Publications

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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-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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
temperature-dependent function of the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel and coupling with glycinamide ribonucleotide synthetase in a hyperthermophile.	genes encoding glutamine phosphoribosylpyrophosphate amidotransferase (gpat) and glycinamide ribonucleotide synthetase (gars) from aquifex aeolicus were expressed in escherichia coli, and the enzymes were purified to near homogeneity. both enzymes were maximally active at a temperature of at least 90 degrees c, with half-lives of 65 min for gpat and 60 h for gars at 80 degrees c. gpat activity is known to depend upon channeling of nh(3) from a site in an n-terminal glutaminase domain to a distal ...	2000	10850988
cyanobacterial sulfide-quinone reductase: cloning and heterologous expression.	the gene encoding sulfide-quinone reductase (sqr; e.c.1.8.5.'), the enzyme catalyzing the first step of anoxygenic photosynthesis in the filamentous cyanobacterium oscillatoria limnetica, was cloned by use of amino acid sequences of tryptic peptides as well as sequences conserved in the rhodobacter capsulatus sqr and in an open reading frame found in the genome of aquifex aeolicus. sqr activity was also detected in the unicellular cyanobacterium aphanothece halophytica following sulfide inductio ...	2000	10852862
characterization of a solvent resistant and thermostable aminopeptidase from the hyperthermophillic bacterium, aquifex aeolicus.	a leucine aminopeptidase gene of aquifex aeolicus, a hyperthermophilic bacterium, was cloned and expressed in escherichia coli, and its expression product was purified and characterized. the expressed protein was purified to homogeneity by using heat to denature contaminating proteins followed by ion-exchange chromatography to purify the heat-stable product. the purified enzyme gave a single band on sds-page with a molecular weight of 54 kda. kinetic studies on the purified enzyme confirmed that ...	2000	10862905
structure of a thioredoxin-like [2fe-2s] ferredoxin from aquifex aeolicus.	the 2.3 a resolution crystal structure of a [2fe-2s] cluster containing ferredoxin from aquifex aeolicus reveals a thioredoxin-like fold that is novel among iron-sulfur proteins. the [2fe-2s] cluster is located near the surface of the protein, at a site corresponding to that of the active-site disulfide bridge in thioredoxin. the four cysteine ligands are located near the ends of two surface loops. two of these ligands can be substituted by non-native cysteine residues introduced throughout a st ...	2000	10884354
three-dimensional model of human tip30, a coactivator for hiv-1 tat-activated transcription, and cc3, a protein associated with metastasis suppression.	human tip30 is a cofactor that specifically enhances human immunodeficiency virus-1 (hiv-1) tat-activated transcription. the sequence of tip30 is identical to that of cc3, a protein associated with metastasis suppression. tip30/cc3 is a member of the short-chain dehydrogenases/reductases (sdr) family. of the several experimentally determined sdr structures, escherichia coli uridine diphosphate (udp) galactose-4 epimerase is most similar to tip30/cc3. because the direct sequence similarity betwee ...	2000	10892349
a soxa gene, encoding a diheme cytochrome c, and a sox locus, essential for sulfur oxidation in a new sulfur lithotrophic bacterium.	a mobilizable suicide vector, psup5011, was used to introduce tn5-mob in a new facultative sulfur lithotrophic bacterium, kct001, to generate mutants defective in sulfur oxidation (sox(-)). the sox(-) mutants were unable to oxidize thiosulfate while grown mixotrophically in the presence of thiosulfate and succinate. the mutants were also impaired in oxidizing other reduced sulfur compounds and elemental sulfur as evident from the study of substrate oxidation by the whole cells. sulfite oxidase a ...	2000	10894738
