Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
|---|
| sulfide:quinone oxidoreductase in membranes of the hyperthermophilic bacterium aquifex aeolicus (vf5). | the sulfide-dependent reduction of exogenous ubiquinone by membranes of the hyperthermophilic chemotrophic bacterium aquifex aeolicus (vf5), the sulfide-dependent consumption of oxygen and the reduction of cytochromes by sulfide in membranes were studied. sulfide reduced decyl-ubiquinone with a maximal rate of up to 3.5 micromol (mg protein)(-1) min(-1) at 20 degrees c. rates of 220 nmol (mg protein)(-1) min(-1)] for the sulfide-dependent consumption of oxygen and 480 nmol (mg protein)(-1) min(- ... | 2000 | 10816041 |
| a metal bridge between two enzyme families. 3-deoxy-d-manno-octulosonate-8-phosphate synthase from aquifex aeolicus requires a divalent metal for activity. | the enzymes 3-deoxy-d-manno-octulosonic acid-8-phosphate synthase (kdo8ps) and 3-deoxy-d-arabino-heptulosonic acid-7-phosphate synthase (dahps) catalyze analogous condensation reactions between phosphoenolpyruvate and d-arabinose 5-phosphate or d-erythrose 4-phosphate, respectively. while several similarities exist between the two enzymatic reactions, classic studies on the escherichia coli enzymes have established that dahps is a metalloenzyme, whereas kdo8ps has no metal requirement. here, we ... | 2000 | 10811802 |
| phylogenetic depth of the bacterial genera aquifex and thermotoga inferred from analysis of ribosomal protein, elongation factor, and rna polymerase subunit sequences. | the phylogenetic placement of the aquifex and thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins s10, l3, l4, l23, l2, s19, l22, and s3 encoded in the s10 operon (833 aa positions); (ii) the joint sequences of the elongation factors tu(1alpha) and g(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint rna polymerase beta- and beta'-type subunits encoded in the rpobc operon (1130 aa positions). phylogenies of r-protein and ef sequenc ... | 2000 | 10795828 |
| the biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. | the bacterial transcription factor sigma(n) (sigma-n, sigma-54, rpon) confers upon rna polymerase (rnap) properties distinct from those of the major house-keeping form of rnap, which contains sigma(70) (sigma-70, rpod). transcription by rnap containing sigma(n) is subject to enhancer-dependent regulation. far from being an 'oddity' or 'exception to the rule', the occurrence of sigma(n) in the genome sequences of such diverse bacteria as aquifex aeolicus, bacillus subtilis, chlamydia spp. and bor ... | 2000 | 10779705 |
| characterization of a novel lipid a containing d-galacturonic acid that replaces phosphate residues. the structure of the lipid a of the lipopolysaccharide from the hyperthermophilic bacterium aquifex pyrophilus. | according to the 16 s rrna phylogenetic tree, the hyperthermophilic bacterium aquifex pyrophilus represents the deepest and shortest branching species of the kingdom bacteria. we show for the first time that an organism, which is phylogenetically ancient on the basis of its 16 s rrna and that exists at extreme conditions, may contain lipopolysaccharide (lps). the lps was extracted from dried bacteria using a modified phenol/water method. sds-polyacrylamide gel electrophoresis and silver stain di ... | 2000 | 10753930 |
| antibacterial agents that target lipid a biosynthesis in gram-negative bacteria. inhibition of diverse udp-3-o-(r-3-hydroxymyristoyl)-n-acetylglucosamine deacetylases by substrate analogs containing zinc binding motifs. | udp-3-o-(r-3-hydroxymyristoyl)-n-acetylglucosamine deacetylase (lpxc) catalyzes the second step in the biosynthesis of lipid a, a unique amphiphilic molecule found in the outer membranes of virtually all gram-negative bacteria. since lipid a biosynthesis is required for bacterial growth, inhibitors of lpxc have potential utility as antibiotics. the enzymes of lipid a biosynthesis, including lpxc, are encoded by single copy genes in all sequenced gram-negative genomes. we have now cloned, overexp ... | 2000 | 10753902 |
| extremely thermostable elongation factor g from aquifex aeolicus: cloning, expression, purification, and characterization in a heterologous translation system. | the fus gene of the translation factor g (ef-g) from the hyperthermophilic bacterium aquifex aeolicus was cloned under control of a phage promoter and overexpressed in escherichia coli with the t7 rna polymerase system. a heat denaturation step at 95 degrees c was used to purify the protein from the cell extract. this approach simplified the chromatographic procedures and decreased the protein loss since most of escherichia coli proteins were denatured and precipitated. ten milligrams of the hig ... | 2000 | 10733877 |
