| structure of the archaebacterial 7s rna molecule. | the genes encoding the 7s rnas of the archaebacteria archaeoglobus fulgidus, methanosarcina acetivorans, sulfolobus, solfataricus, and thermococcus celer have been isolated. all four genes occur as single genomic copies and are flanked by sequences containing potential signals for transcriptional promotion and termination. the genes encode rna molecules approximately 300 nucleotides in length which conform strictly to a model of secondary structure common to all described archaebacterial 7s rnas ... | 1990 | 2116588 |
| dissimilatory sulphite reductase from archaeoglobus fulgidus: physico-chemical properties of the enzyme and cloning, sequencing and analysis of the reductase genes. | a dissimilatory sulphite reductase was isolated from the extremely thermophilic dissimilatory sulphate-reducing archaeon archaeoglobus fulgidus. in common with other dissimilatory sulphite reductases thus far characterized, the enzyme has an alpha 2 beta 2-structure and contains sirohaem, non-haem iron atoms and acid labile sulphide. the oxidized enzyme exhibited absorption maxima at 281, 394, 545 and 593 nm with a weak band around 715 nm. we have cloned and sequenced the genes for the alpha and ... | 1993 | 7691984 |
| the primary structure of the split-soret cytochrome c from desulfovibrio desulfuricans atcc 27774 reveals an unusual type of diheme cytochrome c. | the complete amino acid sequence of the unusual diheme split-soret cytochrome c from the sulphate-reducing desulfovibrio desulfuricans strain atcc 27774 has been determined using classical chemical sequencing techniques and mass spectrometry. the 247-residue sequence shows almost no similarity with any other known diheme cytochrome c, but the heme-binding site of the protein is similar to that of the cytochromes c3 from the sulphate reducers. the cytochrome-c-like domain of the protein covers on ... | 1997 | 9346301 |
| abundant microsatellite polymorphism in saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and s. cerevisiae, result from strong mutation pressures and a variety of selective forces. | we examined the distributions of short tandemly repeated dnas (microsatellites) in nine complete microbial genomes (saccharomyces cerevisiae, archaeoglobus fulgidus, escherichia coli, haemophilus influenzae, helicobacter pylori, methanococcus jannaschii, mycoplasma pneumoniae, m. genitalium, and synechocystis pcc6803.) these repeats contribute differently to the global features of these genomes, and we explore the evolutionary implications of these differences by empirical examination of length ... | 1998 | 9465070 |
| strand compositional asymmetry in bacterial and large viral genomes. | several bacterial genomes exhibit preference for g over c on the dna leading strand extending from the origin of replication to the ter-region in the genomes of escherichia coli, mycoplasma genitalium, bacillus subtilis, and marginally in haemophilus influenzae, mycoplasma pneumoniae, and helicobacter pylori. strand compositional asymmetry is not observed in the cyanobacterium synechocystis sp. genome nor in the archaeal genomes of methanococcus jannaschii, methanobacterium thermoautotrophicum, ... | 1998 | 9520433 |
| molecular analysis of the gene encoding f420-dependent glucose-6-phosphate dehydrogenase from mycobacterium smegmatis. | the gene fgd, which codes for f420-dependent glucose-6-phosphate dehydrogenase (fgd), was cloned from mycobacterium smegmatis, and its sequence was determined and analyzed. a homolog of fgd which has a very high similarity to the m. smegmatis fgd-derived amino acid sequence was identified in mycobacterium tuberculosis. fgd showed significant homology with f420-dependent n5,n10-methylene-tetrahydromethanopterin reductase (mer) from methanogenic archaea and with several hypothetical proteins from ... | 1998 | 9555906 |
| structural characteristics of methanogenic cofactors in the non-methanogenic archaebacterium archaeoglobus fulgidus. | archaeoglobus fulgidus is an extremely thermophilic, sulphate reducing archaebacterium thought to represent a biochemical missing-link between sulphur-metabolizing bacteria and methanogenic bacteria. whereas the phylogenetic position of a.fulgidus is closer to the sulphur-metabolizing bacteria, there is a partial overlap in the biochemical machinery of a.fulgidus with both groups of bacteria. in particular, the presence of a number of aberrant cofactors up to now thought to be involved exclusive ... | 1991 | 1905547 |
| spectroscopic studies on aps reductase isolated from the hyperthermophilic sulfate-reducing archaebacterium archaeglobus fulgidus. | adenylyl sulfate (aps) reductase, the key enzyme of the dissimilatory sulfate respiration, catalyzes the reduction of aps (the activated form of sulfate) to sulfite with release of amp. a spectroscopic study was carried out with the aps reductase purified from the extremely thermophilic sulfate-reducing archaebacterium archaeoglobus fulgidus dsm 4304. combined ultraviolet/visible spectroscopy and low temperature electron paramagnetic resonance (epr) studies were used in order to characterize the ... | 1991 | 1659811 |
| salt dependence, kinetic properties and catalytic mechanism of n-formylmethanofuran:tetrahydromethanopterin formyltransferase from the extreme thermophile methanopyrus kandleri. | n-formylmethanofuran(cho-mfr):tetrahydromethanopterin(h4mpt) formyltransferase (formyltransferase) from the extremely thermophilic methanopyrus kandleri was purified over 100-fold to apparent homogeneity with a 54% yield. the monomeric enzyme had an apparent molecular mass of 35 kda. the n-terminal amino acid sequence of the polypeptide was determined. the formyltransferase was found to be absolutely dependent on the presence of phosphate or sulfate salts for activity. the ability of salts to ac ... | 1992 | 1483480 |
| purification and properties of an extremely thermostable nadp+-specific glutamate dehydrogenase from archaeoglobus fulgidus. | nadp+-specific glutamate dehydrogenase (ec 1.4.1.4) was purified to homogeneity from the extremely thermophilic, strictly anaerobic, sulfate-reducing archaeon archaeoglobus fulgidus strain 7324. the native enzyme (263 kda) is composed of subunits of mol. mass 46 kda, suggesting a hexameric structure. the temperature optimum for enzyme activity was > 95 degrees c. the enzyme was highly thermostable, having a half-life of 140 min at 100 degrees c. potassium phosphate, kcl, and nacl enhanced the th ... | 1997 | 9385147 |
| properties and primary structure of a thermostable l-malate dehydrogenase from archaeoglobus fulgidus. | a thermostable l-malate dehydrogenase from the hyperthermophilic sulfate-reducing archaeon archaeoglobus fulgidus was isolated and characterized, and its gene was cloned and sequenced. the enzyme is a homodimer with a molecular mass of 70 kda and catalyzes preferentially the reduction of oxaloacetic acid with nadh. a. fulgidus l-malate dehydrogenase was stable for 5 h at 90 degrees c, and the half-life at 101 degrees c was 80 min. thus, a. fulgidus l-malate dehydrogenase is the most thermostable ... | 1997 | 9211715 |