recombinant superoxide dismutase from a hyperthermophilic archaeon, pyrobaculum aerophilium.	superoxide dismutase (sod) from the hyperthermophilic archaeon pyrobaculum aerophilum (a facultative aerobe) has been cloned and expressed in a mesophilic host (escherichia coli) as a soluble tetrameric apoprotein. the purified apoprotein can be reconstituted with either mn or fe by heating the protein with the appropriate metal salt at an elevated temperature (95 degrees c). both mn- and fe-reconstituted p. aerophilum sod exhibit superoxide dismutase activity, with the mn-containing enzyme havi ...	2000	10907751
structural and genomic correlates of hyperthermostability.	while most organisms grow at temperatures ranging between 20 and 50 degrees c, many archaea and a few bacteria have been found capable of withstanding temperatures close to 100 degrees c, or beyond, such as pyrococcus or aquifex. here we report the results of two independent large scale unbiased approaches to identify global protein properties correlating with an extreme thermophile lifestyle. first, we performed a comparative proteome analyses using 30 complete genome sequences from the three k ...	2000	10940293
letter to the editor: 1h, 13c and 15n resonance assignments of aquifex aeolicus shikimate kinase in complex with the substrate shikimate.		2000	10959638
the phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes.	the evolutionary relationships of proteobacteria, which comprise the largest and phenotypically most diverse division among prokaryotes, are examined based on the analyses of available molecular sequence data. sequence alignments of different proteins have led to the identification of numerous conserved inserts and deletions (referred to as signature sequences), which either are unique characteristics of various proteobacterial species or are shared by only members from certain subdivisions of p ...	2000	10978543
survey and summary: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.	holliday junction resolvases (hjrs) are key enzymes of dna recombination. a detailed computer analysis of the structural and evolutionary relationships of hjrs and related nucleases suggests that the hjr function has evolved independently from at least four distinct structural folds, namely rnase h, endonuclease, endonuclease vii-colicin e and rusa. the endonuclease fold, whose structural prototypes are the phage lambda exonuclease, the very short patch repair nuclease (vsr) and type ii restrict ...	2000	10982859
the alternative sigma factor sigma(28) of the extreme thermophile aquifex aeolicus restores motility to an escherichia coli flia mutant.	sigma factor sigma(28) (sigma(f), flia, sigd) directs rna polymerase to transcribe the genes required for flagellar biosynthesis and chemotaxis in many bacteria, including bacillus subtilis, legionella pneumophila, salmonella typhimurium, escherichia coli, yersinia enterolytica, treponema maltophilum and pseudomonas aeruginosa. remarkably the flia gene from the extreme thermophile aquifex aeolicus restored motility to the e. coli mutant at relatively low temperature, albeit partially. this clear ...	2000	11004406
genomic analysis of the genes encoding ribosomal proteins in eight eubacterial species and saccharomyces cerevisiae.	the complete genomic nucleotide sequence data of more than 10 unicellular organisms have become available. during the past years, we have been focusing our attention to the analysis of the structure and function of the ribosome and its protein components. by making use of the genomic sequence data, our work can now be extended to comparative analysis of the ribosomal components at the genomic level. such analysis will contribute to our understanding of the structure-function relationship of the ...	1998	11072316
crystal structure of trbp111: a structure-specific trna-binding protein.	trbp111 is a 111 amino acid aquifex aeolicus structure-specific trna-binding protein that has homologous counterparts distributed throughout evolution. a dimer is the functional unit for binding a single trna. here we report the 3d structures of the a.aeolicus protein and its escherichia coli homolog at resolutions of 2.50 and 1.87 a, respectively. the structure shows a symmetrical dimer of two core domains and a central dimerization domain where the n- and c-terminal regions of trbp111 form an ...	2000	11101501
