| heterogeneity of primer extension products in asymmetric pcr is due both to cleavage by a structure-specific exo/endonuclease activity of dna polymerases and to premature stops. | in pcr, dna polymerases from thermophilic bacteria catalyze the extension of primers annealed to templates as well as the structure-specific cleavage of the products of primer extension. here we show that cleavage by thermus aquaticus and thermus thermophilus dna polymerases can be precise and substantial: it occurs at the base of the stem-loop structure assumed by the single strand products of primer extension using as template a common genetic element, the promoter-operator of the escherichia ... | 1996 | 8610108 |
| cloning, sequencing, and expression of ruvb and characterization of ruvb proteins from two distantly related thermophilic eubacteria. | the ruvb genes of the highly divergent thermophilic eubacteria thermus thermophilus and thermotoga maritima were cloned, sequenced, and expressed in escherichia coli. both thermostable ruvb proteins were purified to homogeneity. like e. coli ruvb protein, both purified thermostable ruvb proteins showed strong double-stranded dna-dependent atpase activity at their temperature optima (> or = 70 degrees c). in the absence of atp, t. thermophilus ruvb protein bound to linear double-stranded dna with ... | 1996 | 8626340 |
| isolation of thermus strains from hot composts (60 to 80 degrees c). | high numbers (10(7) to 10(10) cells per g [dry weight]) of heterotrophic, gram-negative, rod-shaped, non-sporeforming, aerobic, thermophilic bacteria related to the genus thermus were isolated from thermogenic composts at temperatures between 65 and 82 degrees c. these bacteria were present in different types of wastes (garden and kitchen wastes and sewage sludge) and in all the industrial composting systems studied (open-air windows, boxes with automated turning and aeration, and closed bioreac ... | 1996 | 8633870 |
| crystal structure of the rna binding ribosomal protein l1 from thermus thermophilus. | l1 has a dual function as a ribosomal protein binding rrna and as a translational repressor binding mrna. the crystal structure of l1 from thermus thermophilus has been determined at 1.85 angstroms resolution. the protein is composed of two domains with the n- and c-termini in domain i. the eight n-terminal residues are very flexible, as the quality of electron density map shows. proteolysis experiments have shown that the n-terminal tail is accessible and important for 23s rrna binding. most of ... | 1996 | 8635468 |
| the crystal structure of the ternary complex of t.thermophilus seryl-trna synthetase with trna(ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. | the low temperature crystal structure of the ternary complex of thermus thermophilus seryl-trna synthetase with trna(ser) (gga) and a non-hydrolysable seryl-adenylate analogue has been refined at 2.7 angstrom resolution. the analogue is found in both active sites of the synthetase dimer but there is only one trna bound across the two subunits. the motif 2 loop of the active site into which the single trna enters interacts within the major groove of the acceptor stem. in particular, a novel ring- ... | 1996 | 8654381 |
| variant minihelix rnas reveal sequence-specific recognition of the helical trna(ser) acceptor stem by e.coli seryl-trna synthetase. | aminoacylation rate determinations for a series of variant rna minihelix substrates revealed that escherichia coli seryl-trna synthetase (serrs) recognizes the 1--72 through 5--68 base pairs of the e.coli trna(ser) acceptor stem with the major recognition elements clustered between positions 2--71 and 4--69. the rank order of effects of canonical base pair substitutions at each position on kcat/km was used to assess the involvement of major groove functional groups in recognition. conclusions ba ... | 1996 | 8654382 |
| differential domain accessibility to monoclonal antibodies in three different morphological assemblies built up by the s-layer protein of thermus thermophilus hb8. | a collection of 27 monoclonal antibodies (mabs) against the s-layer protein (p100) of thermus thermophilus hb8 has been obtained. they have been classified according to their ability to recognize s-layer regions expressed in e. coli from plasmids containing different fragments of its coding gene, slpa. the accessibility of the binding sites in hexagonal, trigonal, or tetragonal assemblies of p100 was analyzed by enzyme-linked immunosorbent assays with six of these mabs and their respective fab f ... | 1996 | 8655568 |
| a conserved motif in s-layer proteins is involved in peptidoglycan binding in thermus thermophilus. | there is experimental evidence to suggest that the 100-kda s-layer protein from thermus thermophilus hb8 binds to the peptidoglycan cell wall. this property could be related to the presence of a region (slh) of homology with other s-layer proteins and extracellular enzymes (a. lupas, h. engelhardt, j. peters, u. santarius, s. volker, and w. baumeister, j. bacteriol. 176:1224-1233, 1994). by using specific monoclonal antibodies, we show that similar regions are present in different members of the ... | 1996 | 8759836 |
| improving the fidelity of thermus thermophilus dna ligase. | the dna ligase from thermus thermophilus (tth dna ligase) seals single-strand breaks (nicks) in dna duplex substrates. the specificity and thermostability of this enzyme are exploited in the ligase chain reaction (lcr) and ligase detection reaction (ldr) to distinguish single base mutations associated with genetic diseases. herein, we describe a quantitative assay using fluorescently labeled substrates to study the fidelity of tth dna ligase. the enzyme exhibits significantly greater discriminat ... | 1996 | 8760896 |
| identification of essential residues in thermus thermophilus dna ligase. | dna ligases play a pivotal role in dna replication, repair and recombination. reactions catalyzed by dna ligases consist of three steps: adenylation of the ligase in the presence of atp or nad+, transferring the adenylate moiety to the 5'-phosphate of the nicked dna substrate (deadenylation) and sealing the nick through the formation of a phosphodiester bond. thermus thermophilus hb8 dna ligase (tth dna ligase) differs from mesophilic atp-dependent dna ligases in three ways: (i) it is nad+ depen ... | 1996 | 8760897 |
| an unusual route to thermostability disclosed by the comparison of thermus thermophilus and escherichia coli inorganic pyrophosphatases. | the structures of escherichia coli soluble inorganic pyrophosphatase (e-ppase) and thermus thermophilus soluble inorganic pyrophosphatase (t-ppase) have been compared to find the basis for the superior thermostability of t-ppase. both enzymes are d3 hexamers and crystallize in the same space group with very similar cell dimensions. two rather small changes occur in the t-ppase monomer: a systematic removal of ser residues and insertion of arg residues, but only in the c-terminal part of the prot ... | 1996 | 8762133 |
| pyrimidine biosynthesis genes (pyre and pyrf) of an extreme thermophile, thermus thermophilus. | we have isolated uracil auxotrophic mutants of an extreme thermophile, thermus thermophilus. a part of the pyrimidine biosynthetic operon including genes for orotate phosphoribosyltransferase (pyre) and for orotidine-5'-monophosphate decarboxylase (pyrf) was cloned and sequenced. the pyre gene can be a bidirectional marker for the gene manipulation system of the thermophile. | 1996 | 8787418 |
| development of a temperature-inducible expression system for streptomyces spp. | pcr mutagenesis of a 0.9-kbp fragment, containing a repressor gene, trar, and its target promoter, ptra, from streptomyces nigrifaciens plasmid psn22, produced streptomyces lividans clones with temperature-inducible ptra expression. using the promoterless gene for the thermostable thermus flavus malate dehydrogenase as an indicator, an induction of enzyme activity of as much as was observed in a temperature shift from 28 to 37 degrees c. temperature downshift reestablished repression of ptra, ma ... | 1996 | 8808949 |
| a stable intermediate in the thermal unfolding process of a chimeric 3-isopropylmalate dehydrogenase between a thermophilic and a mesophilic enzymes. | the thermal unfolding process of a chimeric 3-isopropylmalate dehydrogenase made of parts from an extreme thermophile, thermus thermophilus, and a mesophile, bacillus subtilis, enzymes was studied by cd spectrophotometry and differential scanning calorimetry (dsc). the enzyme is a homodimer with a subunit containing two structural domains. the dsc melting profile of the chimeric enzyme in 20 mm nahco3, ph 10.4, showed two endothermic peaks, whereas that of the t. thermophilus wild-type enzyme ha ... | 1996 | 8868488 |
| spontaneous tandem sequence duplications reverse the thermal stability of carboxyl-terminal modified 3-isopropylmalate dehydrogenase. | a mutant strain of thermus thermophilus which contains deletions in the 3'-terminal region of its leub gene showed a temperature-sensitive growth phenotype in the absence of leucine. three phenotypically thermostable mutants were isolated from the temperature-sensitive strain by spontaneous evolution. each pseudorevertant carried a tandem sequence duplication in the 3' region of its leub gene. the mutated 3-isopropylmalate dehydrogenases encoded by the leub genes from the pseudorevertants were m ... | 1996 | 8892833 |
| redesigning secondary structure to invert coenzyme specificity in isopropylmalate dehydrogenase. | rational engineering of enzymes involves introducing key amino acids guided by a knowledge of protein structure to effect a desirable change in function. to date, all successful attempts to change specificity have been limited to substituting individual amino acids within a protein fold. however, the infant field of protein engineering will only reach maturity when changes in function can be generated by rationally engineering secondary structures. guided by x-ray crystal structures and molecula ... | 1996 | 8901552 |
| the 16s rrna binding site of thermus thermophilus ribosomal protein s15: comparison with escherichia coli s15, minimum site and structure. | binding of escherichia coli and thermus thermophilus ribosomal proteins s15 to a 16s ribosomal rna fragment from t. thermophilus (nt 559-753) has been investigated in detail by extensive deletion analysis, filter-binding assays, gel mobility shift, structure probing, footprinting with chemical, enzymatic, and hydroxyl radical probes. both s15 proteins recognize two distinct sites. the first one maps in the bottom of helix 638-655/717-734 (h22) and in the three-way junction between helix 560-570/ ... | 1996 | 8903343 |
| electron paramagnetic resonance studies of the soluble cua protein from the cytochrome ba3 of thermus thermophilus. | the electron paramagnetic resonance (epr) spectrum of the binuclear cua center in the water-soluble subunit ii fragment from cytochrome ba3 of thermus thermophilus was recorded at 3.93, 9.45, and 34.03 ghz, and the epr parameters were determined by computer simulations. the frequency and m1 dependence of the linewidth was discussed in terms of g strain superimposed on a correlation between the a and g values. the g values were found to be gx = 1.996, gy = 2.011, gz = 2.187, and the two cu ions c ... | 1996 | 8913619 |
| the crystal structures of t. thermophilus lysyl-trna synthetase complexed with e. coli trna(lys) and a t. thermophilus trna(lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. | the crystal structures of thermus thermophilus lysyl-trna synthetase, a class iib aminoacyl-trna synthetase, complexed with escherchia coli trna(lys)(mnm5 s2uuu) at 2.75 a resolution and with a t. thermophilus trna(lys)(cuu) transcript at 2.9 a resolution are described. in both complexes only the trna anticodon stem-loop is well ordered. the mode of binding of the anticodon stem-loop to the n-terminal beta-barrel domain is similar to that previously found for the homologous class iib aspartyl-tr ... | 1996 | 8947055 |
| ethanolic fermentation of xylose with saccharomyces cerevisiae harboring the thermus thermophilus xyla gene, which expresses an active xylose (glucose) isomerase. | the thermus thermophilus xyla gene encoding xylose (glucose) isomerase was cloned and expressed in saccharomyces cerevisiae under the control of the yeast pgk1 promoter. the recombinant xylose isomerase showed the highest activity at 85 degrees c with a specific activity of 1.0 u mg-1. a new functional metabolic pathway in s. cerevisiae with ethanol formation during oxygen-limited xylose fermentation was demonstrated. xylitol and acetic acid were also formed during the fermentation. | 1996 | 8953736 |
| chaperone activity and structure of monomeric polypeptide binding domains of groel. | the chaperonin groel is a large complex composed of 14 identical 57-kda subunits that requires atp and groes for some of its activities. we find that a monomeric polypeptide corresponding to residues 191 to 345 has the activity of the tetradecamer both in facilitating the refolding of rhodanese and cyclophilin a in the absence of atp and in catalyzing the unfolding of native barnase. its crystal structure, solved at 2.5 a resolution, shows a well-ordered domain with the same fold as in intact gr ... | 1996 | 8986757 |
| a novel transporter involved in cobalt uptake. | cobalt is an essential component of a low molecular-mass nitrile hydratase (l-nhase) from rhodococcus rhodochrous j1. we have found a new gene, nhlf, in the dna region sandwiched between nhlba encoding l-nhase and amda encoding amidase, which are involved in the degradation of nitriles. the product of nhlf, nhlf, shows a significant sequence similarity with those of hoxn from alcaligenes eutrophus, hupn from bradyrhizobium japonicum, nixa from helicobacter pylori, and ureh from bacillus sp., whi ... | 1997 | 8990157 |
| mitochondrial dna damage is more extensive and persists longer than nuclear dna damage in human cells following oxidative stress. | a significant amount of reactive oxygen species (ros) is generated during mitochondrial oxidative phosphorylation. several studies have suggested that mtdna may accumulate more oxidative dna damage relative to nuclear dna. this study used quantitative pcr to examine the formation and repair of hydrogen peroxide-induced dna damage in a 16.2-kb mitochondrial fragment and a 17.7-kb fragment flanking the beta-globin gene. simian virus 40-transformed fibroblasts treated with 200 microm hydrogen perox ... | 1997 | 9012815 |
| selective amplification of rna utilizing the nucleotide analog ditp and thermus thermophilus dna polymerase. | the ability to selectively amplify rna in the presence of genomic dna of analogous sequence is cumbersome and requires implementation of critical controls for genes lacking introns. the convenient approaches of either designing oligonucleotide primers at the splice junction or differentiating the target sequence based on the size difference obtained by the presence of the intron are not possible. our strategy for the selective amplification of rna targets is based on the enzymology of a single t ... | 1996 | 9016675 |
| protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase. | evolutionary analysis indicates that eubacterial nadp-dependent isocitrate dehydrogenases (ec 1.1.1.42) first evolved from an nad-dependent precursor about 3.5 billion years ago. selection in favor of utilizing nadp was probably a result of niche expansion during growth on acetate, where isocitrate dehydrogenase provides 90% of the nadph necessary for biosynthesis. amino acids responsible for differing coenzyme specificities were identified from x-ray crystallographic structures of escherichia c ... | 1997 | 9096353 |
