Publications

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
mismatch dna recognition protein from an extremely thermophilic bacterium, thermus thermophilus hb8.	the muts gene, implicated in dna mismatch repair, was cloned from an extremely thermophilic bacterium, thermus thermophilus hb8. its nucleotide sequence encoded a 819-amino acid protein with a molecular mass of 91.4 kda. its predicted amino acid sequence showed 56 and 39% homology with escherichia coli muts and human hmsh2 proteins, respectively. the t.thermophilus muts gene complemented the hypermutability of the e.coli muts mutant, suggesting that t.thermophilus muts protein was active in e.co ...	1996	8604304
antideterminants present in minihelix(sec) hinder its recognition by prokaryotic elongation factor tu.	during protein biosynthesis, all aminoacylated elongator trnas except selenocysteine-inserting trna sec form ternary complexes with activated elongation factor. trna sec is bound by its own translation factor, an elongation factor analogue, e.g. the selb factor in prokaryotes. an apparent reason for this discrimination could be related to the unusual length of trna sec amino acid-acceptor branch formed by 13 bp. however, it has been recently shown that an aspartylated minihelix of 13 bp derived ...	1996	8599948
the reca protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of recas and 16s rrnas from the same species.	the evolution of the reca protein was analyzed using molecular phylogenetic techniques. phylogenetic trees of all currently available complete reca proteins were inferred using multiple maximum parsimony and distance matrix methods. comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. the reca trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the alpha, ...	1995	8587109
inhibition of pcr by aqueous and vitreous fluids.	the detection of viral nucleic acids in intraocular fluids and tissues by pcr has become increasingly important in clinical ophthalmology. while much attention has been directed toward minimizing false-positive reactions resulting from specimen contamination or amplicor carryover, relatively little attention has been given to the causes of false-negative pcrs. this report describes a pcr inhibitor in normal aqueous and vitreous fluids that can produce false-negative pcr results. as little as 0.5 ...	1995	8567898
structural similarities in the noncatalytic domains of phenylalanyl-trna and biotin synthetases.	detailed comparison between the structures of the escherichia coli biotin synthetase/repressor protein (bira) and the recently solved thermus thermophilus phenylalanyl-trna synthetase (phers) reveals significant similarities outside their respective catalytic domains. these comprise a dna-binding alpha+beta domain and an src-homology 3 (sh3)-like domain that were observed in both enzymes. this similarity provides a novel example in which all domains of one multidomain protein appear to be consti ...	1995	8563641
further stabilization of 3-isopropylmalate dehydrogenase of an extreme thermophile, thermus thermophilus, by a suppressor mutation method.	we succeeded in further improvement of the stability of 3-isopropylmalate dehydrogenase (ipmdh) from an extreme thermophile, thermus thermophilus, by a suppressor mutation method. we previously constructed a chimeric ipmdh consisting of portions of thermophile and mesophile enzymes. the chimeric enzyme is less thermostable than the thermophile enzyme. the gene encoding the chimeric enzyme was subjected to random mutagenesis and integrated into the genome of a leub-deficient mutant of t. thermoph ...	1996	8550506
slpm, a gene coding for an "s-layer-like array" overexpressed in s-layer mutants of thermus thermophilus hb8.	s-layer deletion mutants of thermus thermophilus hb8 overproduce a regular array which surrounds groups of several cells. averages of two-dimensional projections revealed a detailed architecture similar in general morphology and unit cell dimensions to that of the s-layer but having a different mass distribution. the structural components of these "s-layer-like arrays" are a group of three proteins of 52 (p52), 50 (p50), and 36 (p36) kda, which are overexpressed in s-layer mutants. these three p ...	1996	8550453
the role of glutamate 87 in the kinetic mechanism of thermus thermophilus isopropylmalate dehydrogenase.	the kinetic mechanism of the oxidative decarboxylation of 2r,3s-isopropylmalate by the nad-dependent isopropylmalate dehydrogenase of thermus thermophilus was investigated. initial rate results typical of random or steady-state ordered sequential mechanisms are obtained for both the wild-type and two mutant enzymes (e87g and e87q) regardless of whether natural or alternative substrates (2r-malate, 2r,3s-tartrate and/or nadp) are utilized. initial rate data fail to converge on a rapid equilibrium ...	1995	8535253
