Publications

recognition of trna by aminoacyl-trna synthetase from hyperthermophilic archaea, aeropyrum pernix k1.	to study the recognition sites of trna for archaeal aminoacyl-trna synthetase, several aminoacyl-trna synthetase genes from hyperthermophilic archaeon, aeropyrum pernix k1 were cloned and expressed. all the expressed enzymes showed extreme thermostability. expressed threonyl-trna synthetase threonylated not only archaeal (a. pernix and haloferax volcanii) threonine trnas but also escherichia coli threonine trna. however, threonyl-trna synthetase from h. volcanii did not threonylate e. coli threo ...	2001	12836292
conserved 'hypothetical' proteins: new hints and new puzzles.	conserved hypothetical proteins, i.e. conserved proteins whose functions are still unknown, pose a challenge not just to functional genomics but also to general biology. for many conserved proteins, computational analysis provides only a general prediction of biochemical function; their exact biological functions have to be established through direct experimentation. in the few cases when this has been accomplished, the results were remarkable, revealing the deoxyxylulose pathway and a new essen ...	2001	18628897
towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (cogs).	standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. we used the database of clusters of orthologous groups of proteins (cogs) to reannotate the genomes of two archaea, aeropyrum pernix, the first member of the crenarchaea to be sequenced, and pyrococcus abyssi.	2000	11178258
novel prenyltransferase gene encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, aeropyrum pernix. molecularevolution with alteration in product specificity.	prenyltransferases catalyse sequential condensations of isopentenyl diphosphate with allylic diphosphates. previously, we reported the presence of farnesylgeranyl diphosphate (fgpp) synthase activity synthesizing c25 isoprenyl diphosphate in natronobacterium pharaonis which is a haloalkaliphilic archaeon having c20-c25 diether lipids in addition to c20-c20 diether lipids commonly occurring in archaea [tachibana, a. (1994) febs lett. 341, 291-294]. recently, it was found that a newly isolated aer ...	2000	10632701
cloning and characterization of a family b dna polymerase from the hyperthermophilic crenarchaeon pyrobaculum islandicum.	in order to extend the limited knowledge about crenarchaeal dna polymerases, we cloned a gene encoding a family b dna polymerase from the hyperthermophilic crenarchaeon pyrobaculum islandicum. the enzyme shared highest sequence identities with a group of phylogenetically related dna polymerases, designated b3 dna polymerases, from members of the kingdom crenarchaeota, pyrodictium occultum and aeropyrum pernix, and several members of the kingdom euryarchaeota. six highly conserved regions as well ...	2000	10633098
characterization of a thermostable dna glycosylase specific for u/g and t/g mismatches from the hyperthermophilic archaeon pyrobaculum aerophilum.	u/g and t/g mismatches commonly occur due to spontaneous deamination of cytosine and 5-methylcytosine in double-stranded dna. this mutagenic effect is particularly strong for extreme thermophiles, since the spontaneous deamination reaction is much enhanced at high temperature. previously, a u/g and t/g mismatch-specific glycosylase (mth-mig) was found on a cryptic plasmid of the archaeon methanobacterium thermoautotrophicum, a thermophile with an optimal growth temperature of 65 degrees c. we re ...	2000	10671447
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
sequence analysis of three family b dna polymerases from the thermoacidophilic crenarchaeon sulfurisphaera ohwakuensis.	three family b dna polymerase genes, designated b1, b2, and b3, were cloned from the thermoacidophilic crenarchaeon sulfurisphaera ohwakuensis, and sequenced. deduced amino acid sequences of b1 and b3 dna polymerases have all exonuclease and polymerase motifs which include critical residues for catalytic activities. furthermore, a yxgg/a motif, which is located between 3'-5' exonuclease and polymerization domains of family b dna polymerases, was also found in each of the b1 and b3 sequences. the ...	2000	10997874
status of genome projects for nonpathogenic bacteria and archaea.	since the first microbial genome was sequenced in 1995, 30 others have been completed and an additional 99 are known to be in progress. although the early emphasis of microbial genomics was on human pathogens for obvious reasons, a significant number of sequencing projects have focused on nonpathogenic organisms, beginning with the release of the complete genome sequence of the archaeon methanococcus jannaschii in 1996. the past 18 months have seen the completion of the genomes of several unusua ...	2000	11017041
links from genome proteins to known 3-d structures.	we describe a genome annotation service provided by the entrez browser, http://www.ncbi.nlm.nih.gov/entrez. all protein products identified in fully sequenced microbial genomes have been compared with proteins with known 3-d structure by use of the blast sequence comparison algorithm. for the approximately 20% of genome proteins in which unambiguous sequence similarity is detected, entrez provides a link from the gene product to its predicted structure. the service uses the cn3d molecular graphi ...	2000	11042161
glutamate dehydrogenase from the aerobic hyperthermophilic archaeon aeropyrum pernix k1: enzymatic characterization, identification of the encoding gene, and phylogenetic implications.	nadp-dependent glutamate dehydrogenase (l-glutamate: nadp oxidoreductase, deaminating, ec 1.4.1.4) from the aerobic hyperthermophilic archaeon aeropyrum pernix k1 (jcm 9820) was purified to homogeneity for characterization. the enzyme retained its full activity on heating at 95 degrees c for 30 min, and the maximum activity in l-glutamate deamination was obtained around 100 degrees c. the enzyme showed a strict specificity for l-glutamate and nadp on oxidative deamination and for 2-oxoglutarate ...	2000	11139075