| expression of a gene encoding a trna synthetase-like protein is enhanced in tumorigenic human myeloid leukemia cells and is cell cycle stage- and differentiation-dependent. | we cloned a tumorigenic phenotype-associated cdna encoding a trna synthetase-like protein from an acute-phase human myeloid leukemia cell line. the cdna was isolated by reiterative subtraction of cdnas synthesized from tumor-generating parental leukemia cells versus those from a nontumorigenic variant of the same cells. the selected cdna encodes a protein that is a close homolog of one subunit of prokaryote and yeast phenylalanyl-trna synthetase (phers). the expressed protein reacts specificiall ... | 1997 | 9177188 |
| a biologically active 53 kda fragment of overproduced alanyl-trna synthetase from thermus thermophilus hb8 specifically interacts with trna ala acceptor helix. | the alas gene encoding the alanyl-trna synthetase (alars) from thermus thermophilus hb8 was cloned and sequenced. the gene comprises 2646 bp, corresponding to 882 amino acids, 45% of which are identical to the enzyme from escherichia coli . the t. thermophilus alars was overproduced in e.coli , purified and characterized. it has high thermal stability up to approximately 65 degrees c, with a temperature optimum of aminoacylation activity at approximately 60 degrees c, and will be valuable for cr ... | 1997 | 9207019 |
| the first step of aminoacylation at the atomic level in histidyl-trna synthetase. | the crystal structure of an enzyme-substrate complex with histidyl-trna synthetase from escherichia coli, atp, and the amino acid analog histidinol is described and compared with the previously obtained enzyme-product complex with histidyl-adenylate. an active site arginine, arg-259, unique to all histidyl-trna synthetases, plays the role of the catalytic magnesium ion seen in seryl-trna synthetase. when arg-259 is substituted with histidine, the apparent second order rate constant (kcat/km) for ... | 1997 | 9207058 |
| cloning of a polycistronic cdna from tomato encoding gamma-glutamyl kinase and gamma-glutamyl phosphate reductase. | we isolated from a tomato cdna library the tompro1 locus, which encodes gamma-glutamyl kinase (gk) and gamma-glutamyl phosphate reductase (gpr). this locus is unusual among eukaryotic genetic elements because it contains two open reading frames, and thus resembles prokaryotic polycistronic operons. the first open reading frame, specifying gk, is terminated by a taa codon, which is followed by five nucleotides, an atg translation initiation codon, and the second open reading frame, encoding gpr. ... | 1997 | 9223347 |
| a new thermus-escherichia coli shuttle integration vector system. | we established a thermus thermophilus strain in which the pyre gene (coding for orotate phosphoribosyltransferase of the pyrimidine biosynthetic pathway) was totally deleted. we also constructed an integration vector, which consisted of the escherichia coli plasmid vector pbluescript and a 2.1-kb segment of the t. thermophilus leu operon sequence, for the integration of a foreign gene into a chromosome of the thermophile. pyre and leub genes were used as probes to test the integration vector. th ... | 1997 | 9244269 |
| effects of base mismatches on joining of short oligodeoxynucleotides by dna ligases. | the requirement for watson-crick base pairing surrounding a nick in duplex dna to be sealed by dna ligase is the basis for oligonucleotide ligation assays that distinguish single base mutations in dna targets. experiments in a model system demonstrate that the minimum length of oligonucleotide that can be joined differs for different ligases. thermus thermophilus (tth) dna ligase is unable to join any oligonucleotide of length six or less, while t4 dna ligase and t7 dna ligase are both able to j ... | 1997 | 9254695 |
| replication of dna templates containing 5-formyluracil, a major oxidative lesion of thymine in dna. | 5-formyluracil (5-fou) is a major lesion of thymine produced in dna by ionizing radiation and various chemical oxidants. to assess its biochemical effects on dna replication, 22mer oligonucleotide templates containing an internal 5-fou at defined sites were synthesized by the phosphoramidite method and examined for ability to serve as a template for various dna polymerases in vitro . klenow fragments with and without 3'-->5'exonuclease of dna polymerase i, thermus thermophilus dna polymerase (ex ... | 1997 | 9321644 |
| characterization of a thermostable dna photolyase from an extremely thermophilic bacterium, thermus thermophilus hb27. | the photolyase gene from thermus thermophilus was cloned and sequenced. the characteristic absorption and fluorescence spectra of the purified t. thermophilus photolyase suggested that the protein has flavin adenine dinucleotide as a chromophore. the second chromophore binding site was not conserved in t. thermophilus photolyase. the purified enzyme showed light-dependent photoreactivation activity in vitro at 35 and 65 degrees c and was stable when subjected to heat and acidic ph. | 1997 | 9335302 |
| archaeal-type lysyl-trna synthetase in the lyme disease spirochete borrelia burgdorferi. | lysyl-trnas are essential for protein biosynthesis by ribosomal mrna translation in all organisms. they are synthesized by lysyl-trna synthetases (ec 6.1.1.6), a group of enzymes composed of two unrelated families. in bacteria and eukarya, all known lysyl-trna synthetases are subclass iic-type aminoacyl-trna synthetases, whereas some archaea have been shown to contain an unrelated class i-type lysyl-trna synthetase. examination of the preliminary genomic sequence of the bacterial pathogen borrel ... | 1997 | 9405621 |
| a mitochondrial-like chaperonin 60 gene in giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. | diplomonads, parabasalids, as represented by trichomonads, and microsporidia are three protist lineages lacking mitochondria that branch earlier than all other eukaryotes in small subunit rrna and elongation factor phylogenies. the absence of mitochondria and plastids in these organisms suggested that they diverged before the origin of these organelles. however, recent discoveries of mitochondrial-like heat shock protein 70 and/or chaperonin 60 (cpn60) genes in trichomonads and microsporidia imp ... | 1998 | 9419358 |
| a dnak homolog in myxococcus xanthus is involved in social motility and fruiting body formation. | myxococcus xanthus is a gram-negative soil bacterium which exhibits a complex life cycle and social behavior. in this study, two developmental mutants of m. xanthus were isolated through tn5 transposon mutagenesis. the mutants were found to be defective in cellular aggregation as well as in sporulation. further phenotypic characterization indicated that the mutants were defective in social motility but normal in directed cell movements. both mutations were cloned by a transposon-tagging method. ... | 1998 | 9440508 |
| in vitro assembly of a ribonucleoprotein particle corresponding to the platform domain of the 30s ribosomal subunit. | a fragment of the 16s rna of thermus thermophilus corresponding to the central domain (nucleotides 547-895) has been prepared by transcription in vitro. incubation of this fragment with the total 30s ribosomal proteins has resulted in the formation of a compact 12s ribonucleoprotein particle. this particle contained five t. thermophilus proteins corresponding to escherichia coli ribosomal proteins s6, s8, s11, s15, and possibly s18, all of which were previously shown to interact with the central ... | 1998 | 9448274 |
