda protein of the large subunit of the ribosome and binds to both 5 s and 23 s rrna. in the uncomplexed state l18 folds to a mixed alpha/beta globular structure with a long disordered n-terminal region. we compared our high-resolution structure with rna-complexed l18 from haloarcula marismortui and t. thermophilus to examine rna-induced as well as species-dependent structural differences. ... | 2002 | 11964156 |
| stability and interactions of the amino-terminal domain of clpb from escherichia coli. | clpb is a member of a multichaperone system in escherichia coli (with dnak, dnaj, and grpe) that reactivates aggregated proteins. the sequence of clpb contains two atp-binding regions that are enclosed between the n- and c-terminal extensions. whereas it has been found that the n-terminal region of clpb is essential for the chaperone activity, the structure of this region is not known, and its biochemical properties have not been studied. we expressed and purified the n-terminal fragment of clpb ... | 2002 | 11967375 |
| the crystal structure of exonuclease recj bound to mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity. | recj, a 5' to 3' exonuclease specific for single-stranded dna, functions in dna repair and recombination systems. we determined the crystal structure of recj bound to mn(2+) ion essential for its activity. recj has a novel fold in which two domains are interconnected by a long helix, forming a central groove. mn(2+) is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes recj proteins. the groove is composed of re ... | 2002 | 11972066 |
| modulation of trnaala identity by inorganic pyrophosphatase. | a highly sensitive assay of trna aminoacylation was developed that directly measures the fraction of aminoacylated trna by following amino acid attachment to the 3'-(32)p-labeled trna. when applied to escherichia coli alanyl-trna synthetase, the assay allowed accurate measurement of aminoacylation of the most deleterious mutants of trna(ala). the effect of trna(ala) identity mutations on both aminoacylation efficiency (k(cat)/k(m)) and steady-state level of aminoacyl-trna was evaluated in the ab ... | 2002 | 11983895 |
| infection of tick cells and bovine erythrocytes with one genotype of the intracellular ehrlichia anaplasma marginale excludes infection with other genotypes. | anaplasma marginale, a tick-borne rickettsial pathogen of cattle, is endemic in several areas of the united states. many geographic isolates of a. marginale that occur in the united states are characterized by the major surface protein 1a, which varies in sequence and molecular weight due to different numbers of tandem repeats of 28 or 29 amino acids. recent studies (g. h. palmer, f. r. rurangirwa, and t. f. mcelwain, j. clin. microbiol. 39:631-635, 2001) of an a. marginale-infected herd of catt ... | 2002 | 11986275 |
| protein coding palindromes are a unique but recurrent feature in rickettsia. | rickettsia are unique in inserting in-frame a number of palindromic sequences within protein coding regions. in this study, we extensively analyzed repeated sequences in the genome of rickettsia conorii and examined their locations in regard to coding versus noncoding regions. we identified 656 interspersed repeated sequences classified into 10 distinct families. of the 10 families, three palindromic sequence families showed clear cases of insertions into open reading frames (orfs). the location ... | 2002 | 11997347 |
| a novel type of uracil-dna glycosylase mediating repair of hydrolytic dna damage in the extremely thermophilic eubacterium thermus thermophilus. | spontaneous hydrolytic deamination of dna cytosine and 5-methyl-cytosine residues is an abundant source of c/g (5-mec/g) to t/a transition mutations. as a result of this pressure, at least six different families of enzymes have evolved that initiate repair at u/g (t/g) mispairs, the relevant pre-mutagenic intermediates. the necessarily higher rate of the process at elevated temperatures must pose a correspondingly accentuated problem to contemporary thermophilic organisms and may have been a ser ... | 2002 | 12000829 |
| occurrence of leu+ revertants under starvation cultures in escherichia coli is growth-dependent. | many investigations have reported that advantageous mutations occurred more frequently under selective conditions than those under non-selective conditions. this phenomenon is referred to as adaptive mutation. their characteristics are that adaptive mutations are directed and growth-independent. the idea of directed adaptive mutation had been objected by some reports, however, the idea of growth-independent adaptive mutation has been held till today. | 2002 | 12019019 |
| mefloquine and new related compounds target the f(0) complex of the f(0)f(1) h(+)-atpase of streptococcus pneumoniae. | the activities of mefloquine (mfl) and related compounds against previously characterized streptococcus pneumoniae strains carrying defined amino acid substitutions in the c subunit of the f(0)f(1) h(+)-atpase were studied. in addition, a series of mfl-resistant (mfl(r)) strains were isolated and characterized. a good correlation was observed between inhibition of growth and inhibition of the membrane-associated f(0)f(1) h(+)-atpase activity. mfl was about 10-fold more active than optochin and a ... | 2002 | 12019076 |
| unique presence of a manganese catalase in a hyperthermophilic archaeon, pyrobaculum calidifontis va1. | we had previously isolated a facultatively anaerobic hyperthermophilic archaeon, pyrobaculum calidifontis strain va1. here, we found that strain va1, when grown under aerobic conditions, harbors high catalase activity. the catalase was purified 91-fold from crude extracts and displayed a specific activity of 23,500 u/mg at 70 degrees c. the enzyme exhibited a k(m) value of 170 mm toward h(2)o(2) and a k(cat) value of 2.9 x 10(4) s(-1).subunit(-1) at 25 degrees c. gel filtration chromatography in ... | 2002 | 12029047 |
| thermoadaptation of alpha-galactosidase agab1 in thermus thermophilus. | the evolutionary potential of a thermostable alpha-galactosidase, with regard to improved catalytic activity at high temperatures, was investigated by employing an in vivo selection system based on thermophilic bacteria. for this purpose, hybrid alpha-galactosidase genes of agaa and agab from bacillus stearothermophilus kve39, designated agaa1 and agab1, were cloned into an autonomously replicating thermus vector and introduced into thermus thermophilus of1053gd (deltaagat) by transformation. th ... | 2002 | 12029056 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |