Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| characterization of a heme-dependent catalase from methanobrevibacter arboriphilus. | recently it was reported that methanogens of the genus methanobrevibacter exhibit catalase activity. this was surprising, since methanobrevibacter species belong to the order methanobacteriales, which are known not to contain cytochromes and to lack the ability to synthesize heme. we report here that methanobrevibacter arboriphilus strains az and dh1 contained catalase activity only when the growth medium was supplemented with hemin. the heme catalase was purified and characterized, and the enco ... | 2001 | 11425719 |
| natural transformation in mesophilic and thermophilic bacteria: identification and characterization of novel, closely related competence genes in acinetobacter sp. strain bd413 and thermus thermophilus hb27. | the mesophile acinetobacter sp. strain bd413 and the extreme thermophile thermus thermophilus hb27 display high frequencies of natural transformation. in this study we identified and characterized a novel competence gene in acinetobacter sp. strain bd413, coma, whose product displays significant similarities to the competence proteins coma and comec in neisseria and bacillus species. transcription of coma correlated with growth phase-dependent transcriptional regulation of the recently identifie ... | 2001 | 11425734 |
| molecular characterization of desulfovibrio gigas neelaredoxin, a protein involved in oxygen detoxification in anaerobes. | desulfovibrio gigas neelaredoxin is an iron-containing protein of 15 kda, having a single iron site with a his(4)cys coordination. neelaredoxins and homologous proteins are widespread in anaerobic prokaryotes and have superoxide-scavenging activity. to further understand its role in anaerobes, its genomic organization and expression in d. gigas were studied and its ability to complement escherichia coli superoxide dismutase deletion mutant was assessed. in d. gigas, neelaredoxin is transcribed a ... | 2001 | 11443075 |
| rad54 protein stimulates the postsynaptic phase of rad51 protein-mediated dna strand exchange. | rad54 and rad51 are important proteins for the repair of double-stranded dna breaks by homologous recombination in eukaryotes. as previously shown, rad51 protein forms nucleoprotein filaments on single-stranded dna, and rad54 protein directly interacts with such filaments to enhance synapsis, the homologous pairing with a double-stranded dna partner. here we demonstrate that saccharomyces cerevisiae rad54 protein has an additional role in the postsynaptic phase of dna strand exchange by stimulat ... | 2001 | 11459988 |
| high stability of a ferredoxin from the hyperthermophilic archaeon a. ambivalens: involvement of electrostatic interactions and cofactors. | the ferredoxin from the thermophilic archaeon acidianus ambivalens is a small monomeric seven-iron protein with a thermal midpoint (t(m)) of 122 degrees c (ph 7). to gain insight into the basis of its thermostability, we have characterized unfolding reactions induced chemically and thermally at various phs. thermal unfolding of this ferredoxin, in the presence of various guanidine hydrochloride (guhcl) concentrations, yields a linear correlation between unfolding enthalpies (deltah[t(m)]) and t( ... | 2001 | 11468351 |
| assessment, by transcription-mediated amplification, of virologic response in patients with chronic hepatitis c virus treated with peginterferon alpha-2a. | transcription-mediated amplification (tma) is an isothermal, autocatalytic target amplification method which has the potential to detect less than 50 hepatitis c virus (hcv) rna copies/ml (10 iu/ml). the tma assay was used to assess the presence of residual hcv rna in plasma from patients treated with polyethylene glycol-modified interferon alpha-2a (peginterferon alpha-2a) who showed a virologic relapse after the end of therapy. stored end-of-treatment and end-of-follow-up plasma samples from 1 ... | 2001 | 11474002 |
| the kink-turn: a new rna secondary structure motif. | analysis of the haloarcula marismortui large ribosomal subunit has revealed a common rna structure that we call the kink-turn, or k-turn. the six k-turns in h.marismortui 23s rrna superimpose with an r.m.s.d. of 1.7 a. there are two k-turns in the structure of thermus thermophilus 16s rrna, and the structures of u4 snrna and l30e mrna fragments form k-turns. the structure has a kink in the phosphodiester backbone that causes a sharp turn in the rna helix. its asymmetric internal loop is flanked ... | 2001 | 11483524 |
| functional and evolutionary relationship between arginine biosynthesis and prokaryotic lysine biosynthesis through alpha-aminoadipate. | our previous studies revealed that lysine is synthesized through alpha-aminoadipate in an extremely thermophilic bacterium, thermus thermophilus hb27. sequence analysis of a gene cluster involved in the lysine biosynthesis of this microorganism suggested that the conversion from alpha-aminoadipate to lysine proceeds in a way similar to that of arginine biosynthesis. in the present study, we cloned an argd homolog of t. thermophilus hb27 which was not included in the previously cloned lysine bios ... | 2001 | 11489859 |
| peplomycin, a bleomycin derivative, induces myofibroblasts in pulmonary fibrosis. | to analyse the mechanism by which a bleomycin derivative, peplomycin (plm) induces pulmonary fibrosis, we investigated differentiation of rat pulmonary fibroblasts to myofibroblasts (mf). in intraperitoneally plm (5 mg/kg/day)-injected rats, the peripheries of lungs adjacent to the pleura revealed advanced fibrosis with a small number of alpha-smooth muscle actin (alpha-sma)-positive mf, which ultrastructurally possessed abundant microfilaments and cellular organelles. in the fibrotic tissue, th ... | 2001 | 11493347 |
| functional relevance of the disulfide-linked complex of the n-terminal pdz domain of inad with norpa. | in drosophila, phototransduction is mediated by g(q)-activation of phospholipase c and is a well studied model system for understanding the kinetics of signal initiation, propagation and termination controlled by g proteins. the proper intracellular targeting and spatial arrangement of most proteins involved in fly phototransduction require the multi-domain scaffolding protein inad, composed almost entirely of five pdz domains, which independently bind various proteins including norpa, the relev ... | 2001 | 11500369 |
| resistance of streptococcus pneumoniae to deformylase inhibitors is due to mutations in defb. | resistance to peptide deformylase inhibitors in escherichia coli or staphylococcus aureus is due to inactivation of transformylase activity. knockout experiments in streptococcus pneumoniae r6x indicate that the transformylase (fmt) and deformylase (defb) genes are essential and that a def paralog (defa) is not. actinonin-resistant mutants of s. pneumoniae atcc 49619 harbor mutations in defb but not in fmt. reintroduction of the mutated defb gene into wild-type s. pneumoniae r6x recreates the re ... | 2001 | 11502510 |
| high-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification. | single nucleotide polymorphisms (snps) are the foundation of powerful complex trait and pharmacogenomic analyses. the availability of large snp databases, however, has emphasized a need for inexpensive snp genotyping methods of commensurate simplicity, robustness, and scalability. we describe a solution-based, microtiter plate method for snp genotyping of human genomic dna. the method is based upon allele discrimination by ligation of open circle probes followed by rolling circle amplification o ... | 2001 | 11511324 |
| hybrid protein between ribosomal protein s16 and rimm of escherichia coli retains the ribosome maturation function of both proteins. | the rimm protein in escherichia coli is associated with free 30s ribosomal subunits but not with 70s ribosomes and is important for efficient maturation of the 30s subunits. a mutant lacking rimm shows a sevenfold-reduced growth rate and a reduced translational efficiency. here we show that a double alanine-for-tyrosine substitution in rimm prevents it from associating with the 30s subunits and reduces the growth rate of e. coli approximately threefold. several faster-growing derivatives of the ... | 2001 | 11514519 |
| recombinational transfer of 100-kilobase genomic dna to plasmid in bacillus subtilis 168. | transformation of bacillus subtilis by a plasmid requires a circular multimeric form. in contrast, linearized plasmids can be circularized only when homologous sequences are present in the host genome. a recombinational transfer system was constructed with this intrinsic b. subtilis recombinational repair pathway. the vector, pgets103, a derivative of the theta-type replicating plasmid ptb19 of thermophilic bacillus, had the full length of escherichia coli plasmid pbr322. a multimeric form of pg ... | 2001 | 11514534 |
| a conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. | the ribosome is a dynamic particle that undergoes many structural changes during translation. we show through chemical probing with dimethyl sulfate (dms) that conformational changes occur at several nucleotides in the peptidyl transferase center upon alterations in ph, temperature, and monovalent ion concentration, consistent with observations made by elson and coworkers over 30 years ago. moreover, we have found that the ph-dependent dms reactivity of a2451 in the center of the 23s rrna peptid ... | 2001 | 11517305 |
| electrostatics of nanosystems: application to microtubules and the ribosome. | evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. foremost among the models used to elucidate the electrostatic potential is the poisson-boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. here we present the application of numerical methods to enable the trivially parallel solution of the poisson-boltzmann eq ... | 2001 | 11517324 |
| production of recombinant alpha-galactosidases in thermus thermophilus. | a thermus thermophilus selector strain for production of thermostable and thermoactive alpha-galactosidase was constructed. for this purpose, the native alpha-galactosidase gene (agat) of t. thermophilus th125 was inactivated to prevent background activity. in our first attempt, insertional mutagenesis of agat by using a cassette carrying a kanamycin resistance gene led to bacterial inability to utilize melibiose (alpha-galactoside) and galactose as sole carbohydrate sources due to a polar effec ... | 2001 | 11526023 |
| xylulokinase overexpression in two strains of saccharomyces cerevisiae also expressing xylose reductase and xylitol dehydrogenase and its effect on fermentation of xylose and lignocellulosic hydrolysate. | fermentation of the pentose sugar xylose to ethanol in lignocellulosic biomass would make bioethanol production economically more competitive. saccharomyces cerevisiae, an efficient ethanol producer, can utilize xylose only when expressing the heterologous genes xyl1 (xylose reductase) and xyl2 (xylitol dehydrogenase). xylose reductase and xylitol dehydrogenase convert xylose to its isomer xylulose. the gene xks1 encodes the xylulose-phosphorylating enzyme xylulokinase. in this study, we determi ... | 2001 | 11526030 |
| the structure of an asprs-trna(asp) complex reveals a trna-dependent control mechanism. | the 2.6 a resolution crystal structure of an inactive complex between yeast trna(asp) and escherichia coli aspartyl-trna synthetase reveals the molecular details of a trna-induced mechanism that controls the specificity of the reaction. the dimer is asymmetric, with only one of the two bound trnas entering the active site cleft of its subunit. however, the flipping loop, which controls the proper positioning of the amino acid substrate, acts as a lid and prevents the correct positioning of the t ... | 2001 | 11566892 |
| multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. | a large fragment of the dissimilatory sulfite reductase genes (dsrab) was pcr amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. in addition, the sequence of the dsrab gene homologs of the sulfite reducer desulfitobacterium dehalogenans was determined. in contrast to previous reports, comparative analysis of all available dsrab sequences produced a tree topology partially inconsistent with the corresponding 16s rrna phylogen ... | 2001 | 11567003 |
| characterization of a highly thermostable alkaline phosphatase from the euryarchaeon pyrococcus abyssi. | this work reports the first isolation and characterization of an alkaline phosphatase (ap) from a hyperthermophilic archaeon. an ap gene from pyrococcus abyssi, a euryarchaeon isolated from a deep-sea hydrothermal vent, was cloned and the enzyme expressed in escherichia coli. analysis of the sequence showed conservation of the active site and structural elements of the e. coli ap. the recombinant ap was purified and characterized. monomeric and homodimeric active forms were detected, with a mono ... | 2001 | 11571149 |
| mutations in the listerial prob gene leading to proline overproduction: effects on salt tolerance and murine infection. | the observed sensitivity of listeria monocytogenes to the toxic proline analogue l-azetidine-2-carboxylic acid (az) suggested that proline synthesis in listeria may be regulated by feedback inhibition of gamma-glutamyl kinase (gk), the first enzyme of the proline biosynthesis pathway, encoded by the prob gene. taking advantage of the epicurian coli mutator strain xl1-red, we performed random mutagenesis of the recently described proba operon and generated three independent mutations in the liste ... | 2001 | 11571156 |