| pathways of autotrophic co2 fixation and of dissimilatory nitrate reduction to n2o in ferroglobus placidus | the strictly anaerobic archaeon ferroglobus placidus was grown chemolithoautotrophically on h2 and nitrate and analyzed for enzymes and coenzymes possibly involved in autotrophic co2 fixation. the following enzymes were found [values in parentheses = μmol min-1 (mg protein)-1]: formylmethanofuran dehydrogenase (0.2), formylmethanofuran:tetrahydromethanopterin formyltransferase (0.6), methenyltetrahydromethanopterin cyclohydrolase (10), f420-dependent methylenetetrahydromethanopterin dehydrogenas ... | 1997 | 9000337 |
| catalytic properties, molecular composition and sequence alignments of pyruvate: ferredoxin oxidoreductase from the methanogenic archaeon methanosarcina barkeri (strain fusaro). | methanosarcina barkeri (strain fusaro) was grown on pyruvate as methanogenic substrate [bock, a. k., prieger-kraft, a. & schönheit, p. (1994) arch. microbiol. 161, 33-46]. the first enzyme of pyruvate catabolism, pyruvate oxidoreductase, which catalyzes oxidation of pyruvate to acetyl-coa was purified about 90-fold to apparent electrophoretic homogeneity. the purified enzyme catalyzed the coa-dependent oxidation of pyruvate with ferredoxin as an electron acceptor which defines the enzyme as a py ... | 1996 | 8620891 |
| formylmethanofuran: tetrahydromethanopterin formyltransferase and n5,n10-methylenetetrahydromethanopterin dehydrogenase from the sulfate-reducing archaeoglobus fulgidus: similarities with the enzymes from methanogenic archaea. | the sulfate-reducing archaeoglobus fulgidus contains a number of enzymes previously thought to be unique for methanogenic archaea. the purification and properties of two of these enzymes, of formylmethanofuran: tetrahydromethanopterin formyltransferase and of n5,n10-methylenetetrahydromethanopterin dehydrogenase (coenzyme f420 dependent) are described here. a comparison of the n-terminal amino acid sequences and of other molecular properties with those of the respective enzymes from three methan ... | 1993 | 8481089 |
| n5,n10-methenyltetrahydromethanopterin cyclohydrolase from the extremely thermophilic sulfate reducing archaeoglobus fulgidus: comparison of its properties with those of the cyclohydrolase from the extremely thermophilic methanopyrus kandleri. | archaeoglobus fulgidus and methanopyrus kandleri are both extremely thermophilic archaea with a growth temperature optimum at 83 degrees c and 98 degrees c, respectively. both archaea contain an active n5,n10-methenyltetrahydromethanopterin cyclohydrolase. the enzyme from m. kandleri has recently been characterized. we describe here the purification and properties of the enzyme from a. fulgidus. the cyclohydrolase from a. fulgidus was purified 180-fold to apparent homogeneity and its properties ... | 1993 | 8481088 |
| 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 |
| identification of a gene for a rubrerythrin/nigerythrin-like protein in spirillum volutans by using amino acid sequence data from mass spectrometry and nh2-terminal sequencing. | a hydrogen peroxide-resistant mutant of the catalase-negative microaerophile, spirillum volutans, constitutively expresses a 21.5 kda protein that is undetectable and non-inducible in the wild-type cells. part of the gene that encodes the protein was cloned using amino acid sequence data obtained by both mass spectrometry and nh2-terminal sequencing. the deduced 158 amino acid polypeptide shows high relatedness to rubrerythrin and nigerythrin previously described in the anaerobes clostridium per ... | 1998 | 9830123 |
| two n5,n10-methylenetetrahydromethanopterin dehydrogenases in the extreme thermophile methanopyrus kandleri: characterization of the coenzyme f420-dependent enzyme. | it was recently reported that the extreme thermophile methanopyrus kandleri contains only a h2-forming n5,n10-methylenetetrahydromethanopterin dehydrogenase which uses protons as electron acceptor. we describe here the presence in this archaeon of a second n5,n10-methylenetetrahydromethanopterin dehydrogenase which is coenzyme f420-dependent. this enzyme was purified and characterized. the enzyme was colourless, had an apparent molecular mass of 300 kda, an isoelectric point of 3.7 +/- 0.2 and w ... | 1993 | 8215796 |
| adenylylsulphate reductase from the sulphate-reducing archaeon archaeoglobus fulgidus: cloning and characterization of the genes and comparison of the enzyme with other iron-sulphur flavoproteins. | adenylylsulphate (adenosine-5'-phosphosulphate, aps) reductase from the extremely thermophilic sulphate-reducing archaeon archaeoglobus fulgidus is an iron-sulphur flavoprotein containing one non-covalently bound flavin group, eight non-haem iron and six labile sulphide atoms per molecule. reevaluation of the enzyme structure revealed the presence of two different subunits with molecular masses of 80 and 18.5 kda. the subunits are arranged in an alpha 2 beta subunit structure. we have cloned and ... | 1994 | 8081492 |
| the serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait. | inspection of the genomes for the bacteria bacillus subtilis 168, borrelia burgdorferi b31, escherichia coli k-12, haemophilus influenzae kw20, helicobacter pylori 26695, mycoplasma genitalium g-37, and synechocystis sp pcc 6803 and for the archaeons archaeoglobus fulgidus vc-16 dsm4304, methanobacterium thermoautotrophicum delta h, and methanococcus jannaschii dsm2661 revealed that each contains at least one orf whose predicted product displays sequence features characteristic of eukaryote-like ... | 1998 | 9862122 |
| genes from nine genomes are separated into their organisms in the dinucleotide composition space. | a set of 16 kinds of dinucleotide compositions was used to analyze the protein-encoding nucleotide sequences in nine complete genomes: escherichia coli, haemophilus influenzae, helicobacter pylori, mycoplasma genitalium, mycoplasma pneumoniae, synechocystis sp., methanococcus jannaschii, archaeoglobus fulgidus, and saccharomyces cerevisiae. the dinucleotide composition was significantly different between the organisms. the distribution of genes from an organism was clustered around its center in ... | 1998 | 9872449 |
| f420h2: quinone oxidoreductase from archaeoglobus fulgidus. characterization of a membrane-bound multisubunit complex containing fad and iron-sulfur clusters. | archaeoglobus fulgidus, a hyperthermophilic sulfate-reducing archaeon, was found to contain a membrane-bound f420h2: quinone oxidoreductase complex presumed to be involved in energy conservation during growth on lactate plus sulfate. after solubilization with dodecyl-beta-d-maltoside the complex was purified 32-fold with a yield of 24%. using both gel filtration and native page, an apparent molecular mass of approximately 270 kda was determined. sds/page revealed the presence of at least seven p ... | 1994 | 8055920 |