| host mutations (miaa and rpsl) reduce tetracycline resistance mediated by tet(o) and tet(m). | the effects of mutations in host genes on tetracycline resistance mediated by the tet(o) and tet(m) ribosomal protection proteins, which originated in campylobacter spp. and streptococcus spp., respectively, were investigated by using mutants of salmonella typhimurium and escherichia coli. the miaa, miab, and miaab double mutants of s. typhimurium specify enzymes for trna modification at the adenosine at position 37, adjacent to the anticodon in trna. in s. typhimurium, this involves biosynthesi ... | 1998 | 9449261 |
| thermostable repair enzyme for oxidative dna damage from extremely thermophilic bacterium, thermus thermophilus hb8. | the mutm (fpg) gene, which encodes a dna glycosylase that excises an oxidatively damaged form of guanine, was cloned from an extremely thermophilic bacterium, thermus thermophilus hb8. its nucleotide sequence encoded a 266 amino acid protein with a molecular mass of approximately 30 kda. its predicted amino acid sequence showed 42% identity with the escherichia coli protein. the amino acid residues cys, asn, gln and met, known to be chemically unstable at high temperatures, were decreased in num ... | 1998 | 9461446 |
| initiator-elongator discrimination in vertebrate trnas for protein synthesis. | initiator trnas are used exclusively for initiation of protein synthesis and not for the elongation step. we show, in vivo and in vitro, that the primary sequence feature that prevents the human initiator trna from acting in the elongation step is the nature of base pairs 50:64 and 51:63 in the tpsic stem of the initiator trna. various considerations suggest that this is due to sequence-dependent perturbation of the sugar phosphate backbone in the tpsic stem of initiator trna, which most likely ... | 1998 | 9488462 |
| genetic analysis of the nuo locus, which encodes the proton-translocating nadh dehydrogenase in escherichia coli. | complex i (ec 1.6.99.3) of the bacterium escherichia coli is considered to be the minimal form of the type i nadh dehydrogenase, the first enzyme complex in the respiratory chain. because of its small size and relative simplicity, the e. coli enzyme has become a model used to identify and characterize the mechanism(s) by which cells regulate the synthesis and assembly of this large respiratory complex. to begin dissecting the processes by which e. coli cells regulate the expression of nuo and th ... | 1998 | 9495756 |
| specific peptide-activated proteolytic cleavage of escherichia coli elongation factor tu. | phage exclusion is a form of programmed cell death in prokaryotes in which death is triggered by infection with phage, a seemingly altruistic response that limits multiplication of the phage and its spread through the population. one of the best-characterized examples of phage exclusion is the exclusion of t-even phages such as t4 by the e14-encoded lit protein in many escherichia coli k-12 strains. in this exclusion system, transcription and translation of a short region of the major head coat ... | 1998 | 9501186 |
| method for reduction of inhibition in a mycobacterium tuberculosis-specific ligase chain reaction dna amplification assay. | the present study describes the identification of inhibitors of a mycobacterium tuberculosis-specific gap ligase chain reaction (lcr) dna amplification assay as well as a method for their removal. a major contributor to inhibition was deduced to be a calcium phosphate precipitate, cahpo4. the precipitate forms during n-acetyl-l-cysteine-sodium hydroxide (nalc-naoh) decontamination, digestion, and concentration of respiratory specimens. the solubility product of cahpo4 precipitate at ph 7.8, the ... | 1998 | 9508309 |
| intra-assay performance characteristics of five assays for quantification of human immunodeficiency virus type 1 rna in plasma. | three kits (roche amplicor human immunodeficiency virus type 1 [hiv-1] monitor, chiron enhanced-sensitivity bdna, and organon teknika nasba hiv-1 qt) and two in-house assays (from national genetics institute and baylor college of medicine) were compared with a blinded panel. the results were evaluated as to intra-assay sensitivity, precision, and ability to detect differences in a dilution series. | 1998 | 9508327 |
| balance between endogenous superoxide stress and antioxidant defenses. | cells devoid of cytosolic superoxide dismutase (sod) suffer enzyme inactivation, growth deficiencies, and dna damage. it has been proposed that the scant superoxide (o2-) generated by aerobic metabolism harms even cells that contain abundant sod. however, this idea has been difficult to test. to determine the amount of o2- that is needed to cause these defects, we modulated the o2- concentration inside escherichia coli by controlling the expression of sod. an increase in o2- of more than twofold ... | 1998 | 9515906 |
| the s-layer proteins of two bacillus stearothermophilus wild-type strains are bound via their n-terminal region to a secondary cell wall polymer of identical chemical composition. | two bacillus stearothermophilus wild-type strains were investigated regarding a common recognition and binding mechanism between the s-layer protein and the underlying cell envelope layer. the s-layer protein from b. stearothermophilus pv72/p6 has a molecular weight of 130,000 and assembles into a hexagonally ordered lattice. the s-layer from b. stearothermophilus atcc 12980 shows oblique lattice symmetry and is composed of subunits with a molecular weight of 122,000. immunoblotting, peptide map ... | 1998 | 9515918 |
| analysis of hepatitis c virus-inoculated chimpanzees reveals unexpected clinical profiles. | the clinical course of hepatitis c virus (hcv) infections in a chimpanzee cohort was examined to better characterize the outcome of this valuable animal model. results of a cross-sectional study revealed that a low percentage (39%) of hcv-inoculated chimpanzees were viremic based on reverse transcription (rt-pcr) analysis. a correlation was observed between viremia and the presence of anti-hcv antibodies. the pattern of antibodies was dissimilar among viremic chimpanzees and chimpanzees that cle ... | 1998 | 9525575 |
| serial increase in the thermal stability of 3-isopropylmalate dehydrogenase from bacillus subtilis by experimental evolution. | we improved the thermal stability of 3-isopropylmalate dehydrogenase from bacillus subtilis by an in vivo evolutionary technique using an extreme thermophile, thermus thermophilus, as a host cell. the leub gene encoding b. subtilis 3-isopropylmalate dehydrogenase was integrated into the chromosome of a leub-deficient strain of t. thermophilus. the resulting transformant showed a leucine-autotrophy at 56 degrees c but not at 61 degrees c and above. phenotypically thermostabilized strains that can ... | 1998 | 9541402 |
| expression and regulation of the sodf gene encoding iron- and zinc-containing superoxide dismutase in streptomyces coelicolor müller. | streptomyces coelicolor müller contains two superoxide dismutases (sods), nickel-containing (nisod) and iron- and zinc-containing sod (feznsod). the sodf gene encoding feznsod was isolated by using pcr primers corresponding to the n-terminal peptide sequence of the purified feznsod and a c-terminal region conserved among known fesods and mnsods. the deduced amino acid sequence exhibited highest similarity to mn- and fesods from propionibacterium shermanii and mycobacterium spp. the transcription ... | 1998 | 9555880 |
| truncation of peptide deformylase reduces the growth rate and stabilizes solvent production in clostridium beijerinckii ncimb 8052. | the wild-type strain of clostridium beijerinckii ncimb 8052 tends to degenerate (i.e., lose the ability to form solvents) after prolonged periods of laboratory culture. several tn1545 mutants of this organism showing enhanced long-term stability of solvent production were isolated. four of them harbor identical insertions within the fms (def) gene, which encodes peptide deformylase (pdf). the c. beijerinckii fms gene product contains four diagnostic residues involved in the zn2+ coordination and ... | 1998 | 9572951 |
