| gene arrangements characteristic of the phylum actinobacteria. | the availability of genomic sequence data allows new challenges to various biological problems. one of such attempts is the extraction of phylogenetic information from gene order data of genomes. phylogenetic inferences are most commonly carried out on the basis of 16s rrna trees, which sometimes produce unresolved or unreliable branching orders. one example for such a low resolution is recognized in the branching pattern among the phylum actinobacteria. here, gene arrangements characteristic of ... | 2007 | 17558547 |
| identification of indole derivatives as self-growth inhibitors of symbiobacterium thermophilum, a unique bacterium whose growth depends on coculture with a bacillus sp. | symbiobacterium thermophilum is a syntrophic bacterium whose growth depends on coculture with a bacillus sp. recently, we discovered that co(2) generated by bacillus is the major inducer for the growth of s. thermophilum; however, the evidence suggested that an additional element is required for its full growth. here, we studied the self-growth-inhibitory substances produced by s. thermophilum. we succeeded in purifying two substances from an ether extract of the culture supernatant of s. thermo ... | 2007 | 17693561 |
| tree of life based on genome context networks. | efforts in phylogenomics have greatly improved our understanding of the backbone tree of life. however, due to the systematic error in sequence data, a sequence-based phylogenomic approach leads to well-resolved but statistically significant incongruence. thus, independent test of current phylogenetic knowledge is required. here, we have devised a distance-based strategy to reconstruct a highly resolved backbone tree of life, on the basis of the genome context networks of 195 fully sequenced rep ... | 2008 | 18852873 |
| lessons from studies of symbiobacterium thermophilum, a unique syntrophic bacterium. | symbiobacterium thermophilum is a syntrophic bacterium whose growth depends on coculture with a cognate bacillus sp. we have been studying the unique features of s. thermophilum in terms of taxonomy, ecology, genome biology, and physiology. here we overview current knowledge of this bacterium. although s. thermophilum shows several physiological properties of gram-negative bacteria, 16s rrna gene-based phylogeny indicated that it represents a distinct lineage of gram-positive bacteria with deep ... | 2007 | 17485837 |
| data mining for proteins characteristic of clades. | a synapomorphy is a phylogenetic character that provides evidence of shared descent. ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. with the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. we h ... | 2006 | 16936320 |
| co2 supply induces the growth of symbiobacterium thermophilum, a syntrophic bacterium. | symbiobacterium thermophilum is a unique syntrophic bacterium that exhibits marked growth only in coculture with a cognate bacillus sp. in this study, we found that the bacterium is capable of marked mono-growth when supplied with co2 or bicarbonate. the evidence suggests that the genetic defect for carbonic anhydrase in this bacterium is a reason for the syntrophic property based on co2 requirement. | 2006 | 16557001 |
| conserved indels in protein sequences that are characteristic of the phylum actinobacteria. | gram-positive bacteria with a high g+c content are currently recognized as a distinct phylum, actinobacteria, on the basis of their branching in 16s rrna trees. except for an insert in the 23s rrna, there are no unique biochemical or molecular characteristics known at present that can distinguish this group from all other bacteria. in this work, three conserved indels (i.e. inserts or deletions) are described in three widely distributed proteins that are distinctive characteristics of the actino ... | 2005 | 16280504 |
| intramolecular cross-linking in a bacterial homolog of mammalian slc6 neurotransmitter transporters suggests an evolutionary conserved role of transmembrane segments 7 and 8. | the extracellular concentration of the neurotransmitters dopamine, serotonin, norepinephrine, gaba and glycine is tightly controlled by plasma membrane transporters belonging to the slc6 gene family. a very large number of putative transport proteins with a remarkable homology to the slc6 transporters has recently been identified in prokaryotes. here we have probed structural relationships in a 'microdoman' corresponding to the extracellular ends of transmembrane segments (tm) 7 and 8 in one of ... | 2005 | 16129457 |