substrate and metal complexes of 3-deoxy-d-manno-octulosonate-8-phosphate synthase from aquifex aeolicus at 1.9-a resolution. implications for the condensation mechanism.	3-deoxy-d-manno-octulosonate-8-phosphate synthase (kdo8ps) from the hyperthermophilic bacterium aquifex aeolicus differs from its escherichia coli counterpart in the requirement of a divalent metal for activity (duewel, h. s., and woodard, r. w. (2000) j. biol. chem. 275, 22824-22831). here we report the crystal structure of the a. aeolicus enzyme, which was determined by molecular replacement using e. coli kdo8ps as a model. the structures of the metal-free and cd(2+) forms of the enzyme were d ...	2001	11115499
cloning and characterization of thermostable endoglucanase (cel8y) from the hyperthermophilic aquifex aeolicus vf5.	aquifex aeolicus is the hyperthermophilic bacterium known, with growth-temperature maxima near 95 degrees c. the cel8y gene, encoding a thermostable endoglucanase (cel8y) from aquifex aeolicus vf5, was cloned into a vector for expression and expressed in escherichia coli xl1-blue. a clone of 1.7 kb fragment containing endoglucanase activity, designated pkycy100, was sequenced and found to contain an orf of 978 bp encoding a protein of 325 amino acid residues, with a calculated molecular mass of ...	2000	11118302
site-directed mutagenesis of the bacterial metalloamidase udp-(3-o-acyl)-n-acetylglucosamine deacetylase (lpxc). identification of the zinc binding site.	udp-3-o-(acyl)-n-acetylglucosamine deacetylase (lpxc) catalyzes the second step in the biosynthesis of lipid a in gram-negative bacteria. compounds targeting this enzyme are proposed to chelate the single, essential zinc ion bound to lpxc and have been demonstrated to stop the growth of escherichia coli. a comparison of lpxc sequences from diverse bacteria identified 10 conserved his, asp, and glu residues that might play catalytic roles. each amino acid was altered in both e. coli and aquifex a ...	2001	11148046
genome of aquifex aeolicus.		2001	11210496
phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria.	the genome sequence of thermotoga maritima revealed that 24% of its open reading frames (orfs) showed the highest similarity scores to archaeal genes in blast analyses. here we screened 16 strains from the genus thermotoga and other related thermotogales for the occurrence of two of these "archaeal" genes: the gene encoding the large subunit of glutamate synthase (gltb) and the myo-inositol 1p synthase gene (ino1). both genes were restricted to the thermotoga species within the thermotogales. th ...	2001	11230537
x-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile aquifex aeolicus at 1.6 a resolution: determinants of thermostability revealed from structural comparisons.	an open reading frame optimized for expression of 6,7-dimethyl-8-ribityl-lumazine synthase of the hyperthermophilic bacterium aquifex aeolicus in escherichia coli was synthesized and expressed in a recombinant e. coli strain to a level of around 15 %. the recombinant protein was purified by heat-treatment and gel-filtration. the protein was crystallized in the cubic space group i23 with the cell dimensions a = b = c = 180.8 a, and diffraction data were collected to 1.6 a resolution. the structur ...	2001	11237620
molecular cloning, expression, purification, and characterization of fructose-1,6-bisphosphate aldolase from thermus aquaticus.	fructose-1,6-bisphosphate aldolase from the thermophilic eubacteria, thermus aquaticus yt-1, was cloned and sequenced. nucleotide-sequence analysis revealed an open reading frame coding for a 33-kda protein of 305 amino acids having amino acid sequence typical of thermophilic adaptation. multiple sequence alignment classifies the enzyme as a class ii b aldolase that shares similarity with aldolases from other extremophiles: thermotoga maritima, aquifex aeolicus, and helicobacter pylori (49--54% ...	2001	11237691
aquifex aeolicus 3-deoxy-d-manno-2-octulosonic acid 8-phosphate synthase: a new class of kdo 8-p synthase?	the relationship between 3-deoxy-d-manno-2-octulosonic acid 8-phosphate (kdo 8-p) synthase and 3-deoxy-d-arabino-2-heptulosonic acid 7-phosphate (dah 7-p) synthase has not been adequately addressed in the literature. based on recent reports of a metal requiring kdo 8-p synthase and the newly solved x-ray crystal structures of both escherichia coli kdo 8-p synthase and dah 7-p synthase, we begin to address the evolutionary kinship between these catalytically similar enzymes. using a maximum likel ...	2001	11244581