| conservation of the genes for dissimilatory sulfite reductase from desulfovibrio vulgaris and archaeoglobus fulgidus allows their detection by pcr. | the structural genes for dissimilatory sulfite reductase (desulfoviridin) from desulfovibrio vulgaris hilden-borough were cloned as a 7.2-kbp sacii dna fragment. nucleotide sequencing indicated the presence of a third gene, encoding a protein of only 78 amino acids, immediately downstream from the genes for the alpha and beta subunits (dsva and dsvb). we designated this protein dsvd and the gene encoding it the dsvd gene. the alpha- and beta-subunit sequences are highly homologous to those of th ... | 1995 | 7887608 |
| enzymology and molecular biology of sulfate reduction in extremely thermophilic archaeon archaeoglobus fulgidus. | | 1994 | 7830617 |
| pyruvate: ferredoxin oxidoreductase from the sulfate-reducing archaeoglobus fulgidus: molecular composition, catalytic properties, and sequence alignments. | archaeoglobus fulgidus is a hyperthermophilic sulfate-reducing archaeon. in this communication we describe the purification and properties of pyruvate: ferredoxin oxidoreductase from this organism. the catabolic enzyme was purified 250-fold to apparent homogeneity with a yield of 16%. the native enzyme had an apparent molecular mass of 120 kda and was composed of four different subunits of apparent molecular masses of 45, 33, 25, and 13 kda, indicating an alpha beta gamma delta structure. per mo ... | 1995 | 7710318 |
| polymorphism identification and quantitative detection of genomic dna by invasive cleavage of oligonucleotide probes. | flap endonucleases (fens) isolated from archaea are shown to recognize and cleave a structure formed when two overlapping oligonucleotides hybridize to a target dna strand. the downstream oligonucleotide probe is cleaved, and the precise site of cleavage is dependent on the amount of overlap with the upstream oligonucleotide. we have demonstrated that use of thermostable archaeal fens allows the reaction to be performed at temperatures that promote probe turnover without the need for temperature ... | 1999 | 10096299 |
| 5'-methylbenzimidazolyl-cobamides are the corrinoids from some sulfate-reducing and sulfur-metabolizing bacteria. | the sulfate-reducing bacteria desulfobacterium autotrophicum, desulfobulbus propionicus and archaeoglobus fulgidus (vc-16) and the sulfur-metabolizing archaebacteria desulfurolobus ambivalens and thermoplasma acidophilum were found to contain considerable amounts of corrinoids, that were isolated and crystallized in their co beta-cyano form. in three other sulfur-metabolizing archaebacteria, thermoproteus neutrophilus, pyrodictium occultum and staphylothermus marinus significant amounts of corri ... | 1988 | 3416881 |
| structural diversity among methanofurans from different methanogenic bacteria. | an examination of the methanofurans isolated from a wide range of methanogenic bacteria and from archaeoglobus fulgidus has revealed at least five chromatographically distinct methanofurans. bacteria from each major genus of methanogenic bacteria have been found to contain a chemically different methanofuran. the nature of the differences in the methanofurans appears to lie in the modification of the side chain attached to the basic core structure of 4-[n-(gamma-l-glutamyl-gamma-l-glutamyl)-p-(b ... | 1988 | 3170480 |
| vitamin contents of archaebacteria. | the levels of six water-soluble vitamins of seven archaebacterial species were determined and compared with the levels found in a eubacterium, escherichia coli. biotin, riboflavin, pantothenic acid, nicotinic acid, pyridoxine, and lipoic acid contents of halobacterium volcanii, methanobacterium thermoautotrophicum delta h, "archaeoglobus fulgidus" vc-16, thermococcus celer, pyrodictium occultum, thermoproteus tenax, and sulfolobus solfataricus were measured by using bioassays. the archaebacteria ... | 1988 | 3137215 |
| phylogenetic conservation of antigenic determinants in archaebacterial elongation factors (tu proteins). | by using affinity chromatography methods, we have purified elongation factor tu (ef-tu) proteins from a host of archaebacteria covering all known divisions in the archaebacterial tree except halophiles, and from such distantly related eubacteria as thermotoga maritima and escherichia coli. polyclonal antibodies were raised against the tu proteins of sulfolobus solfataricus, thermoproteus tenax, thermococcus celer, pyrococcus wosei, archaeoglobus fulgidus, methanococcus thermolitotrophicus, therm ... | 1989 | 2470483 |
| dissimilatory atp sulfurylase from the hyperthermophilic sulfate reducer archaeoglobus fulgidus belongs to the group of homo-oligomeric atp sulfurylases. | in the hyperthermophilic sulfate reducer archaeoglobus fulgidus dsm 4304t, two open reading frames (sat and orf2) are located upstream of the aprba genes encoding adenosine-5'-phosphosulfate (aps) reductase. sat-orf2-aprba probably form a transcriptional unit, since sat is preceded by putative promoter sequences and termination signals are found downstream of apra. while the 117-residue orf2 product does not show significant similarity to known proteins, the 456-residue, 52.78-kda, sat-encoded p ... | 1998 | 9627961 |
| phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. | microorganisms that use sulfate as a terminal electron acceptor for anaerobic respiration play a central role in the global sulfur cycle. here, we report the results of comparative sequence analysis of dissimilatory sulfite reductase (dsr) genes from closely and distantly related sulfate-reducing organisms to infer the evolutionary history of dsr. a 1.9-kb dna region encoding most of the alpha and beta subunits of dsr could be recovered only from organisms capable of dissimilatory sulfate reduct ... | 1998 | 9603890 |
| acetyl-coa decarbonylase/synthase complex from archaeoglobus fulgidus. | the acetyl-coa decarbonylase/synthase (acds) multienzyme complex catalyzes the reversible cleavage and synthesis of acetyl-coa in methanogens. this report of the enzyme complex in archaeoglobus fulgidus demonstrates the existence of a functional acds complex in an organism that is not a methanogen. the a. fulgidus enzyme complex contained five subunits of 89, 72, 50, 49.5, and 18.5 kda, and it catalyzed the overall synthesis of acetyl-coa according to the following reaction: co2 + 2 fdred(fe2+) ... | 1998 | 9575239 |
| the complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon archaeoglobus fulgidus. | archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. its genome of 2,178,400 base pairs contains 2,436 open reading frames (orfs). the information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon methanococcus jannaschii. the genomes of these two archaea indicate dramatic differences in the way these organisms se ... | 1997 | 9389475 |
| characterization and sequence comparison of temperature-regulated chaperonins from the hyperthermophilic archaeon archaeoglobus fulgidus. | we have cloned and sequenced the genes encoding two chaperonin subunits (cpn-alpha and cpn-beta), from archaeoglobus fulgidus, a sulfate-reducing hyperthermophilic archaeon. the genes encode proteins of 545 amino acids with calculated mr of 58 977 and 59 683. both proteins have been identified in cytoplasmic fractions of a. fulgidus by western analysis using antibodies raised against one of the subunits expressed in escherichia coli, and by n-terminal amino acid sequencing of chaperonin complexe ... | 1998 | 9714842 |