| polypurine.polypyrimidine sequences in complete bacterial genomes: preference for polypurines in protein-coding regions. | the genomes of methanococcus jannaschii, mycoplasma genitalium, haemophilus influenzae, archaeoglobus fulgidus, helicobacter pylori, treponema pallidum, borrelia burgdorferri, rickettsia prowazekeii, mycobacterium tuberculosis, methanobacterium thermoautotrophicum, synechocystis sp. pcc6803, bacillus subtilis, chlamydia trachomatis, pyrococcus horikoshii, aquifex aeolicus, mycoplasma pneumoniae and escherichia coli have been analysed for the presence of polypurine.polypyrimidine tracts, in order ... | 2000 | 10721721 |
| functionality of purified sigma(n) (sigma(54)) and a nifa-like protein from the hyperthermophile aquifex aeolicus. | the genome sequence of the extremely thermophilic bacterium aquifex aeolicus encodes alternative sigma factor sigma(n) (sigma(54), rpon) and five potential sigma(n)-dependent transcriptional activators. although a. aeolicus possesses no recognizable nitrogenase genes, two of the activators have a high degree of sequence similarity to nifa proteins from nitrogen-fixing proteobacteria. we identified five putative sigma(n)-dependent promoters upstream of operons implicated in functions including su ... | 2000 | 10692367 |
| ligation reaction specificities of an nad(+)-dependent dna ligase from the hyperthermophile aquifex aeolicus. | an nad(+)-dependent dna ligase from the hyperthermophilic bacterium aquifex aeolicus was cloned, expressed in escherichia coli and purified to homogeneity. the enzyme is most active in slightly alkaline ph conditions with either mg(2+)or mn(2+)as the metal cofactor. ca(2+)and ni(2+)mainly support formation of dna-adenylate intermediates. the catalytic cycle is characterized by a low k (cat)value of 2 min(-1)with concomitant accumulation of the dna - adenylate intermediate when mg(2+)is used as t ... | 2000 | 10684941 |
| sequences and evolutionary analyses of eukaryotic-type protein kinases from streptomyces coelicolor a3(2). | four eukaryotic-type protein serine/threonine kinases from streptomyces coelicolor a3(2) were cloned and sequenced. to explore evolutionary relationships between these and other protein kinases, the distribution of protein serine/threonine kinase genes in prokaryotes was examined with the tfasta program. genes of this type were detected in only a few species of prokaryotes and their distribution was uneven; streptomyces, mycobacterium, synechocystis and myxococcus each contained more than three ... | 1999 | 10627033 |
| ligase-based detection of mononucleotide repeat sequences. | up to 15% of all colorectal cancers are considered to be replication error positive (rer(+)) and contain mutations at hundreds of thousands of microsatellite repeat sequences. recently, a number of intragenic mononucleotide repeat sequences have been demonstrated to be targets for inactivating genes in rer(+)colorectal tumors. in this study, thermostable dna ligases were tested for the ability to detect alterations in microsatellite sequences in colon tumor samples. ligation profiles on mononucl ... | 1999 | 10572192 |
| studies of codon usage and trna genes of 18 unicellular organisms and quantification of bacillus subtilis trnas: gene expression level and species-specific diversity of codon usage based on multivariate analysis. | we examined codon usage in bacillus subtilis genes by multivariate analysis, quantified its cellular levels of individual trnas, and found a clear constraint of trna contents on synonymous codon choice. individual trna levels were proportional to the copy number of the respective trna genes. this indicates that the trna gene copy number is an important factor to determine in cellular trna levels, which is common with escherichia coli and yeast saccharomyces cerevisiae. codon usage in 18 unicellu ... | 1999 | 10570992 |
| mutational analysis of the recj exonuclease of escherichia coli: identification of phosphoesterase motifs. | the recj gene, identified in escherichia coli, encodes a mg(+2)-dependent 5'-to-3' exonuclease with high specificity for single-strand dna. genetic and biochemical experiments implicate recj exonuclease in homologous recombination, base excision, and methyl-directed mismatch repair. genes encoding proteins with strong similarities to recj have been found in every eubacterial genome sequenced to date, with the exception of mycoplasma and mycobacterium tuberculosis. multiple genes encoding protein ... | 1999 | 10498723 |