| two c or not two c: recurrent disruption of zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. | ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. in prokaryotes, the genes for most ribosomal proteins are clustered in several highly conserved operons, which ensures efficient co-regulation of their expression. duplications of ribosomal-protein genes are infrequent, and given their coordinated expression and functioning, it is generally assumed that ribosomal-protein genes are unlikely to undergo horizontal transfer. howe ... | 2001 | 11574053 |
| screening of active lyssavirus infection in wild bat populations by viral rna detection on oropharyngeal swabs. | brain analysis cannot be used for the investigation of active lyssavirus infection in healthy bats because most bat species are protected by conservation directives. consequently, serology remains the only tool for performing virological studies on natural bat populations; however, the presence of antibodies merely reflects past exposure to the virus and is not a valid marker of active infection. this work describes a new nested reverse transcription (rt)-pcr technique specifically designed for ... | 2001 | 11574590 |
| visualization of protein s1 within the 30s ribosomal subunit and its interaction with messenger rna. | s1 is the largest ribosomal protein, present in the small subunit of the bacterial ribosome. it has a pivotal role in stabilizing the mrna on the ribosome. thus far, s1 has eluded structural determination. we have identified the s1 protein mass in the cryo-electron microscopic map of the escherichia coli ribosome by comparing the map with a recent x-ray crystallographic structure of the 30s subunit, which lacks s1. according to our finding, s1 is located at the junction of head, platform, and ma ... | 2001 | 11593008 |
| characterization of a brucella species 25-kilobase dna fragment deleted from brucella abortus reveals a large gene cluster related to the synthesis of a polysaccharide. | in the present study we completed the nucleotide sequence of a brucella melitensis 16m dna fragment deleted from b. abortus that accounts for 25,064 bp and show that the other brucella spp. contain the entire 25-kb dna fragment. two short direct repeats of four nucleotides, detected in the b. melitensis 16m dna flanking both sides of the fragment deleted from b. abortus, might have been involved in the deletion formation by a strand slippage mechanism during replication. in addition to omp31, co ... | 2001 | 11598046 |
| sequence analysis of four shigella boydii o-antigen loci: implication for escherichia coli and shigella relationships. | shigella strains are in reality clones of escherichia coli and are believed to have emerged relatively recently (g. m. pupo, r. lan, and p. r. reeves, proc. natl. acad. sci. usa 97:10567-10572, 2000). there are 33 o-antigen forms in these shigella clones, of which 12 are identical to o antigens of other e. coli strains. we sequenced o-antigen gene clusters from shigella boydii serotypes 4, 5, 6, and 9 and also studied the o53- and o79-antigen gene clusters of e. coli, encoding o antigens identic ... | 2001 | 11598067 |
| the organization of cytoplasmic ribosomal protein genes in the arabidopsis genome. | eukaryotic ribosomes are made of two components, four ribosomal rnas, and approximately 80 ribosomal proteins (r-proteins). the exact number of r-proteins and r-protein genes in higher plants is not known. the strong conservation in eukaryotic r-protein primary sequence allowed us to use the well-characterized rat (rattus norvegicus) r-protein set to identify orthologues on the five haploid chromosomes of arabidopsis. by use of the numerous expressed sequence tag (est) accessions and the complet ... | 2001 | 11598216 |
| influence of a sulfhydryl cross-link across the allosteric-site interface of e. coli phosphofructokinase. | to assess the role of quaternary stability on the properties of escherichia coli phosphofructokinase (pfk), a disulfide bond has been introduced across the subunit interface containing the allosteric binding sites in e. coli phosphofructokinase by changing n288 to cysteine. n288 is located in close proximity to the equivalent residue on an adjacent subunit. although sds-page of oxidized n288c indicates monomeric protein, blocking the six native cysteine residues with n-ethyl maleimide (nem) reve ... | 2001 | 11604525 |