| 2-hydroxyglutaryl-coa dehydratase from clostridium symbiosum. | component d (hgdab) of 2-hydroxyglutaryl-coa dehydratase from clostridium symbiosum was purified to homogeneity. it is able to use component a from acidaminococcus fermentans (hgdc) to initiate catalysis together with atp, mg2+ and a strong reducing agent such as ti(iii)citrate. component d from c. symbiosum has a 6 x higher specific activity compared with that from a. fermentans and contains a second [4fe-4s] cluster but the same amount of riboflavin 5'-phosphate (1.0 per heterodimeric enzyme, ... | 1999 | 10491198 |
| biochemical and phylogenetic characterization of isocitrate dehydrogenase from a hyperthermophilic archaeon, archaeoglobus fulgidus. | a thermostable homodimeric isocitrate dehydrogenase from the hyperthermophilic sulfate-reducing archaeon archaeoglobus fulgidus was purified and characterized. the mol. mass of the isocitrate dehydrogenase subunit was 42 kda as determined by sds-page. following separation by sds-page, a. fulgidus isocitrate dehydrogenase could be renatured and detected in situ by activity staining. the enzyme showed dual coenzyme specificity with a high preference for nadp+. optimal temperature for activity was ... | 1997 | 9325430 |
| towards the phylogeny of aps reductases and sirohaem sulfite reductases in sulfate-reducing and sulfur-oxidizing prokaryotes. | the genes for adenosine-5'-phosphosulfate (aps) reductase, aprba, and sirohaem sulfite reductase, dsrab, from the sulfur-oxidizing phototrophic bacterium chromatium vinosum strain d (dsmz 180(t)) were cloned and sequenced. statistically significant sequence similarities and similar physicochemical properties suggest that the aprba and dsrab gene products from chr. vinosum are true homologues of their counterparts from the sulfate-reducing chemotrophic archaeon archaeoglobus fulgidus and the sulf ... | 1997 | 9308173 |
| newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for dna substrate binding and catalysis resembling human flap endonuclease-1. | mammalian flap endonuclease-1 (fen-1) is a structure-specific metalloenzyme that acts in processing of both the okazaki fragments during lagging strand dna synthesis and flap intermediates during dna damage repair. we identified and cloned three open reading frames encoding a flap endonuclease from archaeglobus fulgidus, methanococcus jannaschii, and pyrococcus furiosus, respectively. the deduced fen-1 protein sequences share approximately 75% similarity with the human fen-1 nuclease in the cons ... | 1998 | 9765234 |
| 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 |
| bacillus subtilis orf yybq encodes a manganese-dependent inorganic pyrophosphatase with distinctive properties: the first of a new class of soluble pyrophosphatase? | the n-terminal 15 amino acids of the major protein associated with inorganic pyrophosphatase activity in bacillus subtilis wb600 are identical to those of b. subtilis orf yybq. this orf was amplified from b. subtilis wb600 dna by pcr and cloned into an overexpression vector in escherichia coli. induction of overexpression produced a soluble protein of 34,000 da by sds-page and by matrix-assisted laser desorption and ionization mass spectrometry. the overexpressed protein had a high specific acti ... | 1998 | 9782505 |
| purification and characterization of mar1. a mitochondrial associated ribonuclease from leishmania tarentolae. | a relatively thermostable 22-kda endoribonuclease (mar1) was purified more than 10,000-fold from a mitochondrial extract of leishmania tarentolae and the gene cloned. the purified nuclease has a km of 100-145 +/- 33 nm and a vmax of 1.8-2.9 +/- 2 nmol/min, depending on the rna substrate, and yields a 3'-oh and a 5'-phosphate. cleavage was limited to several specific sites in the substrate rnas tested, but cleavage of pre-edited rnas was generally independent of the addition of cognate guide rna. ... | 1998 | 9792721 |
| a functional homolog of a yeast trna splicing enzyme is conserved in higher eukaryotes and in escherichia coli. | trna splicing in the yeast saccharomyces cerevisiae requires an endonuclease to excise the intron, trna ligase to join the trna half-molecules, and 2'-phosphotransferase to transfer the splice junction 2'-phosphate from ligated trna to nad, producing adp ribose 1"-2" cyclic phosphate (appr>p). we show here that functional 2'-phosphotransferases are found throughout eukaryotes, occurring in two widely divergent yeasts (candida albicans and schizosaccharomyces pombe), a plant (arabidopsis thaliana ... | 1998 | 9826666 |
| identification and characterization of a single-stranded dna-binding protein from the archaeon methanococcus jannaschii. | single-stranded dna-binding proteins (ssbs) play essential roles in dna replication, recombination, and repair in bacteria and eukarya. we report here the identification and characterization of the ssb of an archaeon, methanococcus jannaschii. the m. jannaschii ssb (mjassb) has significant amino acid sequence similarity to the eukaryotic ssb, replication protein a (rpa), and contains four tandem repeats of the core single-stranded dna (ssdna) binding domain originally defined by structural studi ... | 1998 | 9843941 |
| cloning and expression of a unique inorganic pyrophosphatase from bacillus subtilis: evidence for a new family of enzymes. | an open reading frame located in the cotf-tetb intergenic region of bacillus subtilis was cloned and expressed in escherichia coli and shown to encode inorganic pyrophosphatase (ppase). the isolated enzyme is mn2+-activated, like the authentic ppase isolated from b. subtilis. although 13 functionally important active site residues are conserved in all 31 soluble ppase sequences so far identified, only two of them are conserved in b. subtilis ppase. this suggests that b. subtilis ppase represents ... | 1998 | 9845334 |
| estimation of genome sizes of hyperthermophiles. | genomes of various hyperthermophilic and extremely thermophilic prokaryotes were analyzed with respect to size, physical organization, and 16s rdna copy number. our results show that all the genomes are circular, and they are in the size range of 1.6-1.8 mb for pyrodictium abyssi, methanococcus igneus, pyrobaculum aerophilum, archaeoglobus fulgidus, archaeoglobus lithotrophicus, and archaeoglobus profundus (the two bacteria fervidobacterium islandicum and thermosipho africanus possess genomes of ... | 1998 | 9672684 |
| 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 |
| evolution of p-type atpases. | | 1998 | 9693719 |
| 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 |