| isolation of a periplasmic molecular chaperone-like protein of rhodobacter sphaeroides f. sp. denitrificans that is homologous to the dipeptide transport protein dppa of escherichia coli. | a periplasmic protein has been found to prevent aggregation of the acid-unfolded dimethyl sulfoxide reductase (dmsor), the periplasmic terminal reductase of dimethyl sulfoxide respiration in the phototroph rhodobacter sphaeroides f. sp. denitrificans, in a manner similar to that of the escherichia coli chaperonin groel (matsuzaki et al., plant cell physiol. 37:333-339, 1996). the protein was isolated from the periplasm of the phototroph. it had a molecular mass of 58 kda and had no subunits. the ... | 1998 | 9573158 |
| acquired thermotolerance and temperature-induced protein accumulation in the extremely thermophilic bacterium rhodothermus obamensis. | temperature-induced changes in thermotolerance and protein composition were examined in heat-shocked cells and high-temperature-grown cells of the extremely thermophilic bacterium rhodothermus obamensis. the survival at temperatures superoptimal for growth (90 and 95 degrees c) was enhanced in both heat-shocked cells and high-temperature-grown cells relative to that of cells grown at optimal temperatures. in a comparison of protein composition using two-dimensional gel electrophoresis, putative ... | 1998 | 9573167 |
| control of 5',5'-dinucleoside triphosphate catabolism by aph1, a saccharomyces cerevisiae analog of human fhit. | the putative human tumor suppressor gene fhit (fragile histidine triad) (m. ohta et al., cell 84:587-597, 1996) encodes a protein behaving in vitro as a dinucleoside 5',5"'-p1,p3-triphosphate (ap3a) hydrolase. in this report, we show that the saccharomyces cerevisiae aph1 gene product, which resembles human fhit protein, also hydrolyzes dinucleoside 5',5'-polyphosphates, with ap3a being the preferred substrate. accordingly, disruption of the aph1 gene produced viable s. cerevisiae cells containi ... | 1998 | 9573184 |
| the crystal structure of asparaginyl-trna synthetase from thermus thermophilus and its complexes with atp and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid. | the crystal structure of thermus thermophilus asparaginyl-trna synthetase has been solved by multiple isomorphous replacement and refined at 2.6 a resolution. this is the last of the three class iib aminoacyl-trna synthetase structures to be determined. as expected from primary sequence comparisons, there are remarkable similarities between the tertiary structures of asparaginyl-trna synthetase and aspartyl-trna synthetase, and most of the active site residues are identical except for three key ... | 1998 | 9582288 |
| visualization of elongation factor g on the escherichia coli 70s ribosome: the mechanism of translocation. | during protein synthesis, elongation factor g (ef-g) binds to the ribosome and promotes the step of translocation, a process in which trna moves from the a to the p site of the ribosome and the mrna is advanced by one codon. by using three-dimensional cryo-electron microscopy, we have visualized ef-g in a ribosome-ef-g-gdp-fusidic acid complex. fitting the crystal structure of ef-g-gdp into the cryo density map reveals a large conformational change mainly associated with domain iv, the domain th ... | 1998 | 9600930 |
| genes for 2,4,5-trichlorophenoxyacetic acid metabolism in burkholderia cepacia ac1100: characterization of the tftc and tftd genes and locations of the tft operons on multiple replicons. | burkholderia cepacia ac1100 uses the chlorinated aromatic compound 2, 4,5-trichlorophenoxyacetic acid (2,4,5-t) as a sole source of carbon and energy. the enzyme which converts the first intermediate in the pathway, 2,4,5-trichlorophenol, to 5-chlorohydroquinone has been purified and consists of two subunits of 58 and 22 kda, encoded by the tftc and tftd genes (48). a degenerate primer was designed from the n terminus of the 58-kda polypeptide and used to isolate a clone containing the tftc and ... | 1998 | 9603818 |
| structure of the beta-galactosidase gene from thermus sp. strain t2: expression in escherichia coli and purification in a single step of an active fusion protein. | the nucleotide sequence of both the bgaa gene, coding for a thermostable beta-galactosidase of thermus sp. strain t2, and its flanking regions was determined. the deduced amino acid sequence of the enzyme predicts a polypeptide of 645 amino acids (mr, 73,595). comparative analysis of the open reading frames located in the flanking regions of the bgaa gene revealed that they might encode proteins involved in the transport and hydrolysis of sugars. the observed homology between the deduced amino a ... | 1998 | 9603833 |
| posttranscriptional modifications in 16s and 23s rrnas of the archaeal hyperthermophile sulfolobus solfataricus. | posttranscriptional modification is common to many types of rna, but the majority of information concerning structure and function of modification is derived principally from trna. by contrast, less is known about modification in rrna in spite of accumulating evidence for its direct participation in translation. the structural identities and approximate molar levels of modifications have been established for 16s and 23s rrnas of the archaeal hyperthermophile sulfolobus solfactaricus by using com ... | 1998 | 9603876 |
| secondary absence of mitochondria in giardia lamblia and trichomonas vaginalis revealed by valyl-trna synthetase phylogeny. | nuclear-coded valyl-trna synthetase (valrs) of eukaryotes is regarded of mitochondrial origin. complete valrs sequences obtained by us from two amitochondriate protists, the diplomonad, giardia lamblia and the parabasalid, trichomonas vaginalis were of the eukaryotic type, strongly suggesting an identical history of valrs in all eukaryotes studied so far. the findings indicate that diplomonads are secondarily amitochondriate and give further evidence for such conclusion reached recently concerni ... | 1998 | 9618503 |
| evaluation of a commercially available reverse transcription-pcr assay for diagnosis of enteroviral infection in archival and prospectively collected cerebrospinal fluid specimens. | a commercially available reverse transcription (rt)-pcr method (amplicor ev; roche diagnostic systems, inc., branchburg, n.j.) was evaluated for detection of enteroviruses in cerebrospinal fluid from patients with neurological disease. this assay was compared with virus isolation in cell culture and an in-house rt-pcr method designed with a nonoverlapping region of the enteroviral genome. a panel of 200 cerebrospinal fluid specimens prospectively collected from patients with a wide variety of ne ... | 1998 | 9620411 |
| anaerobic growth, a property horizontally transferred by an hfr-like mechanism among extreme thermophiles. | despite the fact that the extreme thermophilic bacteria belonging to the genus thermus are classified as strict aerobes, we have shown that thermus thermophilus hb8 (atcc 27634) can grow anaerobically when nitrate is present in the growth medium. this strain-specific property is encoded by a respiratory nitrate reductase gene cluster (nar) whose expression is induced by anoxia and nitrate (s. ramírez-arcos, l. a. fernández-herrero, and j. berenguer, biochim. biophys. acta, 1396:215-1997). we sho ... | 1998 | 9620963 |
| an autonomously replicating transforming vector for sulfolobus solfataricus. | a plasmid able to transform and to be stably maintained both in sulfolobus solfataricus and in escherichia coli was constructed by insertion into an e. coli plasmid of the autonomously replicating sequence of the virus particle ssv1 and a suitable mutant of the hph (hygromycin phosphotransferase) gene as the transformation marker. the vector suffered no rearrangement and/or chromosome integration, and its copy number in sulfolobus was increased by exposure of the cells to mitomycin c. | 1998 | 9620978 |