| functional and biochemical characterization of a recombinant 3-deoxy-d-manno-octulosonic acid 8-phosphate synthase from the hyperthermophilic bacterium aquifex aeolicus. | the kdsa gene from the hyperthermophilic bacterium aquifex aeolicus was cloned into a vector for expression in escherichia coli and the kdsa gene product, 3-deoxy-d-manno-octulosonic acid 8-phosphate synthase (kdsa), was overexpressed under optimized growth conditions. the thermophilic kdsa was purified using an efficient purification procedure including a heat-treatment step. purified kdsa was shown to catalyze the formation of 3-deoxy-d-manno-octulosonic acid 8-phosphate from phosphoenolpyruva ... | 1999 | 10491295 |
| structures of a histone deacetylase homologue bound to the tsa and saha inhibitors. | histone deacetylases (hdacs) mediate changes in nucleosome conformation and are important in the regulation of gene expression. hdacs are involved in cell-cycle progression and differentiation, and their deregulation is associated with several cancers. hdac inhibitors, such as trichostatin a (tsa) and suberoylanilide hydroxamic acid (saha), have anti-tumour effects, as they can inhibit cell growth, induce terminal differentiation and prevent the formation of tumours in mice models, and they are ... | 1999 | 10490031 |
| molecular cloning, expression, and characterization of a thermostable glutamate racemase from a hyperthermophilic bacterium, aquifex pyrophilus. | a gene encoding glutamate racemase has been cloned from aquifex pyrophilus, a hyperthermophilic bacterium, and expressed in escherichia coli. the a. pyrophilus glutamate racemase is composed of 254 amino acids and shows high homology with glutamate racemase from escherichia coli, bacillus subtilis, or lactobacillus brevis. this racemase converts l- or d-glutamate to d- or l-glutamate, respectively, but not other amino acids such as alanine, aspartate, and glutamine. the cloned gene was expressed ... | 1999 | 10484173 |
| a novel rieske iron-sulfur protein from the hyperthermophilic crenarchaeon pyrobaculum aerophilum: sequencing of the gene, expression in e. coli and characterization of the protein. | the crenarchaeon pyrobaculum aerophilum is with an optimal growth temperature of 100 degrees c one of the most thermophilic organisms known to possess an aerobic respiratory chain. the analysis of dna sequences from the pyrobaculum genome project lead to the identification of an open reading frame potentially coding for a rieske iron-sulfur protein. the complete gene (named parr) was cloned and sequenced. the deduced amino acid sequence displays unusual amino acid exchanges and a so far unknown ... | 1999 | 10449238 |
| a [2fe-2s] protein from the hyperthermophilic bacterium aquifex aeolicus. | overexpression in escherichia coli of the fdx4 gene from aquifex aeolicus has allowed isolation and characterization of the first hyperthermophilic [2fe-2s](scys)(4) protein, a homodimer of m = 2 x 12.4 kda with one [2fe-2s] cluster per subunit. this protein is undamaged by heating to 100 degrees c for at least three hours. the primary structure, in particular the characteristic distribution of the four cysteine ligands of the metal site, and the spectroscopic properties of the a. aeolicus prote ... | 1999 | 10441520 |
| structural models of the ktrb, trkh, and trk1,2 symporters based on the structure of the kcsa k(+) channel. | three-dimensional computer modeling is used to further investigate the hypothesis forwarded in the accompanying paper of an evolutionary relationship between four related families of k(+) sympoter proteins and the superfamily of k(+) channel proteins. atomic-scale models are developed for the transmembrane regions of one member from each of the three more distinct symporter families, i.e., a trkh protein from escherichia coli, a ktrb protein from aquifex aeolicus, and a trk1,2 protein from schiz ... | 1999 | 10423426 |
| complete nucleotide sequence of a cryptic plasmid from the ruminal bacterium selenomonas ruminantium hd4 and identification of two predicted open reading frames. | a cryptic plasmid (psr1) isolated from selenomonas ruminantium hd4 was previously cloned into the hindiii site of pbr322 and a restriction map was constructed using hindiii, clai, bamhi, and pvuii (s. a. martin and r. g. dean, appl. environ. microbiol. 55(12), 3035-3038, 1989). analysis of the nucleotide sequence of psr1 revealed two major open reading frames (orfs) located in the minus strand at different frames. analysis of orf-1 revealed that it has 325 amino acids with a predicted mw of 36,5 ... | 1999 | 10413665 |