| transcription in archaea. | using the sequences of all the known transcription-associated proteins from bacteria and eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal genomes. through extensive sequence comparisons, we establish the presence of 280 predicted transcription factors or transcription-associated proteins in the four archaeal genomes, of which 168 have homologs only in bacteria, 51 have homologs only in eucarya, and the remaining 61 have homologs in both p ... | 1999 | 10411912 |
| comparative genomics of the archaea (euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. | comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (methanococcus jannaschii, methanobacterium thermoautotrophicum, archaeoglobus fulgidus, and pyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all four species. the proteins that belong to these conserved euryarchaeal families comprise 31%-35% of the gene complement and may be considered the evolutionarily stable core of the arch ... | 1999 | 10413400 |
| evaluation of the invader assay, a linear signal amplification method, for identification of mutations associated with resistance to rifampin and isoniazid in mycobacterium tuberculosis. | we evaluated a recently described linear signal amplification method for sensitivity and specificity in detecting mutations associated with resistance to rifampin (rif) and isoniazid (inh) in mycobacterium tuberculosis. the assay utilizes the thermostable flap endonuclease cleavase viii, derived from archaeoglobus fulgidus, which cleaves a structure formed by the hybridization of two overlapping oligonucleotide probes to a target nucleic acid strand. this method, termed the invader assay, can di ... | 2000 | 10770765 |
| homology modeling and identification of serine 160 as nucleophile of the active site in a thermostable carboxylesterase from the archaeon archaeoglobus fulgidus. | the hyperthermophilic archaeon archaeoglobus fulgidus has a gene (af1763) which encodes a thermostable carboxylesterase belonging to the hormone-sensitive lipase (hsl)-like group of the esterase/lipase family. based on secondary structure predictions and a secondary structure-driven multiple sequence alignment with remote homologous proteins of known three-dimensional structure, we previously hypothesized for this enzyme the alpha/beta-hydrolase fold typical of several lipases and esterases and ... | 2000 | 10775661 |
| control of ribosomal protein l1 synthesis in mesophilic and thermophilic archaea. | the mechanisms for the control of ribosomal protein synthesis have been characterized in detail in eukarya and in bacteria. in archaea, only the regulation of the mval1 operon (encoding ribosomal proteins mval1, mval10, and mval12) of the mesophilic methanococcus vannielii has been extensively investigated. as in bacteria, regulation takes place at the level of translation. the regulator protein mval1 binds preferentially to its binding site on the 23s rrna, and, when in excess, binds to the reg ... | 1999 | 10430567 |
| characterization of the desulforubidin operons from desulfobacter vibrioformis and desulfobulbus rhabdoformis. | the genes encoding the desulforubidin type of dissimilatory sulfite reductase (dsr) from the sulfate-reducing bacteria desulfobacter vibrioformis and desulfobulbus rhabdoformis were cloned and sequenced. similar to the genes for dissimilatory sulfite reductase from the genera archaeoglobus, desulfovibrio and desulfotomaculum the dsr genes were found to form an operon, dsrabd, where dsra and dsrb encode the structural subunits, alpha and beta, of dsr, respectively. dsrd encodes a conserved unknow ... | 2000 | 10779710 |
| identification of the archaeoglobus fulgidus endonuclease iii dna interaction surface using heteronuclear nmr methods. | endonuclease iii is the prototype for a family of dna-repair enzymes that recognize and remove damaged and mismatched bases from dna via cleavage of the n-glycosidic bond. crystal structures for endonuclease iii, which removes damaged pyrimidines, and muty, which removes mismatched adenines, show a highly conserved structure. although there are several models for dna binding by this family of enzymes, no experimental structures with bound dna exist for any member of the family. | 1999 | 10467137 |
| archaeal genomics. | four euryarchaeal genomes have been completely sequenced and are publicly available: methanococcus jannaschii, methanobacterium thermoautotrophicum, pyrococcus horikoshii and archaeoglobus fulgidus. four more genome sequences, two crenarchaeal and two pyrococci, will soon be released. in addition, seven more archaeal genome sequencing projects are under way, including two halophiles, two thermoplasma, and a methanogen. these projects cover all branches of the archaeal domain and will lead to new ... | 1999 | 10508726 |
| the sodium ion translocating glutaconyl-coa decarboxylase from acidaminococcus fermentans: cloning and function of the genes forming a second operon. | glutaconyl-coa decarboxylase from acidaminococcus fermentans (clostridal cluster ix), a strict anaerobic inhabitant of animal intestines, uses the free energy of decarboxylation (delta g(o) approximately -30 kj mol-1) in order to translocate na+ from the inside through the cytoplasmic membrane. the proton, which is required for decarboxylation, most probably comes from the outside. the enzyme consists of four different subunits. the largest subunit, alpha or gcda (65 kda), catalyses the transfer ... | 1999 | 10027965 |
| unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic archaea. | the predominant pool of organic matter on earth is derived from the biological reduction and assimilation of carbon dioxide gas, catalyzed primarily by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco). by virtue of its capacity to use molecular oxygen as an alternative and competing gaseous substrate, the catalytic efficiency of rubisco and the enzyme's ability to assimilate co2 may be severely limited, with consequent environmental and agricultural effects. recent genomic se ... | 1999 | 10049390 |
| diversity of dissimilatory bisulfite reductase genes of bacteria associated with the deep-sea hydrothermal vent polychaete annelid alvinella pompejana. | a unique community of bacteria colonizes the dorsal integument of the polychaete annelid alvinella pompejana, which inhabits the high-temperature environments of active deep-sea hydrothermal vents along the east pacific rise. the composition of this bacterial community was characterized in previous studies by using a 16s rrna gene clone library and in situ hybridization with oligonucleotide probes. in the present study, a pair of pcr primers (p94-f and p93-r) were used to amplify a segment of th ... | 1999 | 10049872 |
| dissimilatory sulfite reductase from archaeoglobus profundus and desulfotomaculum thermocisternum: phylogenetic and structural implications from gene sequences. | the genes encoding the alpha- and beta-subunits of dissimilatory sulfite reductase, dsrab, from the hyperthermophilic archaeon archaeoglobus profundus and the thermophilic gram-positive bacterium desulfotomaculum thermocisternum were cloned and sequenced. the dsrab genes are contiguous, and most probably comprise an operon also including a dsrd homolog, a conserved gene of unknown function located downstream of dsrab in all four sulfate reducers so far sequenced. sequence comparison confirms tha ... | 1999 | 10086846 |