| phylogenetic and guanine-cytosine content analysis of symbiobacterium thermophilum genes. | although the bacterium symbiobacterium thermophilum has a genome with a high guanine-cytosine (gc) content (69%), it belongs to a low gc content bacterial group. we detected only 18 low gc content regions with 5 or more consecutive genes whose gc contents were below 65% in the genome of this organism. s. thermophilum has 66 transposase genes, which are markers of transposable genetic elements, and 38 (58%) of them were located in the low gc content regions, suggesting that symbiobacterium has a ... | 2010 | 21350632 |
| genome sequence of symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. | symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. the 16s ribosomal dna-based phylogeny suggests that this bacterium belongs to an unknown taxon in the gram-positive bacterial cluster. here, we describe the 3.57 mb genome sequence of s.thermophilum. the genome consists of 3338 protein-coding sequences, out of which 2082 have functional assignments. despite the high g + c content (68.7%), the genome is closest to that of firmic ... | 2004 | 15383646 |
| characterization of a functional bacterial homologue of sodium-dependent neurotransmitter transporters. | the tnat gene of symbiobacterium thermophilum encodes a protein homologous to sodium-dependent neurotransmitter transporters. expression of the tnat gene product in escherichia coli conferred the ability to accumulate tryptophan from the medium and the ability to grow on tryptophan as a sole source of carbon. transport was na(+)-dependent and highly selective. the k(m) for tryptophan was approximately 145 nm, and tryptophan transport was unchanged in the presence of 100 microm concentrations of ... | 2003 | 12569103 |
| development of a membrane dialysis bioreactor and its application to a large-scale culture of a symbiotic bacterium, symbiobacterium thermophilum. | a simple membrane dialysis bioreactor was developed for a large-scale axenic culture of symbiobacterium thermophilum, a symbiotic thermophile that requires co-cultivation with an associating thermophilic bacillus strain s for normal growth. the bioreactor consisted of an outer- and an inner-coaxial cylindrical compartment bordered across a dialyzing membrane, which enabled a 1 l-scale dialysis culture with exchange of low molecular metabolites between the two compartments to be performed. using ... | 2002 | 12436311 |
| characterization of symbiobacterium toebii, an obligate commensal thermophile isolated from compost. | a symbiotic thermophilic bacterium, strain sc-1, was isolated from hay compost (toebi) in korea. the new isolate exhibited an obligate commensal interaction with a thermophilic geobacillus strain and required crude extracts and/or culture supernatant from geobacillus sp. sk-1 for axenic growth. the growth factors from geobacillus sp. sk-1 were irreversibly inactivated by phenol or protease treatment, suggesting that they might be proteins. the cells of strain sc-1 were non-spore forming, nonmoti ... | 2002 | 11878563 |
| distribution and diversity of symbiotic thermophiles, symbiobacterium thermophilum and related bacteria, in natural environments. | symbiobacterium thermophilum is a tryptophanase-positive thermophile which shows normal growth only in coculture with its supporting bacteria. analysis of the 16s rrna gene (rdna) indicated that the bacterium belongs to a novel phylogenetic branch at the outermost position of the gram-positive bacterial group without clustering to any other known genus. here we describe the distribution and diversity of s. thermophilum and related bacteria in the environment. thermostable tryptophanase activity ... | 2001 | 11525967 |
| symbiobacterium thermophilum gen. nov., sp. nov., a symbiotic thermophile that depends on co-culture with a bacillus strain for growth. | a gram-negative and tryptophanase-positive thermophile, whose growth is dependent on co-culture with an associating bacillus strain, had been reported and tentatively named symbiobacterium thermophilum strain t(t). axenic culture of strain t(t) was recently established by dialysing cultures with the supporting bacterial strains or adding their culture broth. phylogenetic analysis of strain t(t), based on the 16s rdna sequence, was conducted for the validation of s. thermophilum. the sequence of ... | 2000 | 11034494 |