| a new member of the endonuclease iii family of dna repair enzymes that removes methylated purines from dna. | dna is constantly exposed to endogenous andexogenous alkylating agents that can modify its bases,resulting in mutagenesis in the absence of dna repair [1,2]. alkylation damage is removed by the action of dna glycosylases, which initiate the base excision repair pathway and protect the sequence information of the genome [3-5]. we have identified a new class of methylpurine dna glycosylase, designated mpgii, that is a member of the endonuclease iii family of dna repair enzymes. we expressed and pu ... | 1999 | 10375529 |
| structure-specific trna-binding protein from the extreme thermophile aquifex aeolicus. | the genome of the bacterium aquifex aeolicus encodes a polypeptide which is related to a small portion of a sequence found in one prokaryotic and two eukaryotic trna synthetases. it also is related to a portion of arc1p, a trna-binding protein believed to be important for nuclear trafficking of trnas. here we cloned, expressed and purified the 111 amino acid polypeptide (designated trbp111) and showed by ultracentrifugation analysis that it is a stable dimer in solution. the protein was also cry ... | 1999 | 10369686 |
| evolutionary relationships among photosynthetic prokaryotes (heliobacterium chlorum, chloroflexus aurantiacus, cyanobacteria, chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. | the presence of shared conserved insertions or deletions in proteins (referred to as signature sequences) provides a powerful means to deduce the evolutionary relationships among prokaryotic organisms. this approach was used in the present work to deduce the branching orders of various eubacterial taxa consisting of photosynthetic organisms. for this purpose, portions of the hsp60 and hsp70 genes, covering known signature sequence regions, were pcr-amplified and sequenced from heliobacterium chl ... | 1999 | 10361294 |
| structure and mechanism of glutamate racemase from aquifex pyrophilus. | glutamate racemase (muri) is responsible for the synthesis of d-glutamate, an essential building block of the peptidoglycan layer in bacterial cell walls. the crystal structure of glutamate racemase from aquifex pyrophilus, determined at 2.3 a resolution, reveals that the enzyme forms a dimer and each monomer consists of two alpha/beta fold domains, a unique structure that has not been observed in other racemases or members of an enolase superfamily. a substrate analog, d-glutamine, binds to the ... | 1999 | 10331867 |
| a common ancestor for a subunit in the mitochondrial proton-translocating nadh:ubiquinone oxidoreductase (complex i) and short-chain dehydrogenases/reductases. | the proton-translocating nadh:ubiquinone oxidoreductase or complex i is located in the inner membranes of mitochondria, where it catalyzes the transfer of electrons from nadh to ubiquinone. here we report that one of the subunits in complex i is homologous to short-chain dehydrogenases and reductases, a family of enzymes with diverse activities that include metabolizing steroids, prostaglandins and nucleotide sugars. we discovered that a subunit of complex i in human, cow, neurospora crassa and ... | 1999 | 10228558 |
| rna polymerase of aquifex pyrophilus: implications for the evolution of the bacterial rpobc operon and extremely thermophilic bacteria. | a 16,226-bp fragment from the genome of aquifex pyrophilus was sequenced, containing the genes for ribosomal proteins l1, l10, and l7/12 (rplajl), dna-directed rna polymerase subunits beta and beta' (rpobc), alanyl-trna synthetase (alas), and subunit a of proteinase clp (clpa). enzymatic activity and extreme thermostability of purified a. pyrophilus rna polymerase were verified. transcription initiation on a dna construct harboring the t7 a1 promoter was demonstrated by elongation of a 32p-label ... | 1999 | 10198119 |
| crystallization and preliminary x-ray analysis of glutamate racemase from aquifex pyrophilus, a hyperthermophilic bacterium. | glutamate racemase catalyzes the reversible reaction of l-glutamate to d-glutamate, an essential component of the bacterial cell wall. glutamate racemase from aquifex pyrophilus has been crystallized by the hanging-drop vapor-diffusion method using polyethylene glycol 6000 as a precipitant. the crystals belong to space group p6122 or p6522 with unit-cell parameters a = b = 72.1, c = 185.02 a. the asymmetric unit contains one molecule, corresponding to a vm value of 2.35 a3 da-1. complete data se ... | 1999 | 10089337 |