simultaneous binding of two proteins to opposite sides of a single transfer rna.	transfer rna (trna) is a small nucleic acid (typically 76 nucleotides) that forms binary complexes with proteins, such as aminoacyl trna synthetases (rs) and trbp111. the latter is a widely distributed structure-specific trna-binding protein that is incorporated into cell signaling molecules. the structure of trbp111 was modeled onto to the outer, convex side of the l-shaped trna. here we present rna footprints that are consistent with this model. this binding mode is in contrast to that of trna ...	2001	11276256
analysis of codon usage patterns of bacterial genomes using the self-organizing map.	codon usage varies both between organisms and between different genes in the same organism. this observation has been used as a basis for earlier work in identifying highly expressed and horizontally transferred genes in escherichia coli. in this work, we applied kohonen's self-organizing map to analysis of the codon usage pattern of the escherichia coli, aquifex aeolicus, archaeoglobus fulgidus, haemophilus influenzae rd:, methanococcus jannaschii, methanobacterium thermoautotrophicum, and pyro ...	2001	11319263
solution structure of the ribosome recycling factor from aquifex aeolicus.	the solution structure of ribosome recycling factor (rrf) from hyperthermophilic bacterium, aquifex aeolicus, was determined by heteronuclear multidimensional nmr spectroscopy. fifteen structures were calculated using restraints derived from noe, j-coupling, and t1/t2 anisotropies. the resulting structure has an overall l-shaped conformation with two domains and is similar to that of a trna molecule. the domain i (corresponding to the anticodon stem of trna) is a rigid three alpha-helix bundle. ...	2001	11327859
mutational analyses of aquifex pyrophilus dna ligase define essential domains for self-adenylation and dna binding activity.	we constructed nine deletion mutants of nad+-dependent dna ligase from aquifex pyrophilus to characterize the functional domains. all of dna ligase deletion mutants were analyzed in biochemical assays for nad+-dependent self-adenylation, dna binding, and nick-closing activity. although the mutant lsub1 (91-362) included the active site lysine (kxdg), self-adenylation was not shown. however, the mutants lsub6 (1-362), lsub7 (1-516), and lsub9 (1-635) showed the same adenylation activity as that o ...	2001	11368162
purification and properties of aquifex aeolicus dna polymerase expressed in escherichia coli.	the gene encoding aquifex aeolicus (aae) dna polymerase was expressed under the control of the trp promoter on a high-copy plasmid, ptrpns, in escherichia coli. the expressed enzyme was purified 11-fold with a 13.8% yield and a specific activity of 2268.3 u mg(-1). the optimum ph of the enzyme was 6.8-7.2. the optimal concentrations of kcl and mg(2+) were 20-30 mm and 4-5 mm, respectively. aae dna polymerase contained a double-strand-dependent 3'-->5' proofreading exonuclease activity but lacked ...	2001	11445170
molecular cloning and characterization of thermostable dna ligase from aquifex pyrophilus, a hyperthermophilic bacterium.	a dna ligase gene from the hyperthermophilic bacterium aquifex pyrophilus (ap) was cloned and sequenced. an open reading frame of 2,157 bp that codes for a 82-kda protein showed 40%-60% homology with a series of nad+-dependent dna ligases from different organisms. the recombinant enzyme ap dna ligase expressed in escherichia coli was purified to homogeneity and characterized. the activity of ap dna ligase gradually increased in proportion to the concentration of monovalent salt up to 200 mm nacl ...	2001	11453459
expression and characterization of the terminal heme synthetic enzymes from the hyperthermophile aquifex aeolicus.	the terminal two heme biosynthetic pathway enzymes, protoporphyrinogen oxidase and ferrochelatase, of the hyperthermophilic bacterium aquifex aeolicus have been expressed in escherichia coli, purified to homogeneity, and biochemically characterized. ferrochelatase and protoporphyrinogen oxidase of this organism are both monomeric, as was found for the corresponding enzymes of bacillus subtilis. however, unlike the b. subtilis proteins, both a. aeolicus enzymes are membrane-associated. both prote ...	2001	11506917