| engineered isoprenoid pathway enhances astaxanthin production in escherichia coli. | the isoprenoid pathway is a versatile biosynthetic network leading to over 23,000 compounds. similar to other biosynthetic pathways, the production of isoprenoids in microorganisms is controlled by the supply of precursors, among other factors. to engineer a host that has the capability to supply geranylgeranyl diphosphate (ggpp), a common precursor of isoprenoids, we cloned and overexpressed isopentenyl diphosphate (ipp) isomerase (encoded by idi) from escherichia coli and ggpp synthase (encode ... | 1999 | 10099534 |
| identification of protein-tyrosine phosphatases in archaea. | protein-tyrosine dephosphorylation is a major mechanism in cellular regulation. a large number of protein-tyrosine phosphatases is known from eukarya, and more recently bacterial homologues have also been identified. by employing conserved sequence patterns from both eukaryotic and bacterial protein-tyrosine phosphatases, we have identified three homologous sequences in two of the four complete archaeal genomes. two hypothetical open reading frames in the genome of methanococcus jannaschii (mj02 ... | 1999 | 10198128 |
| purification, characterization, dna sequence and cloning of a pimeloyl-coa synthetase from pseudomonas mendocina 35. | a pimeloyl-coa synthetase from pseudomonas mendocina 35 was purified and characterized, the dna sequence determined, and the gene cloned into escherichia coli to yield an active enzyme. the purified enzyme had a ph optimum of approximately 8.0, km values of 0.49 mm for pimelic acid, 0.18 mm for coa and 0.72 mm for atp, a subunit mr of approximately 80000 as determined by sds/page, and was found to be a tetramer by gel-filtration chromatography. the specific activity of the purified enzyme was 77 ... | 1999 | 10359666 |
| a fast algorithm for genome-wide analysis of proteins with repeated sequences. | we present a fast algorithm to search for repeating fragments within protein sequences. the technique is based on an extension of the smith-waterman algorithm that allows the calculation of sub-optimal alignments of a sequence against itself. we are able to estimate the statistical significance of all sub-optimal alignment scores. we also rapidly determine the length of the repeating fragment and the number of times it is found in a sequence. the technique is applied to sequences in the swisspro ... | 1999 | 10382671 |
| a comparison of eubacterial and archaeal structure-specific 5'-exonucleases. | the 5'-exonuclease domains of the dna polymerase i proteins of eubacteria and the fen1 proteins of eukarya and archaea are members of a family of structure-specific 5'-exonucleases with similar function but limited sequence similarity. their physiological role is to remove the displaced 5' strands created by dna polymerase during displacement synthesis, thereby creating a substrate for dna ligase. in this paper, we define the substrate requirements for the 5'-exonuclease enzymes from thermus aqu ... | 1999 | 10409700 |
| overexpression, purification, and analysis of complementation behavior of e. coli suhb protein: comparison with bacterial and archaeal inositol monophosphatases. | the e. coli suhb gene product, which has been suggested to participate in posttranscriptional control of gene expression, also possesses inositol-1-phosphatase (i-1-pase) activity. to test if suhb i-1-pase activity is sufficient for its function in cells, we have cloned the genes for three other i-1-pases (from the archaea methanococcus jannaschii and archaeoglobus fulgidus, and from the bacterium thermotoga maritima) into the e. coli expression vector pet23a(+) and examined if these extragenic ... | 2000 | 10747806 |
| uracil-dna glycosylase in the extreme thermophile archaeoglobus fulgidus. | uracil-dna glycosylase (udg) is an essential enzyme for maintaining genomic integrity. here we describe a udg from the extreme thermophile archaeoglobus fulgidus. the enzyme is a member of a new class of enzymes found in prokaryotes that is distinct from the udg enzyme found in escherichia coli, eukaryotes, and dna-containing viruses. the a. fulgidus udg is extremely thermostable, maintaining full activity after heating for 1.5 h at 95 degrees c. the protein is capable of removing uracil from do ... | 2000 | 10777501 |
| inositol-1-phosphate synthase from archaeoglobus fulgidus is a class ii aldolase. | a gene putatively identified as the archaeoglobus fulgidus inositol-1-phosphate synthase (ips) gene was overexpressed to high level (about 30-40% of total soluble cellular proteins) in escherichia coli. the recombinant protein was purified to homogeneity by heat treatment followed by two column chromatographic steps. the native enzyme was a tetramer of 168 +/- 4 kda (subunit molecular mass of 44 kda). at 90 degrees c the k(m) values for glucose-6-phosphate and nad(+) were estimated as 0.12 +/- 0 ... | 2000 | 11015222 |
| genetic analysis of carboxydothermus hydrogenoformans carbon monoxide dehydrogenase genes coof and coos. | carboxydothermus hydrogenoformans is an extremely thermophilic, gram-positive bacterium growing on carbon monoxide (co) as single carbon and energy source and producing only h(2) and co(2). carbon monoxide dehydrogenase is a key enzyme for co metabolism. the carbon monoxide dehydrogenase genes coof and coos from c. hydrogenoformans were cloned and sequenced. these genes showed the highest similarity to the coof genes from the archaeon archaeoglobus fulgidus and the coos gene from the bacterium r ... | 2000 | 11024270 |
| the archean sulfur cycle and the early history of atmospheric oxygen. | the isotope record of sedimentary sulfides can help resolve the history of oxygen accumulation into the atmosphere. we measured sulfur isotopic fractionation during microbial sulfate reduction up to 88 degrees c and show how sulfate reduction rate influences the preservation of biological fractionations in sediments. the sedimentary sulfur isotope record suggests low concentrations of seawater sulfate and atmospheric oxygen in the early archean (3.4 to 2.8 billion years ago). the accumulation of ... | 2000 | 10784446 |
| thermostabilization of proteins by diglycerol phosphate, a new compatible solute from the hyperthermophile archaeoglobus fulgidus. | diglycerol phosphate accumulates under salt stress in the archaeon archaeoglobus fulgidus (l. o. martins, r. huber, h. huber, k. o. stetter, m. s. da costa, and h. santos, appl. environ. microbiol. 63:896-902, 1997). this solute was purified after extraction from the cell biomass. in addition, the optically active and the optically inactive (racemic) forms of the compound were synthesized, and the ability of the solute to act as a protecting agent against heating was tested on several proteins d ... | 2000 | 10788369 |