| the clpb atpase of streptomyces albus g belongs to the hspr heat shock regulon. | the clpb gene of streptomyces albus was cloned by polymerase chain reaction (pcr) using degenerate oligonucleotides. transcriptional analysis showed that the clpb gene was heat induced. primer extension identified a transcription start site preceded by typical vegetative -10 and -35 hexamer sequences. the streptomyces hspr repressor is known to bind to three inverted repeat motifs (ir1, ir2, ir3) upstream from the s. coelicolor dnak operon. we identified an inverted repeat motif identical to ir3 ... | 1999 | 10027969 |
| identification of three aspartic acid residues essential for catalysis by the rusa holliday junction resolvase. | rusa is a holliday junction resolvase encoded by the cryptic prophage dlp12 of escherichia coli k-12 that can be activated to promote homologous recombination and dna repair in resolution-deficient mutants lacking the ruvabc proteins. database searches with the 120 amino acid residue rusa sequence identified 11 homologues from diverse species, including one from the extreme thermophile aquifex aeolicus, which suggests that rusa may be of ancient bacterial ancestry. a multiple alignment of these ... | 1999 | 9973560 |
| iron superoxide dismutase from the archaeon sulfolobus solfataricus: analysis of structure and thermostability. | the crystal structure of superoxide dismutase (sod) from the hyper thermophile sulfolobus solfataricus has been determined at 2.3 a resolution by molecular replacement and refined to a crystallographic r-factor of 16.8 % (rfree 19.8 %). the crystals belong to the space group c2 (a=76.3 a, b=124.3 a, c=60.3 a, beta=128.8 degrees) with two identical monomers in the asymmetric unit. the monomer has a molecular weight of 24 kda and consists of 210 amino acid residues of which 205 are visible in the ... | 1999 | 9931259 |
| 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 |
| refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon sulfolobus acidocaldarius at 2.2 a resolution. | the extremely thermostable superoxide dismutase from the hyperthermophilic archaeon sulfolobus acidocaldarius was crystallized and the three-dimensional structure was determined by x-ray diffraction methods. the enzyme crystallized in the monoclinic spacegroup c2 with the cell dimensions a=168.1 a, b=91.3 a, c=85.7 a, beta=91.4 degrees. the diffraction limit of these crystals was 2.2 a. the crystals were very stable in the x-ray beam and measured diffraction data of a single crystal had a comple ... | 1999 | 9878438 |
| extremely thermostable serine-type protease from aquifex pyrophilus. molecular cloning, expression, and characterization. | a gene encoding a serine-type protease has been cloned from aquifex pyrophilus using a sequence tag containing the consensus sequence of proteases as a probe. sequence analysis of the cloned gene reveals an open reading frame of 619 residues that has three canonical residues (asp-140, his-184, and ser-502) that form the catalytic site of serine-type proteases. the size of the mature form (43 kda) and its localization in the cell wall fraction indicate that both the nh2- and cooh-terminal sequenc ... | 1999 | 9873027 |
| sequence and phylogenetic position of a class ii aldolase gene in the amitochondriate protist, giardia lamblia. | a giardia lamblia gene, glfba, was cloned and sequenced. this gene codes for a 324-residue-long putative class ii fructose-1, 6-bisphosphate aldolase. the positions of gaps and phylogenetic analysis with maximum likelihood and maximum parsimony methods showed the sequence to be most closely related to the as-yet uncharacterized aldolases of helicobacter pylori and aquifex aeolicus and to the group that comprises the calvin-cycle aldolases of photosynthetic proteobacteria and cyanobacteria. in co ... | 1998 | 9831644 |
| analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination. | free energy values of mrna tertiary structures around stop codons were systematically calculated to surmise the hairpin-forming potential for all genes in each of the 16 complete prokaryote genomes. instead of trying to detect each individual hairpin, we averaged the free energy values around the stop codons over the entire genome to predict how extensively the organism relies on hairpin formation in the process of transcription termination. the free energy values of escherichia coli k-12 shows ... | 1998 | 9826772 |