| identification of the gene encoding the tryptophan synthase beta-subunit from chlamydomonas reinhardtii. | we report the isolation of a chlamydomonas reinhardtii cdna that encodes the beta-subunit of tryptophan synthase (tsb). this cdna was cloned by functional complementation of a trp-operon-deleted strain of escherichia coli. hybridization analysis indicated that the gene exists in a single copy. the predicted amino acid sequence showed the greatest identity to tsb polypeptides from other photosynthetic organisms. with the goal of identifying mutations in the gene encoding this enzyme, we isolated ... | 1998 | 9625698 |
| immunological and molecular characterization of three variant subtype p1.14 strains of neisseria meningitidis. | epidemic outbreaks of group b meningococcal disease exhibit a clonal nature consisting of a common serotype-subtype. subtype-specific monoclonal antibodies (mabs) directed toward two variable regions (vr1 and vr2) of the class 1 protein of neisseria meningitidis are used in this classification scheme. a new mab was developed to classify a nonsubtypeable (nst) strain of n. meningitidis, 7967. this mab bound to both the nst strain and the prototype subtype p1. 14 strain, s3446, by dot blot analysi ... | 1998 | 9632588 |
| adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. | 3-isopropylmalate dehydrogenase (ipmdh, e.c. 1.1.1.85) from the thermophilic bacterium thermus thermophilus hb8 is homologous to ipmdh from the mesophilic escherichia coli, but has an approximately 17 degreesc higher melting temperature. its temperature optimum is 22-25 degreesc higher than that of the e. coli enzyme; however, it is hardly active at room temperature. the increased conformational rigidity required to stabilize the thermophilic enzyme against heat denaturation might explain its di ... | 1998 | 9636162 |
| does disparate occurrence of autoregulatory programmed frameshifting in decoding the release factor 2 gene reflect an ancient origin with loss in independent lineages? | in escherichia coli an autoregulatory mechanism of programmed ribosomal frameshifting governs the level of polypeptide chain release factor 2. from an analysis of 20 sequences of genes encoding release factor 2, we infer that this frameshift mechanism was present in a common ancestor of a large group of bacteria and has subsequently been lost in three independent lineages. | 1998 | 9642202 |
| thermotoga neapolitana homotetrameric xylose isomerase is expressed as a catalytically active and thermostable dimer in escherichia coli. | the xyla gene from thermotoga neapolitana 5068 was expressed in escherichia coli. gel filtration chromatography showed that the recombinant enzyme was both a homodimer and a homotetramer, with the dimer being the more abundant form. the purified native enzyme, however, has been shown to be exclusively tetrameric. the two enzyme forms had comparable stabilities when they were thermoinactivated at 95 degrees c. differential scanning calorimetry revealed thermal transitions at 99 and 109.5 degrees ... | 1998 | 9647799 |
| solution structure of the cytohesin-1 (b2-1) sec7 domain and its interaction with the gtpase adp ribosylation factor 1. | cytohesin-1 (b2-1) is a guanine nucleotide exchange factor for human adp ribosylation factor (arf) gtpases, which are important for vesicular protein trafficking and coatamer assembly in the cell. cytohesin-1 also has been reported to promote cellular adhesion via binding to the beta2 integrin cytoplasmic domain. the solution structure of the sec7 domain of cytohesin-1, which is responsible for both the protein's guanine nucleotide exchange factor function and beta2 integrin binding, was determi ... | 1998 | 9653114 |
| single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons. | prokaryotic translational release factors, rf1 and rf2, catalyze polypeptide release at uag/uaa and uga/uaa stop codons, respectively. in this study, we isolated a bacterial rf2 mutant (rf2*) containing an e167k substitution that restored the growth of a temperature-sensitive rf1 strain of escherichia coli and the viability of a chromosomal rf1/rf2 double knockout. in both in vivo and in vitro polypeptide termination assays, rf2* catalyzed uag/uaa termination, as does rf1, as well as uga termina ... | 1998 | 9653158 |
| diversity of cytochrome bc complexes: example of the rieske protein in green sulfur bacteria. | the rieske 2fe2s cluster of chlorobium limicola forma thiosulfatophilum strain tassajara was studied by electron paramagnetic resonance spectroscopy. two distinct orientations of its g tensor were observed in oriented samples corresponding to differing conformations of the protein. only one of the two conformations persisted after treatment with 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone. a redox midpoint potential (em) of +160 mv in the ph range of 6 to 7.7 and a decreasing em (-60 to -80 ... | 1998 | 9658021 |
| influence of the secondary cell wall polymer on the reassembly, recrystallization, and stability properties of the s-layer protein from bacillus stearothermophilus pv72/p2. | the high-molecular-weight secondary cell wall polymer (scwp) from bacillus stearothermophilus pv72/p2 is mainly composed of n-acetylglucosamine (glcnac) and n-acetylmannosamine (mannac) and is involved in anchoring the s-layer protein via its n-terminal region to the rigid cell wall layer. in addition to this binding function, the scwp was found to inhibit the formation of self-assembly products during dialysis of the guanidine hydrochloride (ghcl)-extracted s-layer protein. the degree of assemb ... | 1998 | 9696762 |
| multicenter evaluation of the amplicor enterovirus pcr test with cerebrospinal fluid from patients with aseptic meningitis. the european union concerted action on viral meningitis and encephalitis. | the amplicor enterovirus pcr test was compared with viral culture for the detection of enteroviruses in cerebrospinal fluid (csf) specimens. in a multicenter study in which nine laboratories participated, a total of 476 csf specimens were collected from patients with suspected aseptic meningitis. sixty-eight samples were positive by pcr (14.4%), whereas 49 samples were positive by culture (10.4%), demonstrating that the amplicor enterovirus pcr test was significantly more sensitive than culture ... | 1998 | 9705409 |
| domain organization and functional analysis of thermus thermophilus muts protein. | muts protein binds to dna and specifically recognizes mismatched or small looped out heteroduplex dna. in order to elucidate its structure-function relationships, the domain structure of thermus thermophilus muts protein was studied by performing denaturation experiments and limited proteolysis. the former suggested that t. thermophilus muts consists of at least three domains with estimated stabilities of 12.3, 22.9 and 30.7 kcal/mol and the latter revealed that it consists of four domains: a1 ( ... | 1998 | 9722634 |
| fidelity of dna ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides. | complete libraries of oligonucleotides were used as substrates for thermus thermophilus dna ligase, on a m13mp18 ssdna template. a 17mer primer was used to start a polymerisation process. ladders of ligation products were analysed by gel electrophoresis. octa-, nona- and decanucleotide libraries were compared. nonanucleotides were optimum for polymerisation and up to 15 monomers were ligated. the fidelity of incorporation was studied by sequencing 28 clones (2268 bases) of nonanucleotide polymer ... | 1998 | 9722647 |
| linkage map of escherichia coli k-12, edition 10: the traditional map. | this map is an update of the edition 9 map by berlyn et al. (m. k. b. berlyn, k. b. low, and k. e. rudd, p. 1715-1902, in f. c. neidhardt et al., ed., escherichia coli and salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). it uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. the latter are included as ... | 1998 | 9729611 |