footprinting of trna(phe) transcripts from thermus thermophilus hb8 with the homologous phenylalanyl-trna synthetase reveals a novel mode of interaction.	the phosphates of the trna(phe) transcript from thermus thermophilus interacting with the cognate synthetase were determined by footprinting. backbone bond protection against cleavage by iodine of the phosphorothioate-containing transcripts was found in the anticodon stem-loop, the d stem-loop and the acceptor stem and weak protection was also seen in the variable loop. most of the protected phosphates correspond to regions around known identity elements of trna(phe). enhancement of cleavage at ...	1995	8524648
comparison of the crystal structures of genetically engineered human manganese superoxide dismutase and manganese superoxide dismutase from thermus thermophilus: differences in dimer-dimer interaction.	the three-dimensional x-ray structure of a recombinant human mitochondrial manganese superoxide dismutase (mnsod) (chain length 198 residues) was determined by the method of molecular replacement using the related structure of mnsod from thermus thermophilus as a search model. this tetrameric human mnsod crystallizes in space group p2(1)2(1)2 with a dimer in the asymmetric unit (wagner, u.g., werber, m.m., beck, y., hartman, j.r., frolow, f., & sussman, j.l., 1989, j. mol. biol. 206, 787-788). r ...	1993	8495200
genomic restriction map of the extremely thermophilic bacterium thermus thermophilus hb8.	a physical map of the chromosome of the extremely thermophilic eubacterium thermus thermophilus hb8 has been constructed by using pulsed-field gel electrophoresis techniques. a total of 26 cleavage sites for the rarely cutting restriction endonucleases hpai, muni, and ndei were located on the genome. on the basis of the sizes of the restriction fragments generated, the genome size was estimated to be 1.74 mbp, which is significantly smaller than the chromosomes of escherichia coli and other meso ...	1993	8416889
detection of hepatitis c virus rna by a combined reverse transcription-polymerase chain reaction assay.	amplification of rna by the polymerase chain reaction (pcr) is normally a two-step process requiring separate enzymes and buffer conditions. we describe a combined reverse transcription-pcr (rt-pcr) assay for hepatitis c virus (hcv) rna amplification in which a single enzyme and buffer condition are used. in this assay, both the rt and pcr steps are carried out with the thermoactive dna polymerase of thermus thermophilus. a transcription vector containing hcv sequences has also been constructed ...	1993	8385151
cloning, sequencing, and expression in escherichia coli of the gene coding for phosphofructokinase in lactobacillus bulgaricus.	a fragment of 1,185 bp containing the gene coding for phosphofructokinase (atp:d-fructose-6-phosphate-1-phosphotransferase; ec 2.7.1.11) in lactobacillus bulgaricus has been cloned, sequenced, and expressed in escherichia coli. the amino acid sequence of this enzyme was homologous to those of the atp-dependent phosphofructokinases from e. coli, thermus thermophilus, spiroplasma citri, and bacillus stearothermophilus, suggesting that these enzymes have closely related structures despite their dif ...	1993	8366023
identification of the gene encoding the mitochondrial elongation factor g in mammals.	protein synthesis in cytosolic and rough endoplasmic reticulum associated ribosomes is directed by factors, many of which have been well characterized. although these factors have been the subject of intense study, most of the corresponding factors regulating protein synthesis in the mitochondrial ribosomes remain unknown. in this report we present the cloning and initial characterization of the gene encoding the rat mitochondrial elongation factor-g (ref-gmt). the rat gene encoding ef-gmt (rmef ...	1993	8332461
molecular cloning and sequence analysis of the crtb gene of thermus thermophilus hb27, an extreme thermophile producing carotenoid pigments.	we have cloned and sequenced a 1.5-kb chromosomal fragment of thermus thermophilus which promoted the overproduction of carotenoids in t. thermophilus. an open reading frame (orf-a) coding for a polypeptide with 289 amino acids was responsible for carotenoid overproduction. the putative orf-a protein showed significant homology with the amino acid sequences of crtb gene products (phytoene syntheses) of other microorganisms. the clone containing the orf-a on a multicopy plasmid produced about thr ...	1993	8215386
pullulanase of thermoanaerobacterium thermosulfurigenes em1 (clostridium thermosulfurogenes): molecular analysis of the gene, composite structure of the enzyme, and a common model for its attachment to the cell surface.	the complete pullulanase gene (amyb) from thermoanaerobacterium thermosulfurigenes em1 was cloned in escherichia coli, and the nucleotide sequence was determined. the reading frame of amyb consisted of 5,586 bp encoding an exceptionally large enzyme of 205,991 da. sequence analysis revealed a composite structure of the pullulanase consisting of catalytic and noncatalytic domains. the n-terminal half of the protein contained a leader peptide of 35 amino acid residues and the catalytic domain, whi ...	1994	8195085