| the trna(guanine-26,n2-n2) methyltransferase (trm1) from the hyperthermophilic archaeon pyrococcus furiosus: cloning, sequencing of the gene and its expression in escherichia coli. | the structural gene pftrm1 (genbank accession no. af051912), encoding trna(guanine-26, n 2- n 2) methyltransferase (ec 2.1.1.32) of the strictly anaerobic hyperthermophilic archaeon pyrococcus furiosus, has been identified by sequence similarity to the trm1 gene of saccharomyces cerevisiae (ydr120c). the pftrm1 gene in a 3.0 kb restriction dna fragment of p.furiosus genomic dna has been cloned by library screening using a pcr probe to the 5'-part of the corresponding orf. sequence analysis revea ... | 1998 | 9685492 |
| random sequence analysis of genomic dna of a hyperthermophile: aquifex pyrophilus. | aquifex pyrophilus is one of the hyperthermophilic bacteria that can grow at temperatures up to 95 degrees c. to obtain information about its genomic structure, random sequencing was performed on plasmid libraries containing 0.5-2 kb genomic dna fragments of a. pyrophilus. comparison of the obtained sequence tags with known proteins revealed that 123 tags showed strong similarity to previously identified proteins in the pir or genebank databases. these included three proteases, two amino acid ra ... | 1997 | 9680318 |
| phylogenetic evidence for the existence of novel thermophilic bacteria in hot spring sulfur-turf microbial mats in japan. | so-called sulfur-turf microbial mats, which are macroscopic white filaments or bundles consisting of large sausage-shaped bacteria and elemental sulfur particles, occur in sulfide-containing hot springs in japan. however, no thermophiles from sulfur-turf mats have yet been isolated as cultivable strains. this study was undertaken to determine the phylogenetic positions of the sausage-shaped bacteria in sulfur-turf mats by direct cloning and sequencing of 16s rrna genes amplified from the bulk dn ... | 1998 | 9572936 |
| the complete genome of the hyperthermophilic bacterium aquifex aeolicus. | aquifex aeolicus was one of the earliest diverging, and is one of the most thermophilic, bacteria known. it can grow on hydrogen, oxygen, carbon dioxide, and mineral salts. the complex metabolic machinery needed for a. aeolicus to function as a chemolithoautotroph (an organism which uses an inorganic carbon source for biosynthesis and an inorganic chemical energy source) is encoded within a genome that is only one-third the size of the e. coli genome. metabolic flexibility seems to be reduced as ... | 1998 | 9537320 |
| the crystal structure of an fe-superoxide dismutase from the hyperthermophile aquifex pyrophilus at 1.9 a resolution: structural basis for thermostability. | superoxide dismutase (sod) from aquifex pyrophilus, a hyperthermophilic bacterium, is an extremely heat-stable enzyme that maintains about 70% of its activity after heat treatment for 60 minutes at 100 degrees c. to understand the molecular basis of thermostability of this enzyme, we have determined the crystal structure of a. pyrophilus superoxide dismutase (ap sod), an fe containing homotetrameric enzyme, at 1.9 a resolution, and compared it with sod structures from a mesophile and a thermophi ... | 1997 | 9236127 |
| cloning and expression of superoxide dismutase from aquifex pyrophilus, a hyperthermophilic bacterium. | a superoxide dismutase (sod) gene of aquifex pyrophilus, a marine hyperthermophilic bacterium, was cloned, sequenced, expressed in escherichia coli, and its gene product characterized. this is the first sod from a hyperthermophilic bacterium that has been cloned. it is an iron-containing homo-oligomeric protein with a monomeric molecular mass of 24.2 kda. the dna-derived amino acid sequence is more similar to those of known mn- and fe-sods from thermophilic archaea than of cu, zn-sods. the metal ... | 1997 | 9109405 |
| sensitivity of ribosomes of the hyperthermophilic bacterium aquifex pyrophilus to aminoglycoside antibiotics. | a poly(u)-programmed cell-free system from the hyperthermophilic bacterium aquifex pyrophilus has been developed, and the susceptibility of aquifex ribosomes to the miscoding-inducing and inhibitory actions of all known classes of aminoglycoside antibiotics has been assayed at temperatures (75 to 80 degrees c) close to the physiological optimum for cell growth. unlike thermotoga maritima ribosomes, which are systematically refractory to all known classes of aminoglycoside compounds (p. londei, s ... | 1996 | 8626307 |