| analysis of stability and catalytic properties of two tryptophanases from a thermophile. | two tryptophanases, tna1 and tna2, both of which were cloned from the thermophile symbiobacterium thermophilum, differ in their enzymatic properties, such as thermal stability, catalytic efficiency and activation energy of catalysis, despite the great similarity (92%) in their amino acid sequences. chimeric tryptophanases were constructed by recombination of the two genes to try to elucidate the molecular basis for the difference. the stability of each chimeric enzyme was roughly proportional to ... | 1999 | 10469830 |
| establishing the independent culture of a strictly symbiotic bacterium symbiobacterium thermophilum from its supporting bacillus strain. | symbiobacterium thermophilum is a strictly symbiotic thermophile, the growth of which is dependent on the coexistence of an associating thermophilic bacillus sp., strain s. s. thermophilum grows only in mixed culture with the bacillus strain in liquid media, and does not form visible colonies on solid media. to measure the growth of this symbiotic bacterium and to analyze its growth requirements, we developed a quantitative pcr method by using its specific sequences in a putative membrane transl ... | 1999 | 10427695 |
| thermostable tyrosine phenol-lyase of symbiobacterium sp. sc-1: gene cloning, sequence determination, and overproduction in escherichia coli. | during the screening for tyrosine phenol-lyase-producing thermophiles, we isolated an obligatory symbiotic thermophile, symbiobacterium sp. sc-1, which grew only in coculture with bacillus sp. sk-1. a gene encoding thermostable tyrosine phenol-lyase (tpl) was cloned from the genomic dna of the symbiobacterium sp. sc-1 and the nucleotide sequence of the tpl structural gene was determined. the gene consists of 1374 base pairs encoding a polypeptide of 458 amino acid residues; the molecular mass of ... | 1997 | 9425630 |
| cloning, nucleotide sequence, and overexpression in escherichia coli of the beta-tyrosinase gene from an obligately symbiotic thermophile, symbiobacterium thermophilum. | symbiobacterium thermophilum is an obligately symbiotic thermophile that can grow only in coculture with a specific bacillus strain. the amino acid sequences of fragments obtained by cyanogen bromide decomposition of the thermostable beta-tyrosinase (tyrosine phenol-lyase, e.c. 4.1.99.2) from this organism resembled that of the tryptophanase produced by the same organism. dna-probing with the tryptophanase gene as the hybridization probe led to cloning in escherichia coli of the beta-tyrosinase ... | 1993 | 7763716 |
| purification and properties of thermostable tryptophanase from an obligately symbiotic thermophile, symbiobacterium thermophilum. | a thermostable tryptophanase was extracted from a thermophilic bacterium, symbiobacterium thermophilum strain t, which is obligately symbiotic with the thermophilic bacillus strain s. the enzyme was purified 21-fold to homogeneity with 19% recovery by a series of chromatographies using anion-exchange, hydroxylapatite, hydrophobic interaction, and monoq anion-exchange columns. the molecular weight of the purified enzyme was estimated to be approximately 210,000 by gel filtration, while the molecu ... | 1991 | 1368766 |
| cloning, nucleotide sequences, and overexpression in escherichia coli of tandem copies of a tryptophanase gene in an obligately symbiotic thermophile, symbiobacterium thermophilum. | symbiobacterium thermophilum, a thermophilic bacterium, is a thermostable tryptophanase producer that can grow only in coculture with a specific bacillus strain. two thermostable tryptophanase genes, tna-1 and tna-2, that are located close to each other were cloned into escherichia coli from s. thermophilum by the dna-probing method. the nucleotide and deduced amino acid sequences indicate that tna1 and tna2 share 92% identical amino acids in a total of 453 amino acids. by means of dna manipulat ... | 1992 | 1339259 |
| thermoanaerobacteriaceae oxidize acetate in methanogenic rice field soil at 50 degrees c. | summary rice field soils contain a thermophilic microbial community. incubation of italian rice field soil at 50 degrees c resulted in transient accumulation of acetate, but the microorganisms responsible for methane production from acetate are unknown. without addition of exogenous acetate, the delta(13)c of ch(4) and co(2) indicated that ch(4) was exclusively produced by hydrogenotrophic methanogenesis. when exogenous acetate was added, acetoclastic methanogenesis apparently also operated. nev ... | 2010 | 20629702 |