a phylogenetic analysis of aquifex pyrophilus.	the 16s rrna of the bacterion aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the pcr amplified gene. phylogenetic analyses show the aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. the addition of this deep branching to the bacterial tree further supports the argument that the bacteria are of thermophilic ancestry.	1992	11540077
mapping the interaction of the [2fe-2s] clostridium pasteurianum ferredoxin with nitrogenase mofe protein.	the [2fe-2s] ferredoxin from clostridium pasteurianum had previously been shown to interact specifically with the nitrogenase mofe protein, and electrostatic forces were found to be important contributors to the interaction. this phenomenon has now been analyzed in detail by using ferredoxin variants in which charge inversions or cancellations were introduced on all charged residues. the mutated forms of the ferredoxin were covalently cross-linked to the mofe protein. the reaction products were ...	2001	11566366
a novel carbamoyl-phosphate synthetase from aquifex aeolicus.	aquifex aeolicus, an extreme hyperthermophile, has neither a full-length carbamoyl-phosphate synthetase (cpsase) resembling the enzyme found in all mesophilic organisms nor a carbamate kinase-like cpsase such as those present in several hyperthermophilic archaea. however, the genome has open reading frames encoding putative proteins that are homologous to the major cpsase domains. the glutaminase, cps.a, and cps.b homologs from a. aeolicus were cloned, overexpressed in escherichia coli, and puri ...	2001	11574542
hydrogenothermus marinus gen. nov., sp. nov., a novel thermophilic hydrogen-oxidizing bacterium, recognition of calderobacterium hydrogenophilum as a member of the genus hydrogenobacter and proposal of the reclassification of hydrogenobacter acidophilus as hydrogenobaculum acidophilum gen. nov., comb. nov., in the phylum 'hydrogenobacter/aquifex'.	a novel thermophilic, hydrogen-oxidizing bacterium, vm1t, has been isolated from a marine hydrothermal area of vulcano island, italy. cells of the strain were gram-negative rods, 2-4 microm long and 1-1.5 microm wide with four to seven monopolarly inserted flagella. cells grew chemolithoautotrophically under an atmosphere of h2/co2 (80:20) in the presence of low concentrations of o2 (optimum 1-2%). carbohydrates and peptide substrates were not utilized, neither for energy generation nor as a sou ...	2001	11594618
mutational effects on thermostable superoxide dismutase from aquifex pyrophilus: understanding the molecular basis of protein thermostability.	we designed two mutants of superoxide dismutase (sod), one is thermostable and the other is thermolabile, which provide valuable insight to identify amino acid residues essential for the thermostability of the sod from aquifex pyrophilus (apsod). the mutant k12a, in which lys12 was replaced by ala, had increased thermostability compared to that of the wild type. the t(1/2) value of k12a was 210 min and that of the wild type was 175 min at 95 degrees c. however, the thermostability of the mutant ...	2001	11594783
central domain assembly: thermodynamics and kinetics of s6 and s18 binding to an s15-rna complex.	the 30 s ribosomal subunit assembles in vitro through the hierarchical binding of 21 ribosomal proteins to 16 s rrna. the central domain of 16 s rrna becomes the platform of the 30 s subunit upon binding of ribosomal proteins s6, s8, s11, s15, s18 and s21. the assembly of the platform is nucleated by binding of s15 to 16 s rrna, followed by the cooperative binding of s6 and s18. the prior binding of s6 and s18 is required for binding of s11 and s21. we have studied the mechanism of the cooperati ...	2001	11601845