| arrangement and nucleotide sequence of the gene (fus) encoding elongation factor g (ef-g) from the hyperthermophilic bacterium aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the ef-g/fus sequences. | the gene fus (for ef-g) of the hyperthermophilic bacterium aquifex pyrophilus was cloned and sequenced. unlike the other bacteria, which display the streptomycin-operon arrangement of ef genes (5'-rps12-rps7-fus-tuf-3'), the aquifex fus gene (700 codons) is not preceded by the two small ribosomal subunit genes although it is still followed by a tuf gene (for ef-tu). the opposite strand upstream from the ef-g coding locus revealed an open reading frame (orf) encoding a polypeptide having 52.5% id ... | 1995 | 8587125 |
| the phylogenetic position of hydrogenobacter acidophilus based on 16s rrna sequence analysis. | hydrogenobacter acidophilus strain 3h-1 is a thermoacidophilic, obligately chemolithoautotrophic, hydrogen-oxidizer isolated from a japanese solfataric field. strain 3h-1 requires elemental sulfur for growth. we used pcr to amplify the 16s rrna gene of strain 3h-1, and sequenced the amplification product directly. phylogenetic analyses show strain 3h-1 is closely related to aquifex pyrophilus and may be located in the deepest branch within the eubacterial phylogenetic tree. sulfur-dependency of ... | 1994 | 8039650 |
| phylogenetic position of the genus hydrogenobacter. | the genus hydrogenobacter consists of extremely thermophilic, obligately chemolithotrophic organisms that exhibit anaerobic anabolism but aerobic catabolism. preliminary studies of the phylogenetic position of these organisms based on limited 16s ribosomal dna sequence data suggested that they belong to one of the earliest branching orders of the bacteria. in this study, the complete 16s ribosomal dna sequences of two type strains, hydrogenobacter thermophilus tk-6 and calderobacterium hydrogeno ... | 1994 | 7981093 |
| a physical map of the hyperthermophilic bacterium aquifex pyrophilus chromosome. | a genomic map of the hyperthermophilic hydrogen-oxidizing bacterium aquifex pyrophilus was established with noti (gc/ggccgc), spei (a/ctagt), and xbai (t/ctaga). linking clones and cross-hybridization of restriction fragments revealed a single circular chromosome of 1.6 mbp. a single flagellin gene and six rrna gene units were located on this map by southern hybridization. | 1994 | 7961434 |
| cloning, sequencing, and expression of reca proteins from three distantly related thermophilic eubacteria. | sequences of the reca genes of the highly divergent thermopholic eubacteria thermus aquaticus (and thermus thermophilus), thermotoga maritima, and aquifex pyrophilus were determined from fragments derived by polymerase chain reaction (pcr) with degenerate primers and from inverse pcr products obtained using unique primers based on the fragment sequences. the source of the pcr products was verified by southern hybridization. complete pcr-derived reca genes were cloned into an expression vector re ... | 1994 | 7929298 |
| root of the universal tree of life based on ancient aminoacyl-trna synthetase gene duplications. | universal trees based on sequences of single gene homologs cannot be rooted. iwabe et al. [iwabe, n., kuma, k.-i., hasegawa, m., osawa, s. & miyata, t. (1989) proc. natl. acad. sci. usa 86, 9355-9359] circumvented this problem by using ancient gene duplications that predated the last common ancestor of all living things. their separate, reciprocally rooted gene trees for elongation factors and atpase subunits showed bacteria (eubacteria) as branching first from the universal tree with archaea (a ... | 1995 | 7708661 |
| flagellar structure and hyperthermophily: analysis of a single flagellin gene and its product in aquifex pyrophilus. | the polytrichously inserted flagella of aquifex pyrophilus, a marine hyperthermophilic bacterium growing at 85 degrees c, were isolated and purified. electron micrographs of the 19-nm-diameter flagellar filaments show prominent helical arrays of subunits. the primary structure of these 54-kda flagellin monomers determining the helical shape and heat stability of filaments was of particular interest. the genomic region encoding the flagellin subunit (flaa gene) and an upstream open reading frame ... | 1995 | 7592443 |
| phylogenetic analysis of the hyperthermophilic pink filament community in octopus spring, yellowstone national park. | the phylogenetic diversity of a well-known pink filament community associated with the 84 to 88 degrees c outflow from octopus spring, yellowstone national park, was examined. three phylogenetic types ("phylotypes"), designated em 3, em 17, and em 19, were identified by cloning and sequencing the small subunit rrna genes (16s rdna) obtained by pcr amplification of mixed-population dna. all three phylotypes diverge deeply within the phylogenetic domain bacteria sensu woese (c. r. woese, o. kandle ... | 1994 | 7518219 |