phylogenetic analysis of archaeal pcna homologues.	proliferating cell nuclear antigen (pcna) is an essential component of the dna replication and repair machinery in the domain eucarya. eukaryotes and euryarchaeotes, which belong to one subdomain of archaea, possess a single pcna homologue, whereas two distinct pcna homologues have been identified from sulfolobus solfataricus, which belongs to the other archaeal subdomain, crenarchaeota. we have cloned and sequenced two genes of pcna homologues from the thermoacidophilic crenarchaeon sulfurispha ...	2000	11139078
a novel phosphoglycolipid archaetidyl(glucosyl)inositol with two sesterterpanyl chains from the aerobic hyperthermophilic archaeon aeropyrum pernix k1.	the structures of two novel polar lipids (agi and ai) of an aerobic hyperthermophilic archaeon, aeropyrum pernix, were elucidated. agi and ai were the only two major lipids and accounted for 91 mol% and 9 mol%, respectively, of total polar lipids of this organism. the core lipid of a. pernix total lipids consisted solely of 2,3-di-o-sesterterpanyl-sn-glycerol (c25,25-archaeol). the molecular weights of the free acid forms of agi and ai were shown by fab-mass spectrometry to be 1196 and 1034, res ...	1999	9989273
purification and characterization of an intracellular heat-stable proteinase (pernilase) from the marine hyperthermophilic archaeon aeropyrum pernix k1.	a novel intracellular serine proteinase from the marine aerobic hyperthermophilic archaeon aeropyrum pernix k1 (jcm 9820) that we designated pernilase was purified by ammonium sulfate precipitation, anionic-exchange chromatography, affinity chromatography, and gel filtration chromatography. the purified enzyme was composed of a single polypeptide chain with a molecular mass of 50 kda as determined by sds-page. the proteinase had a broad ph profile (ph 5-10) with an optimum ph of 9.0 for peptide ...	1999	10086839
complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, aeropyrum pernix k1.	the complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, aeropyrum pernix k1, which optimally grows at 95 degrees c, has been determined by the whole genome shotgun method with some modifications. the entire length of the genome was 1,669,695 bp. the authenticity of the entire sequence was supported by restriction analysis of long pcr products, which were directly amplified from the genomic dna. as the potential protein-coding regions, a total of 2,694 open reading fram ...	1999	10382966
a cambialistic sod in a strictly aerobic hyperthermophilic archaeon, aeropyrum pernix.	the superoxide dismutase (sod) gene of aeropyrum pernix, a strictly aerobic hyperthermophilic archaeon, was cloned and expressed in escherichia coli, and its gene product was characterized. the molecular mass of the protein, based on the deduced amino acid sequence, was 24.6 kda. the sequence showed overall similarity to the sequences of known mn- and fe-sods. the metal binding residues conserved in mn- and fe-sods were also found in a. pernix sod. when the sod gene was expressed in e. coli cell ...	1999	10393342
two family b dna polymerases from aeropyrum pernix, an aerobic hyperthermophilic crenarchaeote.	dna polymerase activities in fractionated cell extract of aeropyrum pernix, a hyperthermophilic crenarchaeote, were investigated. aphidicolin-sensitive (fraction i) and aphidicolin-resistant (fraction ii) activities were detected. the activity in fraction i was more heat stable than that in fraction ii. two different genes (pola and polb) encoding family b dna polymerases were cloned from the organism by pcr using degenerated primers based on the two conserved motifs (motif a and b). the deduced ...	1999	10498710
lessons from the aeropyrum pernix genome.	aeropyrum pernix is the first crenarchaeote and first aerobic member of the archaea for which the complete genome sequence has been determined. the sequence confirms the distinct nature of crenarchaeotes and provides new insight into the relationships between the three domains: bacteria, archaea and eukaryotes.	1999	10607556
molecular characterization and postsplicing fate of three introns within the single rrna operon of the hyperthermophilic archaeon aeropyrum pernix k1.	the single rrna operon (arns-arnl) of the hyperthermophilic archaeon aeropyrum pernix k1 was sequenced. the dna sequence data and detailed rna analyses disclosed an unusual feature: the presence of three introns at hitherto undescribed insertion positions within the rrna genes. the 699-nucleotide (nt) intron ialpha was located at position 908 (escherichia coli numbering [h. f. noller, annu. rev. biochem. 53:119-162, 1984]) of the 16s rrna, while the 202-nt intron ibeta and 575-nt intron igamma w ...	1998	9658008
an extremely heat-stable extracellular proteinase (aeropyrolysin) from the hyperthermophilic archaeon aeropyrum pernix k1.	an extracellular metalloproteinase, which we had designated aeropyrolysin, from the aerobic marine hyperthermophilic archaeon aeropyrum pernix k1 (jcm 9820), was purified by ammonium sulfate precipitation, anionic exchange chromatography, and gel filtration chromatography. the purified enzyme was composed of a single polypeptide chain with a molecular mass of 52 kda as determined by sds-page. the proteinase had a broad ph optimum (ph 5-9) with a maximal activity at ph 6-8 for azocasein hydrolysi ...	1997	9357994
aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100 degrees c.	a novel aerobic hyperthermophilic archaeon was isolated from a coastal solfataric vent at kodakara-jima island, japan. the new isolate, strain k1, is the first strictly aerobic organism growing at temperatures up to 100 degrees c. it grows optimally at 90 to 95 degrees c, ph 7.0, and a salinity of 3.5%. the cells are spherical shaped and 0.8 to 1.2 microns in diameter. various proteinaceous complex compounds served as substrates during aerobic growth. thiosulfate stimulates growth without produc ...	1996	8863437