effector region of the translation elongation factor ef-tu.gtp complex stabilizes an orthoester acid intermediate structure of aminoacyl-trna in a ternary complex.	trna(val) from escherichia coli was aminoacylated with [1-13c]valine and its complex with thermus thermophilus elongation factor ef-tu.gtp was analyzed by 13c nmr spectroscopy. the results suggest that the aminoacyl residue of the valyl-trna in ternary complex with bacterial ef-tu and gtp is not attached to trna by a regular ester bond to either a 2'- or 3'-hydroxyl group; instead, an intermediate orthoester acid structure with covalent linkage to both vicinal hydroxyls of the terminal adenosine ...	1994	8183898
overexpression of genes of an extreme thermophile thermus thermophilus, in escherichia coli cells.	the 3-isopropylmalate dehydrogenase gene from an extreme thermophile, thermus thermophilus, was not expressed in escherichia coli unless a palindromic structure around the ribosome binding site was eliminated or a leader open reading frame was introduced into the upstream flanking region of the gene. this report suggests a way to increase the expression of this gene, with a high g+c content, in e. coli.	1994	8169232
properties of the lysyl-trna synthetase gene and product from the extreme thermophile thermus thermophilus.	a dna region carrying lyss, the gene encoding the lysyl-trna synthetase, was cloned from the extreme thermophile prokaryote thermus thermophilus vk-1 and sequenced. the analysis indicated an open reading frame encoding a protein of 492 amino acids. this putative protein has significant homologies to previously sequenced lysyl-trna synthetases and displays the three motifs characteristic of class ii aminoacyl-trna synthetases. the t. thermophilus lyss gene was overexpressed in escherichia coli by ...	1994	8169220
crystal structure of the ribosomal protein s6 from thermus thermophilus.	the amino acid sequence and crystal structure of the ribosomal protein s6 from the small ribosomal subunit of thermus thermophilus have been determined. s6 is a small protein with 101 amino acid residues. the 3d structure, which was determined to 2.0 a resolution, consists of a four-stranded anti-parallel beta-sheet with two alpha-helices packed on one side. similar folding patterns have been observed for other ribosomal proteins and may suggest an original rna-interacting motif. related topolog ...	1994	8137808
domain structure of the acetogenium kivui surface layer revealed by electron crystallography and sequence analysis.	the three-dimensional structure of the acetogenium kivui surface layer (s-layer) has been determined to a resolution of 1.7 nm by electron crystallographic techniques. two independent reconstructions were made from layers negatively stained with uranyl acetate and na-phosphotungstate. the s-layer has p6 symmetry with a center-to-center spacing of approximately 19 nm. within the layer, six monomers combine to form a ring-shaped core surrounded by a fenestrated rim and six spokes that point toward ...	1994	8113161
three-dimensional structure of the ribosomal translocase: elongation factor g from thermus thermophilus.	the crystal structure of thermus thermophilus elongation factor g without guanine nucleotide was determined to 2.85 a. this gtpase has five domains with overall dimensions of 50 x 60 x 118 a. the gtp binding domain has a core common to other gtpases with a unique subdomain which probably functions as an intrinsic nucleotide exchange factor. domains i and ii are homologous to elongation factor tu and their arrangement, both with and without gdp, is more similar to elongation factor tu in complex ...	1994	8070397
the crystal structure of elongation factor g complexed with gdp, at 2.7 a resolution.	elongation factor g (ef-g) catalyzes the translocation step of protein synthesis in bacteria, and like the other bacterial elongation factor, ef-tu--whose structure is already known--it is a member of the gtpase superfamily. we have determined the crystal structure of ef-g--gdp from thermus thermophilus. it is an elongated molecule whose large, n-terminal domain resembles the g domain of ef-tu, except for a 90 residue insert, which covers a surface that is involved in nucleotide exchange in ef-t ...	1994	8070396
crystal structure of a prokaryotic aspartyl trna-synthetase.	the crystal structure of thermus thermophilus aspartyl trna-synthetase (asprs) refined at 2.5 a resolution is described. this molecular structure is a textbook illustration of the modular organization of aminoacyl-trna synthetases. in addition to the three domains found in yeast asprs, each monomer exhibits a module specific to prokaryotic enzymes, which corresponds to a helix-turn-helix motif in yeast asprs, a domain implicated in the stabilization of the complex with trna. its topology matches ...	1994	8045252
a structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.	we propose that arginine side chains often play a previously unappreciated general structural role in the maintenance of tertiary structure in proteins, wherein the positively charged guanidinium group forms multiple hydrogen bonds to backbone carbonyl oxygens. using as a criterion for a "structural" arginine one that forms 4 or more hydrogen bonds to 3 or more backbone carbonyl oxygens, we have used molecular graphics to locate arginines of interest in 4 proteins: arg 180 in thermus thermophilu ...	1994	8003972
characterization of the thermus thermophilus locus encoding peptide deformylase and methionyl-trna(fmet) formyltransferase.	an escherichia coli strain with thermosensitive expression of the gene encoding peptide deformylase (fms) has been constructed. at nonpermissive temperatures, this strain fails to grow. the essential character of the fms gene was further used to clone by heterologous complementation the locus corresponding to thermus thermophilus peptide deformylase. the cloned fragment also carries the methionyl-trna(fmet) formyltransferase gene (fmt). it is located immediately downstream from the fms gene, as ...	1994	7961514
pulvomycin-resistant mutants of e.coli elongation factor tu.	this paper reports the generation of escherichia coli mutants resistant to pulvomycin. together with targeted mutagenesis of the tufa gene, conditions were found to overcome membrane impermeability, thereby allowing the selection of three mutants harbouring elongation factor (ef)-tu arg230-->cys, arg333-->cys or thr334-->ala which confer pulvomycin resistance. these mutations are clustered in the three-domain junction interface of the crystal structure of the gtp form of thermus thermophilus ef- ...	1994	7957075
crystal structure of inorganic pyrophosphatase from thermus thermophilus.	the 3-dimensional structure of inorganic pyrophosphatase from thermus thermophilus (t-ppase) has been determined by x-ray diffraction at 2.0 a resolution and refined to r = 15.3%. the structure consists of an antiparallel closed beta-sheet and 2 alpha-helices and resembles that of the yeast enzyme in spite of the large difference in size (174 and 286 residues, respectively), little sequence similarity beyond the active center (about 20%), and different oligomeric organization (hexameric and dime ...	1994	7920256
phosphorylation of ctp synthetase from saccharomyces cerevisiae by protein kinase c.	phosphorylation of ctp synthetase (ec 6.3.4.2, utp:ammonia ligase (adp-forming)) from saccharomyces cerevisiae protein kinase c was examined. using pure ctp by synthetase as a substrate, protein kinase c activity was dose- and time-dependent and required calcium, diacylglycerol, and phosphatidylserine for full activation. protein kinase c activity was also dependent on the concentration of ctp synthetase. protein kinase c phosphorylated ctp synthetase on serine and threonine residues in vitro wh ...	1995	7797479
genetic and molecular analysis of the trna-tufb operon of the myxobacterium stigmatella aurantiaca.	the tufb gene, encoding elongation factor tu (ef-tu), from the myxobacterium stigmatella aurantiaca was cloned and sequenced. it is preceded by four trna genes, the first ever described in myxobacteria. the trna synthesized from these genes and the general organization of the locus seem identical to that of escherichia coli, but differences of potential importance were found in the trna sequences and in the intergenic regions. the primary structure of ef-tu was deduced from the tufb dna sequence ...	1995	7784178
modeling substrate binding in thermus thermophilus isopropylmalate dehydrogenase.	the thermus thermophilus 3-isopropylmalate dehydrogenase (ipmdh) and escherichia coli isocitrate dehydrogenase (icdh) are two functionally and evolutionarily related enzymes with distinct substrate specificities. to understand the determinants of substrate specificities of the two proteins, the substrate and coenzyme in ipmdh were docked into their respective binding sites based on the published structure for apo ipmdh and its sequence and structural homology to icdh. this modeling study suggest ...	1995	7773180
sulredoxin: a novel iron-sulfur protein of the thermoacidophilic archaeon sulfolobus sp. strain 7 with a rieske-type [2fe-2s] center.	a novel pink [2fe-2s] protein has been purified from the cytosol fraction of the thermoacidophilic archaeon sulfolobus sp. strain 7 (originally named sulfolobus acidocaldarius 7) and called "sulredoxin." its absorption, circular dichroism, and electron paramagnetic resonance spectra suggest the presence of a rieske-type [2fe-2s] cluster (g-factors of 2.01, 1.91, and 1.79; average g-factor [gav] = 1.90) which is remarkably similar to that of thermus thermophilus respiratory rieske fes protein (j. ...	1995	7730295