| adenylylsulfate reductases from archaea and bacteria are 1:1 alphabeta-heterodimeric iron-sulfur flavoenzymes--high similarity of molecular properties emphasizes their central role in sulfur metabolism. | highly active adenylylsulfate (aps) reductase was isolated under n(2)/h(2) from sulfate-reducing and sulfide-oxidizing bacteria and archaea. it was a 1:1 alphabeta-heterodimer of molecular mass approximately 95 kda, and two subunits (alpha approximately 75, beta approximately 20 kda). the specific activity was 11-14 micromol (min mg)(-1); cofactor analysis revealed 0.96+/-0.05 fad, 7.5+/-0.1 fe and 7.9+/-0.25 s(2-). the photochemically reduced enzyme had a multiline epr spectrum resulting from t ... | 2000 | 10802060 |
| whole genome-based phylogenetic analysis of free-living microorganisms. | a phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. past attempts to reconstruct the evolutionary relation-ships of microorganisms have been limited to sets of genes rather than complete genomes. despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. ... | 1999 | 10518613 |
| biofilm formation in hyperthermophilic archaea. | | 1999 | 10547803 |
| early lateral transfer of genes encoding malic enzyme, acetyl-coa synthetase and alcohol dehydrogenases from anaerobic prokaryotes to entamoeba histolytica. | the fermentation enzymes, which enable the microaerophilic protist entamoeba histolytica to parasitize the colonic lumen and tissue abscesses, closely resemble homologues in anaerobic prokaryotes. here, genes encoding malic enzyme and acetyl-coa synthetase (nucleoside diphosphate forming) were cloned from e. histolytica, and their evolutionary origins, as well as those encoding two alcohol dehydrogenases (adhe and adh1), were inferred by means of phylogenetic reconstruction. the e. histolytica m ... | 2000 | 11069669 |
| 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 |
| identification and characterization of a novel ferric reductase from the hyperthermophilic archaeon archaeoglobus fulgidus. | archaeoglobus fulgidus, a hyperthermophilic sulfate-reducing archaeon, contains high fe(3+)-edta reductase activity in its soluble protein fraction. the corresponding enzyme, which constitutes about 0.75% of the soluble protein, was purified 175-fold to homogeneity. based on sds-polyacrylamide gel electrophoresis, the ferric reductase consists of a single subunit with a m(r) of 18,000. the m(r) of the native enzyme was determined by size exclusion chromatography to be 40,000 suggesting that the ... | 1999 | 10593977 |
| the archaeoglobus fulgidus d-lactate dehydrogenase is a zn(2+) flavoprotein. | archaeoglobus fulgidus, a hyperthermophilic, archaeal sulfate reducer, is one of the few organisms that can utilize d-lactate as a sole source for both carbon and electrons. the a. fulgidus open reading frame, af0394, which is predicted to encode a d-(-)-lactate dehydrogenase (dld), was cloned, and its product was expressed in escherichia coli as a fusion with the maltose binding protein (mbp). the 90-kda mbp-dld fusion protein was more efficiently expressed in e. coli when coexpressed with the ... | 1999 | 10601217 |
| cellulosome-like sequences in archaeoglobus fulgidus: an enigmatic vestige of cohesin and dockerin domains. | the distribution of cellulosomal cohesin domains among the sequences currently compiled in various sequence databases was investigated. two cohesin domains were detected in two consecutive open reading frames (orfs) of the recently sequenced genome of the archaeon archaeoglobus fulgidus. otherwise, no cohesin-like sequence could be detected in organisms other than those of the eubacteria. one of the a. fulgidus cohesin-containing orfs also harbored a dockerin domain, but the additional modular p ... | 1999 | 10606737 |
| correlation between shine--dalgarno sequence conservation and codon usage of bacterial genes. | in this study, we analyzed the correlation between codon usage bias and shine--dalgarno (sd) sequence conservation, using complete genome sequences of nine prokaryotes. for codon usage bias, we adopted the codon adaptation index (cai), which is based on the codon usage preference of genes encoding ribosomal proteins, elongation factors, heat shock proteins, outer membrane proteins, and rna polymerase subunit proteins. to compute sd sequence conservation, we used sd motif sequences predicted by t ... | 2001 | 11231896 |
| cysteine biosynthesis pathway in the archaeon methanosarcina barkeri encoded by acquired bacterial genes? | the pathway of cysteine biosynthesis in archaea is still unexplored. complementation of a cysteine auxotrophic escherichia coli strain nk3 led to the isolation of the methanosarcina barkeri cysk gene [encoding o-acetylserine (thiol)-lyase-a], which displays great similarity to bacterial cysk genes. adjacent to cysk is an open reading frame orthologous to bacterial cyse (serine transacetylase) genes. these two genes could account for cysteine biosynthesis in this archaeon. analysis of recent geno ... | 2000 | 10613873 |
| cloning, overexpression, and properties of a new thermophilic and thermostable esterase with sequence similarity to hormone-sensitive lipase subfamily from the archaeon archaeoglobus fulgidus. | a new esterase gene from the hyperthermophilic archaeon archaeoglobus fulgidus, reported to show homology with the mammalian hormone-sensitive lipase (hsl)-like group of the esterase/lipase family, was cloned by means of the polymerase chain reaction from the a. fulgidus genome. in order to compare the biochemical properties of this putative hyperthermophilic enzyme with those of the homologous, thermophilic member of hsl group, namely alicyclobacillus (formerly bacillus) acidocaldarius esterase ... | 2000 | 10620337 |
| cdna-derived amino acid sequence of acetoacetyl-coa synthetase from rat liver. | in order to examine the primary structure of acetoacetyl-coa synthetase (acetoacetate-coa ligase, ec 6.2.1.16; aa-coa synthetase), the cdna clone encoding this enzyme has been isolated from the cdna library which was prepared from the liver of rat fed a diet supplemented with 4% cholestyramine and 0.4% pravastatin for 4 days. nucleotide sequence analysis of cloned cdna revealed that aa-coa synthetase of rat liver contains an open reading frame of 2019 nucleotides, and the deduced amino acid sequ ... | 2000 | 10682835 |
| conservation of dna regulatory motifs and discovery of new motifs in microbial genomes. | regulatory motifs can be found by local multiple alignment of upstream regions from coregulated sets of genes, or regulons. we searched for regulatory motifs using the program alignace together with a set of filters that helped us choose the motifs most likely to be biologically relevant in 17 complete microbial genomes. we searched the upstream regions of potentially coregulated genes grouped by three methods: (1) genes that make up functional pathways; (2) genes homologous to regulons from a w ... | 2000 | 10854408 |