| caldinitratiruptor microaerophilus, gen. nov., sp. nov. isolated from a french hot spring (chaudes-aigues, massif central): a novel cultivated facultative microaerophilic anaerobic thermophile pertaining to the symbiobacterium branch within the firmicutes. | a novel facultative microaerophilic nitrate-reducing bacterium designated ca62n(t) was isolated from a thermal spring in france. cells were non-motile rods (2-3 x 0.2 mum) and showed low cytoplasmic density when observed under a phase-contrast microscope. strain ca62n(t) grew at temperatures between 50 and 75 degrees c (optimum 65 degrees c) and at a ph between 6.3 and 7.9 (optimum 7.0). nacl was not required for growth but was tolerated up to 10 gl(-1). sulfate, thiosulfate, elemental sulfur, s ... | 2010 | 20165893 |
| simultaneous improvement of catalytic activity and thermal stability of tyrosine phenol-lyase by directed evolution. | the tyrosine phenol-lyase from symbiobacterium toebii was engineered to improve both its stability and catalytic activity by the application of random mutagenesis and subsequent reassembly of the acquired mutations. activity screening of the random library produced four mutants with a two-fold improved activity, whereas parallel screening after heat treatment at 65 degrees c identified three mutants with half-inactivation temperatures improved by up to 5.6 degrees c. the selected mutants were th ... | 2009 | 19780833 |
| microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16s rrna gene analysis. | rice paddy soil has been shown to have strong denitrifying activity. however, the microbial populations responsible for nitrate respiration and denitrification have not been well characterized. in this study, we performed a clone library analysis of >1,000 clones of the nearly full-length 16s rrna gene to characterize bacterial community structure in rice paddy soil. we also identified potential key players in nitrate respiration and denitrification by comparing the community structures of soils ... | 2009 | 19767468 |
| symbiobacterium lost carbonic anhydrase in the course of evolution. | recent genetic studies have elucidated that carbonic anhydrase (ca; ec 4.2.1.1), a ubiquitous enzyme catalyzing interconversion between co(2) and bicarbonate, is essential for microbial growth under ambient air but not under high-co(2) air. the irregular distribution of the phylogenetically distinct types of ca in the prokaryotic genome suggests its complex evolutionary history in prokaryotes. this paper deals with the genetic defect of ca in symbiobacterium thermophilum, a syntrophic bacterium ... | 2009 | 19123013 |
| characterization of growth-supporting factors produced by geobacillus toebii for the commensal thermophile symbiobacterium toebii. | symbiobacterium toebii is a commensal symbiotic thermophile that cannot grow without support from a partner bacterium. we investigated the properties of symbiobacterium growth-supporting factors (sgsfs) produced by the partner bacterium geobacillus toebii. sgsfs occurred in both the cell-free extract (cfe) and culture supernatant of g. toebii and might comprise multifarious materials because of their different biological properties. the heavy sgsf contained in the cytosolic component exhibited h ... | 2008 | 18388467 |
| distribution of symbiobacterium thermophilum and related bacteria in the marine environment. | we study the ecological distribution of a unique syntrophic bacterium, symbiobacterium thermophilum, and related bacteria. in this study, we found that they were frequently obtained from seashells and several marine samples. symbiobacterium also grew from sterilized oyster shells incubated undersea for 2 or 3 months on the coast of shimoda, shizuoka, japan. 16s rrna gene-based phylogeny of the clones obtained from the symbiobacterium-positive cultures demonstrated the potential diversity of this ... | 2008 | 18175900 |
| development of bioreactor system for l-tyrosine synthesis using thermostable tyrosine phenol-lyase. | an efficient enzyme system for the synthesis of l-tyrosine was developed using a fed-batch reactor with continuous feeding of phenol, pyruvate, and ammonia. a thermo- and chemostable tyrosine phenol-lyase from symbiobacterium toebii was employed as the biocatalyst in this work. the enzyme was produced using a constitutive expression system in escherichia coli bl21, and prepared as a soluble extract by rapid clarification, involving treatment with 40% methanol in the presence of excess ammonium c ... | 2007 | 18051362 |