sequence of trna(asp) from thermus thermophilus hb8.		1993	7692402
structure of peptidoglycan from thermus thermophilus hb8.	the composition and structure of peptidoglycan (murein) extracted from the extreme thermophilic eubacterium thermus thermophilus hb8 are presented. the structure of 29 muropeptides, accounting for more than 85% of total murein, is reported. the basic monomeric subunit consists of n-acetylglucosamine-n-acetylmuramic acid-l-ala-d-glu-l-orn-d-ala-d-ala, acylated at the delta-nh2 group of orn by a gly-gly dipeptide. in a significant proportion (about 23%) of total muropeptides, the n-terminal gly is ...	1995	7665471
molecular cloning of the pyre gene from the extreme thermophile thermus flavus.	mutants of the extreme thermophile thermus flavus in the pyrimidine biosynthetic pathway (pyr-) were isolated by resistance to 5-fluoroorotic acid. the pyre gene, which codes for the orotate phosphoribosyltransferase, was cloned by recombination with one of the isolated pyr- t. flavus mutant strains. it was subcloned by complementation of an escherichia coli pyre mutant strain and was sequenced. the deduced polypeptide sequence extends over 183 amino acids. several independent pyr- mutations wer ...	1995	7635839
effect of genome size and rrn gene copy number on pcr amplification of 16s rrna genes from a mixture of bacterial species.	in order to assess the effect of genome size and number of 16s rrna genes (rdnas) on the quantities of pcr-generated partial 16s rdna fragments, equimolar amounts of dna from pairs of different species for which these parameters are known were subjected to gene amplification. the experimentally determined ratio of pcr products obtained, as determined by image analysis of sybr-green i-stained amplification products, corresponded well with the predicted ratio calculated from the number of rrn gene ...	1995	7618894
molecular characterization and t-cell-stimulatory capacity of mycobacterium leprae antigen t5.	a mycobacterium leprae lambda gt11 clone designated t5 has previously been selected with sera from tuberculoid leprosy patients. sequence analysis of this clone revealed the presence of two overlapping open reading frames (orfs) present on the two cdna strands. the first orf codes for the serologically recognized antigen, which was fused with the lacz gene in the lambda gt11 clone. the second orf, present on the complementary strand, displays strong sequence homology with the aspartyl-trna synth ...	1995	7591123
horizontal transference of s-layer genes within thermus thermophilus.	the s-layers of thermus thermophilus hb27 and t. thermophilus hb8 are composed of protein units of 95 kda (p95) and 100 kda (p100), respectively. we have selected s-layer deletion mutants from both strains by complete replacement of the slpa gene. mutants of the two strains showed similar defects in growth and morphology and overproduced an external cell envelope inside of which cells remained after division. however, the nature of this external layer is strain specific, being easily stained and ...	1995	7559330
crystal structure of glycyl-trna synthetase from thermus thermophilus.	the sequence and crystal structure at 2.75 a resolution of the homodimeric glycyl-trna synthetase from thermus thermophilus, the first representative of the last unknown class ii synthetase subgroup, have been determined. the three class ii synthetase sequence motifs are present but the structure was essential for identification of motif 1, which does not possess the proline previously believed to be an essential class ii invariant. nevertheless, crucial contacts with the active site of the othe ...	1995	7556056
crystal structure of histidyl-trna synthetase from escherichia coli complexed with histidyl-adenylate.	the crystal structure at 2.6 a of the histidyl-trna synthetase from escherichia coli complexed with histidyl-adenylate has been determined. the enzyme is a homodimer with a molecular weight of 94 kda and belongs to the class ii of aminoacyl-trna synthetases (aars). the asymmetric unit is composed of two homodimers. each monomer consists of two domains. the n-terminal catalytic core domain contains a six-stranded antiparallel beta-sheet sitting on two alpha-helices, which can be superposed with t ...	1995	7556055
contribution of structural elements to thermus thermophilus ribonuclease p rna function.	we have performed a deletion and mutational analysis of the catalytic ribonuclease (rnase) p rna subunit from the extreme thermophilic eubacterium thermus thermophilus hb8. catalytic activity was reduced 600-fold when the terminal helix, connecting the 5' and 3' ends of the molecule, was destroyed by deleting 15 nucleotides from the 3' end. in comparison, the removal of a large portion (94 nucleotides, about one quarter of the rna) of the upper loop region impaired function only to a relatively ...	1994	7525270