| a natural large chromosomal inversion in lactococcus lactis is mediated by homologous recombination between two insertion sequences. | comparative analysis of chromosomal macrorestriction polymorphism of the two closely related lactococcus lactis subsp. cremoris strains mg1363 and ncdo763 revealed the presence of a large inversion covering half of the genome. to determine what kind of genetic element could be implicated in this rearrangement, the two inversion junctions of mg1363 and ncdo763 chromosomes were cloned and characterized. nucleotide sequence analysis showed the presence of one copy of the lactococcal is905 element i ... | 1998 | 9733685 |
| creation of genetic information by dna polymerase of the thermophilic bacterium thermus thermophilus. | genetic information encoded in a template of a genome is replicated in a complementary way by dna polymerase or rna polymerase with high fidelity; no creation of information occurs in this reaction unless an error occurs. we report here that dna polymerase of the thermophilic bacterium thermus thermophilus can synthesize up to 200 kb linear double-stranded dna in vitro in the complete absence of added primer and template dnas, indicating that genetic information is actively created by protein. t ... | 1998 | 9753734 |
| translation elongation factor 2 is part of the target for a new family of antifungals. | translation elongation factor 2 (ef2), which in saccharomyces cerevisiae is expressed from the eft1 and eft2 genes, has been found to be targeted by a new family of highly specific antifungal compounds derived from the natural product sordarin. two complementation groups of mutants resistant to the semisynthetic sordarin derivative gm193663 were found. the major one (21 members) consisted of isolates with mutations on eft2. the minor one (four isolates) is currently being characterized but it is ... | 1998 | 9756779 |
| effects of temperature, salinity, and medium composition on compatible solute accumulation by thermococcus spp | the effects of salinity and growth temperature on the accumulation of intracellular organic solutes were examined by nuclear magnetic resonance spectroscopy (nmr) in thermococcus litoralis, thermococcus celer, thermococcus stetteri, and thermococcus zilligii (strain an1). in addition, the effects of growth stage and composition of the medium were studied in t. litoralis. a novel compound identified as beta-galactopyranosyl-5-hydroxylysine was detected in t. litoralis grown on peptone-containing ... | 1998 | 9758772 |
| capacity of nine thermostable dna polymerases to mediate dna amplification in the presence of pcr-inhibiting samples. | the pcr is an extremely powerful method for detecting microorganisms. however, its full potential as a rapid detection method is limited by the inhibition of the thermostable dna polymerase from thermus aquaticus by many components found in complex biological samples. in this study, we have compared the effects of known pcr-inhibiting samples on nine thermostable dna polymerases. samples of blood, cheese, feces, and meat, as well as various ions, were added to pcr mixtures containing various the ... | 1998 | 9758794 |
| enhancement of the amplicor enterovirus pcr test with a coprecipitant. | the incorporation of a commercially available coprecipitant into the amplicor enterovirus pcr test specimen preparation enhanced the sensitivity and reproducibility of this assay. fifty-five previously tested archived cerebrospinal fluids (csf) specimens were tested in a blind study in duplicate with and without pellet paint coprecipitant (novagen, inc., madison, wis.). of these specimens, 26 had previously been determined to be positive and 29 had previously been determined to be negative. all ... | 1998 | 9774607 |
| lactone-ring-cleaving enzyme: genetic analysis, novel rna editing, and evolutionary implications. | a lactonohydrolase from fusarium oxysporum aku 3702 is an enzyme catalyzing the hydrolysis of aldonate lactones to the corresponding aldonic acids. the amino acid sequences of the nh2 terminus and internal peptide fragments of the enzyme were determined to prepare synthetic oligonucleotides as primers for the pcr. an approximate 1, 000-base genomic dna fragment thus amplified was used as the probe to clone both genomic dna and cdna for the enzyme. the lactonohydrolase genomic gene consists of si ... | 1998 | 9788992 |
| thermus thermophilus: a link in evolution of the trna-dependent amino acid amidation pathways. | thermus thermophilus possesses an aspartyl-trna synthetase (asprs2) able to aspartylate efficiently trnaasp and trnaasn. aspartate mischarged on trnaasn then is converted into asparagine by an omega amidase that differs structurally from all known asparagine synthetases. however, aspartate is not misincorporated into proteins because the binding capacity of aminoacylated trnaasn to elongation factor tu is only conferred by conversion of aspartate into asparagine. t. thermophilus additionally con ... | 1998 | 9789000 |
| glutamyl-trna(gln) amidotransferase in deinococcus radiodurans may be confined to asparagine biosynthesis. | asparaginyl-trna (asn-trna) and glutaminyl-trna (gln-trna) are essential components of protein synthesis. they can be formed by direct acylation by asparaginyl-trna synthetase (asnrs) or glutaminyl-trna synthetase (glnrs). the alternative route involves transamidation of incorrectly charged trna. examination of the preliminary genomic sequence of the radiation-resistant bacterium deinococcus radiodurans suggests the presence of both direct and indirect routes of asn-trna and gln-trna formation. ... | 1998 | 9789001 |
| oxygen-insensitive nitroreductases: analysis of the roles of nfsa and nfsb in development of resistance to 5-nitrofuran derivatives in escherichia coli. | nitroheterocyclic and nitroaromatic compounds constitute an enormous range of chemicals whose potent biological activity has significant human health and environmental implications. the biological activity of nitro-substituted compounds is derived from reductive metabolism of the nitro moiety, a process catalyzed by a variety of nitroreductase activities. resistance of bacteria to nitro-substituted compounds is believed to result primarily from mutations in genes encoding oxygen-insensitive nitr ... | 1998 | 9791100 |
| construction of a proline-producing mutant of the extremely thermophilic eubacterium thermus thermophilus hb27. | growth of thermus thermophilus hb27 was inhibited by a proline analog, 3,4-dehydroproline (dhp). this result suggested that the gamma-glutamyl kinase (the product of the prob gene) was inhibited by feedback inhibition in t. thermophilus. dhp-resistant mutants were reported previously for escherichia coli (a. m. dandekar and s. l. uratsu, j. bacteriol. 170:5943-5945, 1988) and serratia marcescens (k. omori, s. suzuki, y. imai, and s. komatsubara, j. gen. microbiol. 138:693-699, 1992), and their m ... | 1998 | 9797285 |
| gene cloning and characterization of recombinant rnase hii from a hyperthermophilic archaeon. | we have cloned the gene encoding rnase hii (rnase hiipk) from the hyperthermophilic archaeon pyrococcus kodakaraensis kod1 by screening of a library for clones that suppressed the temperature-sensitive growth phenotype of an rnh mutant strain of escherichia coli. this gene was expressed in an rnh mutant strain of e. coli, the recombinant enzyme was purified, and its biochemical properties were compared with those of e. coli rnases hi and hii. rnase hiipk is composed of 228 amino acid residues (m ... | 1998 | 9829929 |