| the t box regulatory element controlling expression of the class i lysyl-trna synthetase of bacillus cereus strain 14579 is functional and can be partially induced by reduced charging of asparaginyl-trnaasn. | lysyl-trna synthetase (lysrs) is unique within the aminoacyl-trna synthetase family in that both class i (lysrs1) and class ii (lysrs2) enzymes exist. lysrs1 enzymes are found in archaebacteria and some eubacteria while all other organisms have lysrs2 enzymes. all sequenced strains of bacillus cereus (except ah820) and bacillus thuringiensis however encode both a class i and a class ii lysrs. the lysk gene (encoding lysrs1) of b. cereus strain 14579 has an associated t box element, the first rep ... | 2010 | 20649968 |
| structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism. | sphingosine-1-phosphate lyase (spl), a key enzyme of sphingolipid metabolism, catalyzes the irreversible degradation of sphingoid base phosphates. its main substrate sphingosine-1-phosphate (s1p) acts both extracellularly, by binding g protein-coupled receptors of the lysophospholipid receptor family, and inside the cell, as a second messenger. there, s1p takes part in regulating various cellular processes and its levels are tightly regulated. spl is a pivotal enzyme regulating s1p intracellular ... | 2010 | 20696404 |
| family m42 aminopeptidase from the syntrophic bacterium symbiobacterium thermophilum: characterization using recombinant protein. | the chromosomal dna of the syntrophic thermophile symbiobacterium thermophilum contains open reading frames of the genes encoding family m42 aminopeptidases, pep1079, pep1080, and pep1081. to characterize these peptidases, the genes were cloned into escherichia coli and overexpressed. our experiments using the recombinant proteins confirmed that pep1079, pep1080, and pep1081 are components of arginyl or lysinyl aminopeptidases that require co²+ for enzymatic activity. coexistence of pep1079 and ... | 2010 | 20970375 |
| unique evolution of symbiobacterium thermophilum suggested from gene content and orthologous protein sequence comparisons. | comparisons of gene content and orthologous protein sequence constitute a major strategy in whole-genome comparison studies. it is expected that horizontal gene transfer between phylogenetically distant organisms and lineage-specific gene loss have greater influence on gene content-based phylogenetic analysis than orthologous protein sequence-based phylogenetic analysis. to determine the evolution of the syntrophic bacterium symbiobacterium thermophilum, we analyzed phylogenetic relationships am ... | 2010 | 21350630 |
| towards reconstructing a metabolic tree of life. | using information from several metabolic databases, we have built our own metabolic database containing 434 pathways and 1157 different enzymes. we have used this information to construct a dendrogram that demonstrates the metabolic similarities between 282 species. the resulting species distribution and the clusters defined in the tree show a certain taxonomic congruence, especially in recent relationships between species. this dendrogram is another representation of the tree of life, based on ... | 2007 | 21670791 |
| a prokaryotic s1p lyase degrades extracellular s1p in vitro and in vivo: implication for treating hyperproliferative disorders. | sphingosine-1-phosphate (s1p) regulates a broad spectrum of fundamental cellular processes like proliferation, death, migration and cytokine production. therefore, elevated levels of s1p may be causal to various pathologic conditions including cancer, fibrosis, inflammation, autoimmune diseases and aberrant angiogenesis. here we report that s1p lyase from the prokaryote symbiobacterium thermophilum (stspl) degrades extracellular s1p in vitro and in blood. moreover, we investigated its effect on ... | 2011 | 21829623 |
| thermoanaerobacteriaceae oxidize acetate in methanogenic rice field soil at 50°c. | rice field soils contain a thermophilic microbial community. incubation of italian rice field soil at 50°c resulted in transient accumulation of acetate, but the microorganisms responsible for methane production from acetate are unknown. without addition of exogenous acetate, the d(13)c of ch(4) and co(2) indicated that ch(4) was exclusively produced by hydrogenotrophic methanogenesis. when exogenous acetate was added, acetoclastic methanogenesis apparently also operated. nevertheless, addition ... | 2010 | 21966924 |
| A commensal symbiotic interrelationship for the growth of Symbiobacterium toebii with its partner bacterium, Geobacillus toebii. | ABSTRACT: | 2011 | 22023733 |