glycolipids from some extreme thermophilic bacteria belonging to the genus thermus.	the lipids of thermus aquaticus yt1, thermus thermophilus hb8, thermus sp. strains h and j (from icelandic hot springs), and thermus sp. strain nh (from domestic hot water) have been investigated. each strain contained two major components, a glycolipid and a glycophospholipid, which have been isolated and analyzed. all of the strains contained as the principal component (41 to 57% of total lipid) a diacyldiglycosyl-(n-acyl)glycosaminylglucosylglycerol, but the five glycolipids differed in carbo ...	1982	7054151
thermally induced biosynthesis of 2'-o-methylguanosine in trna from an extreme thermophile, thermus thermophilus hb27.	the contents of 2'-o-methylguanosine and 1-methyladenosine in unfractionated trna obtained from thermus thermophilus hb27 were found to increase significantly when the bacterium was grown at a higher temperature (80 degrees c). s-adenosyl-l-methionine-dependent trna (guanosine-2')-methyltransferase (ec 2.1.1.34) and trna (adenine-1)-methyltransferase (ec 2.1.1.36) were detected in a cell-free extract of the thermophile, and both of them were partially purified. trna (guanosine-2')-methyltransfer ...	1980	6990416
consensus structure and evolution of 5s rrna.	a consensus structure model of 5s rrna presenting all conserved nucleotides in fixed positions has been deduced from the primary and secondary structure of 71 eubacterial, archaebacterial, eukaryotic cytosolic and organellar molecules. phylogenetically related groups of molecules are characterized by nucleotide deletions in helices iii, iv and v, and by potential base pair interactions in helix iv. the group-specific deletions are correlated with the early branching pattern of a dendrogram calcu ...	1983	6835839
terminal heterogeneity and corrections of the nucleotide sequence of 5s rrna from an extreme thermophile, thermus thermophilus hb8.	the nucleotide sequence of 5s rrna from an extreme thermophile thermusthermophilus hb8 has been re-examined and determined as [formula: see text] the present study could resolve previously ambiguous residues and find two additional residues (g(8 3), c(9 7)), g at position 89 and two terminal heterogeneities which are exactly the same as reported with thermusaquaticus 5s rrna.images	1983	6828381
the number of ribosomal rna genes in thermus thermophilus hb8.	we have examined the number of rrna genes in thermus thermophilus hb8 by hybridization of bam hi -, hind iii - and pst i - digests of dna to 3'- (3 2p) 23s, 16s and 5s rrnas according to the southern procedure. the restriction gels gave two radioactive bands with 23s and 5s rrna. furthermore, band positions were indistinguishable from one another when 23s and 5s rrnas were used as probes to bam hi and hind iii digests, indicating that each band contains sequences corresponding to the 3'-end of 2 ...	1984	6322133
purification and characterization of two new modification methylases: mclai from caryophanon latum l and mtaqi from thermus aquaticus yti.	a method for detecting type ii modification methylases and determining their methylation site by assaying the ability of methylated dna to be cleaved by heterologous restriction enzymes is described and applied to the isolation of the restriction modification methylases from thermus thermophilus hb8, thermus aquaticus yti and caryophanon latum l. m.taqi is shown to have a methylation specificity identical to m.thi (tcgmea). m.clai methylates at adenine and protects a subset of tthi sites indicat ...	1981	6278447
nuclease tt1 from thermus thermophilus hb8 has an endonuclease activity preferential to circular dnas.	homogeneously purified nuclease tt1 from thermus thermophilus hb8 is known as an exonuclease to produce 5'-mononucleotides. besides the exonuclease activity, nuclease tt1 also possesses endonuclease activity preferential to superhelical (form i) and single-stranded circular dna. although the rate of cleavage is slower than that of form i, covalently closed circular dna (form i') is also cleaved. form i dna was nicked to yield relaxed circles (form ii) first, and was then nicked at the opposite s ...	1980	6258147
a second site specific endonuclease from thermus thermophilus 111, tth111ii.	a second site specific endonuclease with novel specificity has been purified from thermus thermophilus strain 111 and named tth111ii. the enzyme is active at temperature up to 80 degrees c and requires mg2+ or mn2+ for endonuclease activity. tth111ii cleaves phi x174rfdna into 11 fragments and lambda na into more than 25 fragments. from the 5'-terminal sequences of tthlllii fragments of phi x174rfdna determined by the two dimensional homochromatography and the survey on nucleotide sequence of ph ...	1980	6255411