| the bacillus subtilis nucleotidyltransferase is a trna cca-adding enzyme. | there has been increased interest in bacterial polyadenylation with the recent demonstration that 3' poly(a) tails are involved in rna degradation. poly(a) polymerase i (pap i) of escherichia coli is a member of the nucleotidyltransferase (ntr) family that includes the functionally related trna cca-adding enzymes. thirty members of the ntr family were detected in a search of the current database of eubacterial genomic sequences. gram-negative organisms from the beta and gamma subdivisions of the ... | 1998 | 9829937 |
| nadp-isocitrate dehydrogenase from pseudomonas nautica: kinetic constant determination and carbon limitation effects on the pool of intracellular substrates. | variations of intracellular concentrations of isocitrate and nadp+ were measured throughout all growth phases of the marine bacterium pseudomonas nautica. the intracellular isocitrate concentration tracked the intracellular protein concentration throughout all phases of growth. it rapidly increased in early exponential phase to a maximum and fell to nearly zero in parallel with pyruvate exhaustion in the culture medium. the intracellular nadp+ and protein concentrations increased in parallel dur ... | 1998 | 9835589 |
| inorganic cation transport and energy transduction in enterococcus hirae and other streptococci. | energy metabolism by bacteria is well understood from the chemiosmotic viewpoint. we know that bacteria extrude protons across the plasma membrane, establishing an electrochemical potential that provides the driving force for various kinds of physiological work. among these are the uptake of sugars, amino acids, and other nutrients with the aid of secondary porters and the regulation of the cytoplasmic ph and of the cytoplasmic concentration of potassium and other ions. bacteria live in diverse ... | 1998 | 9841664 |
| posttranscriptional control of gene expression in yeast. | studies of the budding yeast saccharomyces cerevisiae have greatly advanced our understanding of the posttranscriptional steps of eukaryotic gene expression. given the wide range of experimental tools applicable to s. cerevisiae and the recent determination of its complete genomic sequence, many of the key challenges of the posttranscriptional control field can be tackled particularly effectively by using this organism. this article reviews the current knowledge of the cellular components and me ... | 1998 | 9841679 |
| tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from heliobacillus mobilis. | a dna sequence has been obtained for a 35.6-kb genomic segment from heliobacillus mobilis that contains a major cluster of photosynthesis genes. a total of 30 orfs were identified, 20 of which encode enzymes for bacteriochlorophyll and carotenoid biosynthesis, reaction-center (rc) apoprotein, and cytochromes for cyclic electron transport. donor side electron-transfer components to the rc include a putative rc-associated cytochrome c553 and a unique four-large-subunit cytochrome bc complex consis ... | 1998 | 9843979 |
| the genome of melanoplus sanguinipes entomopoxvirus. | the family poxviridae contains two subfamilies: the entomopoxvirinae (poxviruses of insects) and the chordopoxvirinae (poxviruses of vertebrates). here we present the first characterization of the genome of an entomopoxvirus (epv) which infects the north american migratory grasshopper melanoplus sanguinipes and other important orthopteran pests. the 236-kbp m. sanguinipes epv (msepv) genome consists of a central coding region bounded by 7-kbp inverted terminal repeats and contains 267 open readi ... | 1999 | 9847359 |
| a novel, rapid in cell rna amplification technique for the detection of low copy mrna transcripts. | growing interest now focuses on improvements of in situ polymerase chain reaction (pcr) technology for the detection of dna and rna cellular sequences. in this study, reverse transcription pcr in situ hybridisation (rt pcr-ish) was developed and used to determine gene expression of pyruvate dehydrogenase in a cell model system, using human peripheral blood lymphocytes (pbls). the success of in cell rna amplification depends on the type of cell/tissue fixation, cell permeabilisation, and the effi ... | 1998 | 9850340 |
| campylobacter fetus surface layer proteins are transported by a type i secretion system. | the virulence of campylobacter fetus, a bacterial pathogen of ungulates and humans, is mediated in part by the presence of a paracrystalline surface layer (s-layer) that confers serum resistance. the subunits of the s-layer are s-layer proteins (slps) that are secreted in the absence of an n-terminal signal sequence and attach to either type a or b c. fetus lipopolysaccharide in a serospecific manner. antigenic variation of multiple slps (encoded by sapa homologs) of type a strain 23d occurs by ... | 1998 | 9851986 |
| identification of two binding domains, one for peptidoglycan and another for a secondary cell wall polymer, on the n-terminal part of the s-layer protein sbsb from bacillus stearothermophilus pv72/p2. | first studies on the structure-function relationship of the s-layer protein from b. stearothermophilus pv72/p2 revealed the coexistence of two binding domains on its n-terminal part, one for peptidoglycan and another for a secondary cell wall polymer (scwp). the peptidoglycan binding domain is located between amino acids 1 to 138 of the mature s-layer protein comprising a typical s-layer homologous domain. the scwp binding domain lies between amino acids 240 to 331 and possesses a high serine pl ... | 1998 | 9852032 |
| peptidoglycan fine structure of the radiotolerant bacterium deinococcus radiodurans sark. | peptidoglycan from deinococcus radiodurans was analyzed by high-performance liquid chromatography and mass spectrometry. the monomeric subunit was: n-acetylglucosamine-n-acetylmuramic acid-l-ala-d-glu-(gamma)-l-orn-[(delta)gly-gly]-d-ala-d-ala. cross-linkage was mediated by (gly)2 bridges, and glycan strands were terminated in (1-->6)anhydro-muramic acid residues. structural relations with the phylogenetically close thermus thermophilus are discussed. | 1999 | 9864347 |
| the alpha subunit of toluene dioxygenase from pseudomonas putida f1 can accept electrons from reduced ferredoxintol but is catalytically inactive in the absence of the beta subunit. | the oxygenase component of toluene dioxygenase from pseudomonas putida f1 is an iron-sulfur protein (isptol) consisting of alpha (todc1) and beta (todc2) subunits. purified todc1 gave absorbance and electron paramagnetic resonance spectra identical to those given by purified isptol. todc1 was reduced by nadh and catalytic amounts of reductasetol and ferredoxintol. reduced todc1 did not oxidize toluene, and catalysis was strictly dependent on the presence of purified todc2. | 1999 | 9872799 |
| characterization of functionally active subribosomal particles from thermus aquaticus. | peptidyl transferase activity of thermus aquaticus ribosomes is resistant to the removal of a significant number of ribosomal proteins by protease digestion, sds, and phenol extraction. to define the upper limit for the number of macromolecular components required for peptidyl transferase, particles obtained by extraction of t. aquaticus large ribosomal subunits were isolated and their rna and protein composition was characterized. active subribosomal particles contained both 23s and 5s rrna ass ... | 1999 | 9874776 |
| discontinuous occurrence of the hsp70 (dnak) gene among archaea and sequence features of hsp70 suggest a novel outlook on phylogenies inferred from this protein. | occurrence of the hsp70 (dnak) gene was investigated in various members of the domain archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria aquifex pyrophilus and thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16s rrna sequences. the gene was not detected in 8 of 10 archaea examined but was found in a. pyrophilus and t. maritima, from which it was cloned and sequenced. comparative analyses of the hsp70 amino aci ... | 1999 | 9882656 |