differential effects of replacing escherichia coli ribosomal protein l27 with its homologue from aquifex aeolicus.	the rpma gene, which encodes 50s ribosomal subunit protein l27, was cloned from the extreme thermophile aquifex aeolicus, and the protein was overexpressed and purified. comparison of the a. aeolicus protein with its homologue from escherichia coli by circular dichroism analysis and proton nuclear magnetic resonance spectroscopy showed that it readily adopts some structure in solution that is very stable, whereas the e. coli protein is unstructured under the same conditions. a mutant of e. coli ...	2001	11673426
expression in escherichia coli of the thermostable inorganic pyrophosphatase from the aquifex aeolicus and purification and characterization of the recombinant enzyme.	the gene encoding the inorganic pyrophosphatase from a hyperthermophilic bacterium, aquifex aeolicus (aae), was amplified by pcr. then, the gene was overexpressed in escherichia coli using a pjr-based expression plasmid, paipd. the recombinant aae pyrophosphatase was purified 16.2-fold with a 53.4% yield and a specific activity of 34 u/mg protein by a combination of heating (to denature e. coli proteins) and two steps of deae-sephacel column chromatography (nonabsorbed enzyme at ph 7.3 and absor ...	2001	11676598
signature lipids and stable carbon isotope analyses of octopus spring hyperthermophilic communities compared with those of aquificales representatives.	the molecular and isotopic compositions of lipid biomarkers of cultured aquificales genera have been used to study the community and trophic structure of the hyperthermophilic pink streamers and vent biofilm from octopus spring. thermocrinis ruber, thermocrinis sp. strain hi 11/12, hydrogenobacter thermophilus tk-6, aquifex pyrophilus, and aquifex aeolicus all contained glycerol-ether phospholipids as well as acyl glycerides. the n-c(20:1) and cy-c(21) fatty acids dominated all of the aquificale ...	2001	11679343
cytochromes c555 from the hyperthermophilic bacterium aquifex aeolicus (vf5). 1. characterization of two highly homologous, soluble and membranous, cytochromes c555.	two distinct class i (monoheme) c-type cytochromes from the hyperthermophilic bacterium aquifex aeolicus were studied by biochemical and biophysical methods (i.e., optical and epr spectroscopy, electrochemistry). the sequences of these two heme proteins (encoded by the cycb1 and cycb2 genes) are close to identical (85% identity in the common part of the protein) apart from the presence of an n-terminal stretch of 62 amino acid residues present only in the cycb1 gene. a soluble cytochrome was pur ...	2001	11695917
cytochromes c555 from the hyperthermophilic bacterium aquifex aeolicus. 2. heterologous production of soluble cytochrome c555s and investigation of the role of methionine residues.	the cycb2 gene encoding the soluble cytochrome c555s from aquifex aeolicus, an hyperthermophilic organism, has been cloned and expressed using escherichia coli as the host organism. the cytochrome was successfully produced in the periplasm of an e. coli strain coexpressing the ccmabcdefgh genes involved in the cytochrome c maturation process. comparison of native and recombinant cytochrome c555s shows that both proteins are indistinguishable in terms of spectroscopic and physicochemical properti ...	2001	11695918
isolation and characterisation of the ylme homologue of thermus thermophilus.	screening of a thermus thermophilus genomic library led to the identification of a homologue of the ylme gene. ylme is highly conserved in widely divergent organisms from prokaryotes to mammals, suggesting an important, albeit currently unknown, cellular function. the 633 bp gene has a gc content of 69.2% overall and 90% in the third nucleotide position, while the gene product is predicted to be a soluble cytoplasmic protein of 23,441 da. it belongs to a family of conserved proteins of unknown f ...	2001	11696977
collaboration between cc- and a-adding enzymes to build and repair the 3'-terminal cca of trna in aquifex aeolicus.	the universal 3'-terminal cca sequence of all transfer rnas (trnas) is repaired, and sometimes constructed de novo, by the cca-adding enzyme [atp(ctp):trna nucleotidyltransferase]. this rna polymerase has no nucleic acid template, yet faithfully builds the cca sequence one nucleotide at a time using cytidine triphosphate (ctp) and adenosine triphosphate (atp) as substrates. all previously characterized cca-adding enzymes from all three kingdoms are single polypeptides with cca-adding activity. h ...	2001	11701927