| assembly of archaeal signal recognition particle from recombinant components. | signal recognition particle (srp) takes part in protein targeting and secretion in all organisms. searches for components of archaeal srp in primary databases and completed genomes indicated that archaea possess only homologs of srp rna, and proteins srp19 and srp54. a recombinant srp was assembled from cloned, expressed and purified components of the hyperthermophilic archaeon archaeoglobus fulgidus. recombinant af-srp54 associated with the signal peptide of bovine pre-prolactin translated in v ... | 2000 | 10684931 |
| dissimilatory atp sulfurylase from archaeoglobus fulgidus. | | 2001 | 11265480 |
| sulfite reductase and aps reductase from archaeoglobus fulgidus. | | 2001 | 11265481 |
| the thermophilic esterase from archaeoglobus fulgidus: structure and conformational dynamics at high temperature. | the esterase from the hyperthermophilic archaeon archaeoglobus fulgidus is a monomeric protein with a molecular weight of about 35.5 kda. the enzyme is barely active at room temperature, displaying the maximal enzyme activity at about 80 degrees c. we have investigated the effect of the temperature on the protein structure by fourier-transform infrared spectroscopy. the data show that between 20 degrees c and 60 degrees c a small but significant decrease of the beta-sheet bands occurred, indicat ... | 2000 | 10707022 |
| 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 |
| genomic analysis of the histidine kinase family in bacteria and archaea. | two-component signal transduction systems, consisting of histidine kinase (hk) sensors and dna-binding response regulators, allow bacteria and archaea to respond to diverse environmental stimuli. hks possess a conserved domain (h-box region) which contains the site of phosphorylation and an atp-binding kinase domain. in this study, a genomic approach was taken to analyse the hk family in bacteria and archaea. based on phylogenetic analysis, differences in the sequence and organization of the h-b ... | 2001 | 11320123 |
| mj1647, an open reading frame in the genome of the hyperthermophile methanococcus jannaschii, encodes a very thermostable archaeal histone with a c-terminal extension. | all archaeal histones studied to date have similar lengths, 66 to 69 amino acid residues that form three alpha-helices separated by two beta-strand loop regions which together constitute a histone fold. in contrast, the eukaryal nucleosome core histones are larger, 102 to 135 residues in length, with n-terminal and c-terminal extensions flanking the histone fold that participate in gene regulation and higher-order chromatin assembly. in the methanococcus jannaschii genome, mj1647 was annotated a ... | 2000 | 10741836 |
| 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 |
| fermentation of 4-aminobutyrate by clostridium aminobutyricum: cloning of two genes involved in the formation and dehydration of 4-hydroxybutyryl-coa. | clostridium aminobutyricum ferments 4-aminobutyrate via succinic semialdehyde, 4-hydroxybutyrate, 4-hydroxybutyryl-coa and crotonyl-coa to acetate and butyrate. the genes coding for the enzymes that catalyse the interconversion of these intermediates are arranged in the order abfd (4-hydroxybutyryl-coa dehydratase), abft (4-hydroxybutyrate coa-transferase), and abfh (nad-dependent 4-hydroxybutyrate dehydrogenase). the genes abfd and abft were cloned, sequenced and expressed as active enzymes in ... | 2000 | 11041350 |
| protection of methanosarcina barkeri against oxidative stress: identification and characterization of an iron superoxide dismutase. | methanosarcina barkeri is a methanogenic archaeon that can only grow under strictly anoxic conditions but which can survive oxidative stress. we have recently reported that the organism contains a monofunctional catalase. we describe here that it also possesses an active iron superoxide dismutase. the enzyme was purified in three steps over 130-fold in a 14% yield to a specific activity of 1500 u/mg. sds-page revealed the presence of only one band, at an apparent molecular mass of 25 kda. the pr ... | 2000 | 11041352 |
| role of srp19 in assembly of the archaeoglobus fulgidus signal recognition particle. | previous studies have shown that srp19 promotes association of the highly conserved signal peptide-binding protein, srp54, with the signal recognition particle (srp) rna in both archaeal and eukaryotic model systems. in vitro characterization of this process is now reported using recombinantly expressed components of srp from the hyperthermophilic, sulfate-reducing archaeon archaeoglobus fulgidis. a combination of native gel mobility shift, filter binding, and ni-nta agarose bead binding assays ... | 2000 | 11041851 |
| bacterial origin for the isoprenoid biosynthesis enzyme hmg-coa reductase of the archaeal orders thermoplasmatales and archaeoglobales. | the enzyme 3-hydroxy-3-methylglutaryl coenzyme a reductase (hmg-coa reductase or hmgr) fulfills an essential role in archaea, as it is required for the synthesis of isoprenoid ethers, the main component of archaeal cell membranes. there are two clearly homologous but structurally different classes of the enzyme, one found mainly in eukaryotes and archaea (class 1), and the other found in bacteria (class 2). this feature facilitated the identification of several cases of interdomain lateral gene ... | 2001 | 11420376 |
| a deoxyinosine specific endonuclease from hyperthermophile, archaeoglobus fulgidus: a homolog of escherichia coli endonuclease v. | deoxyadenosine undergoes spontaneous deamination to deoxyinosine in dna. based on amino acids sequence homology, putative homologs of endonuclease v were identified in several organisms including archaebacteria, eubacteria as well as eukaryotes. the translated amino acid sequence of the archaeoglobus fulgidus nfi gene shows 39% identity and 55% similarity to the e. coli nfi gene. a. fulgidus endonuclease v was cloned and expressed in e. coli as a c-terminal hexa-histidine fusion protein. the c-t ... | 2000 | 11056288 |
| complexes with truncated rnas from the large domain of archaeoglobus fulgidus signal recognition particle. | protein srp19 is an important component of the signal recognition particle (srp) as it promotes assembly of protein srp54 with srp rna and recognizes a tetranucleotide loop. structural features and rna binding activities of srp19 of the hyperthermophilic archaeon archaeoglobus fulgidus were investigated. an updated alignment of srp19 sequences predicted three conserved regions and two alpha-helices. with af-srp rna the af-srp54 protein assembled into an a. fulgidus srp which remained intact for ... | 2001 | 11430398 |
| oxygen detoxification in the strict anaerobic archaeon archaeoglobus fulgidus: superoxide scavenging by neelaredoxin. | archaeoglobus fulgidus is a hyperthermophilic sulphate-reducing archaeon. it has an optimum growth temperature of 83 degrees c and is described as a strict anaerobe. its genome lacks any homologue of canonical superoxide (o2.-) dismutases. in this work, we show that neelaredoxin (nlr) is the main o2.- scavenger in a. fulgidus, by studying both the wild-type and recombinant proteins. nlr is a 125-amino-acid blue-coloured protein containing a single iron atom/molecule, which in the oxidized state ... | 2000 | 11069658 |