| differential effects of replacing escherichia coli ribosomal protein l27 with its homologue from aquifex aeolicus. | the rpma gene, which encodes 50s ribosomal subunit protein l27, was cloned from the extreme thermophile aquifex aeolicus, and the protein was overexpressed and purified. comparison of the a. aeolicus protein with its homologue from escherichia coli by circular dichroism analysis and proton nuclear magnetic resonance spectroscopy showed that it readily adopts some structure in solution that is very stable, whereas the e. coli protein is unstructured under the same conditions. a mutant of e. coli ... | 2001 | 11673426 |
| gene cassette pcr: sequence-independent recovery of entire genes from environmental dna. | the vast majority of bacteria in the environment have yet to be cultured. consequently, a major proportion of both genetic diversity within known gene families and an unknown number of novel gene families reside in these uncultured organisms. isolation of these genes is limited by lack of sequence information. where such sequence data exist, pcr directed at conserved sequence motifs recovers only partial genes. here we outline a strategy for recovering complete open reading frames from environme ... | 2001 | 11679351 |
| 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 | |
| aaa proteins: in search of a common molecular basis. international meeting on cellular functions of aaa proteins. | 2001 | 11713188 | |
| 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 |
| 5s ribosomal rna database. | ribosomal 5s rna (5s rrna) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. it is thought to enhance protein synthesis by stabilization of a ribosome structure. this paper presents the updated database of 5s rrna and their genes (5s rdna). its short characteristics are presented in the introduction. the database contains 2280 primary structures of 5s rrna and 5s rrna genes. these include 536 eu ... | 2002 | 11752286 |
| the european database on small subunit ribosomal rna. | the european database on ssu rrna can be consulted via the world wideweb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal rna sequences. sequences are provided in aligned format. the alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also av ... | 2002 | 11752288 |
| mmdb: entrez's 3d-structure database. | three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. the goal of entrez's 3d-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. to this end entrez's search engine provides three powerful features. (i) sequence and structure neighbors; one may select all sequences similar to one of ... | 2002 | 11752307 |
| 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 |
| distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal rna. | the relative substitution rate of each nucleotide site in bacterial small subunit rrna, large subunit rrna and 5s rrna was calculated from sequence alignments for each molecule. two-dimensional and three-dimensional variability maps of the rrnas were obtained by plotting the substitution rates on secondary structure models and on the tertiary structure of the rrnas available from x-ray diffraction results. this showed that the substitution rates are generally low near the centre of the ribosome, ... | 2001 | 11812832 |
| 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 |
| modularity and specialization in superfamily 1 and 2 helicases. | 2002 | 11889086 | |
| 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 accessory subunit of dna polymerase gamma is essential for mitochondrial dna maintenance and development in drosophila melanogaster. | dna polymerase gamma, pol gamma, is the key replicative enzyme in animal mitochondria. the drosophila enzyme is a heterodimer comprising catalytic and accessory subunits of 125 kda and 35 kda, respectively. both subunits have been cloned and characterized in a variety of model systems, and genetic mutants of the catalytic subunit were first identified in drosophila, as chemically induced mutations that disrupt larval behavior (tamas). mutations in the gene encoding the accessory subunit have not ... | 2002 | 11917141 |
| 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 |
| high affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands. | we have isolated 2'-fluoro-substituted rna aptamers that bind to streptavidin (sa) with an affinity around 7 +/- 1.8 nm, comparable with that of recently described peptide aptamers. binding to sa was not prevented by prior saturation with biotin, enabling nucleic acid aptamers to form useful ternary complexes. mutagenesis, secondary structure analysis, ribonuclease footprinting and deletion analysis provided evidence for the essential structural features of sa-binding aptamers. in order to provi ... | 2002 | 12000850 |
| 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 |