prokaryotic structural maintenance of chromosomes (smc) proteins: distribution, phylogeny, and comparison with mukbs and additional prokaryotic and eukaryotic coiled-coil proteins.	structural maintenance of chromosomes (smc) proteins are known to be essential for chromosome segregation in some prokaryotes and in eukaryotes. a systematic search for the distribution of smc proteins in prokaryotes with fully or partially sequenced genomes showed that they form a larger family than previously anticipated and raised the number of known prokaryotic homologs to 54. secondary structure predictions revealed that the length of the globular n-terminal and c-terminal domains is extrem ...	2001	11707343
crystallographic and modeling studies of rnase iii suggest a mechanism for double-stranded rna cleavage.	aquifex aeolicus ribonuclease iii (aa-rnase iii) belongs to the family of mg(2+)-dependent endonucleases that show specificity for double-stranded rna (dsrna). rnase iii is conserved in all known bacteria and eukaryotes and has 1-2 copies of a 9-residue consensus sequence, known as the rnase iii signature motif. the bacterial rnase iii proteins are the simplest, consisting of two domains: an n-terminal endonuclease domain, followed by a double-stranded rna binding domain (dsrbd). the three-dimen ...	2001	11738048
structures of aquifex aeolicus kdo8p synthase in complex with r5p and pep, and with a bisubstrate inhibitor: role of active site water in catalysis.	we have determined the crystal structures of the metalloenzyme 3-deoxy-d-manno-octulosonate 8-phosphate (kdo8p) synthase from aquifex aeolicus in complex with phosphoenolpyruvate (pep) and ribose 5-phosphate (r5p), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. r5p, which is not a substrate for kdo8p synthase, binds in a manner similar to that of arabinose 5-phosphate (a5p), which is the natural substrate. the lack of reactivity of r5p appears to be pri ...	2001	11747443
cloning, expression and preliminary x-ray analysis of the dihydroorotase from the hyperthermophilic eubacterium aquifex aeolicus.	dihydroorotase (dhoase) catalyzes the formation of dihydroorotate in the de novo pyrimidine biosynthetic pathway. the gene encoding the type i dhoase from the hyperthermophilic bacterium aquifex aeolicus has been cloned in escherichia coli with a polyhistidine affinity tag appended to the amino-terminal end and sequenced. the recombinant protein was expressed at high levels and could be purified readily in a single step by ni(2+) affinity chromatography. both native and selenomethionine-labeled ...	2002	11752797
a dna repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis.	during a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most archaea (with the exception of thermoplasma acidophilum and halobacterium nrc-1) and some bacteria, including the hyperthermophiles thermotoga maritima and aquifex aeolicus. the gene composition and gene order in this neighborhood vary greatly between species, but all versions have a stable, conse ...	2002	11788711
the proton-pumping nadh:ubiquinone oxidoreductase (complex i) of aquifex aeolicus.	the proton-pumping nadh:ubiquinone oxidoreductase, also called complex i, is the first energy-transducing complex of many respiratory chains. homologues of complex i are present in the three domains of life. here, we report the properties of complex i in membranes of the hyperthermophilic bacterium aquifex aeolicus. the complex reacted with nadh but not with nadph and f(420)h(2) as electron donors. short-chain analogues of ubiquinone like decyl-ubiquinone and ubiquinone-2 were suitable electron ...	2002	11852056
analysis of a multicomponent thermostable dna polymerase iii replicase from an extreme thermophile.	this report takes a proteomic/genomic approach to characterize the dna polymerase iii replication apparatus of the extreme thermophile, aquifex aeolicus. genes (dnax, hola, and holb) encoding the subunits required for clamp loading activity (tau, delta, and delta') were identified. the dnax gene produces only the full-length product, tau, and therefore differs from escherichia coli dnax that produces two proteins (gamma and tau). nonetheless, the a. aeolicus proteins form a taudeltadelta' comple ...	2002	11859073