| a novel sphingoglycolipid containing galacturonic acid and 2-hydroxy fatty acid in cellular lipids of sphingomonas yanoikuyae. | a novel sphingoglycolipid was isolated from sphingomonas yanoikuyae, and its structure was identified as a galacturonosyl-beta (1-->1)-ceramide. this was a characteristic sphingoglycolipid present in s. yanoikuyae and certain other species of sphingomonas, such as sphingomonas mali, sphingomonas terrae, and sphingomonas macrogoltabidus, but not in the type species of sphingomonas, sphingomonas paucimobilis. | 2000 | 10762275 |
| proposal of sphingomonas wittichii sp. nov. for strain rw1t, known as a dibenzo-p-dioxin metabolizer. | a polyphasic taxonomic study was performed on sphingomonas sp. strain rw1t. the organism was isolated from water of the river elbe and has been known as a potent metabolizer of dibenzo-p-dioxin and its relatives. tlc of a mild alkaline hydrolysate of extractable cellular lipids of strain rw1t and type strains of 21 sphingomonas species gave a spot of sphingoglycolipid (sgl)-1 (glucuronosyl ceramide), which is characteristic of sphingomonads. in addition, strain rw1t and type strains of three sph ... | 2001 | 11321072 |
| proposal of the genus sphingomonas sensu stricto and three new genera, sphingobium, novosphingobium and sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. | phylogenetic analyses of 16s rrna gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus sphingomonas can be divided into four clusters. some chemotaxonomic and phenotypic differences were noted among these clusters. three new genera, sphingobium, novosphingobium and sphingopyxis, are proposed in addition to the genus sphingomonas sensu stricto. the genus sphingobium is proposed to accommodate sphingomonas chlorophenolica, sphingomonas her ... | 2001 | 11491340 |
| correction of the connecting vowel and gender of the specific epithet in the name sphingomonas macrogoltabidus takeuchi et al. 1993 to sphingomonas macrogolitabida. | in accordance with the bacteriological code (1990 revision), the connecting vowel and gender of the specific epithet macrogoltabidus in combination with the generic name sphingomonas must be -i- and the ending must be changed to -a to agree with the gender of the generic name, respectively. thus sphingomonas macroboltabidus takeuchi et al. 1993 should be sphingomonas macrogolitabida corrig. takeuchi et al. 1993. | 2002 | 12054221 |
| sphingopyxis witflariensis sp. nov., isolated from activated sludge. | classification of strain w-50(t), which was isolated from a wastewater treatment plant, was investigated by a polyphasic approach. cells of strain w-50(t) were gram-negative, strictly aerobic, oxidase-positive and yellow-pigmented. ubiquinone q-10 was the main respiratory lipoquinone system and polar lipid fingerprints were characterized by the presence of a sphingoglycolipid, suggesting that strain w-50(t) belongs to the alpha-4 subclass of the proteobacteria. sequencing and comparative analyse ... | 2002 | 12508864 |
| identification and functional characterization of sphingomonas macrogolitabida strain tfa genes involved in the first two steps of the tetralin catabolic pathway. | five genes involved in the two initial steps of the tetralin biodegradation pathway of sphingomonas macrogolitabida strain tfa have been characterized. thna1a2 and thna3a4, components of the ring-hydroxylating dioxygenase, were encoded in divergently transcribed operons. thna1, thna2, and thna3 were essential for tetralin ring-hydroxylating dioxygenase activity. thnb was identified as a dehydrogenase required for tetralin biodegradation. | 2003 | 12618469 |
| sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of sphingomonas alaskensis to sphingopyxis alaskensis comb. nov. | the taxonomic position of a chlorophenol-degrading bacterium, strain s37t, was investigated. the 16s rdna sequence indicated that this strain belongs to the genus sphingopyxis, exhibiting high sequence similarity to the 16s rdna sequences of sphingomonas alaskensis lmg 18877t (98.8%), sphingopyxis macrogoltabida lmg 17324t (98.2%), sphingopyxis terrae ifo 15098t (95%) and sphingomonas adhaesiva gifu 11458t (92%). these strains (except sphingopyxis terrae ifo 15098t, which was not investigated) a ... | 2003 | 12710615 |
| identification and distribution of insertion sequences of paracoccus solventivorans. | three novel insertion sequences (iss) (ispso1, ispso2, and ispso3) of the soil bacterium paracoccus solventivorans dsm 11592 were identified by transposition into entrapment vector pmec1. ispso1 (1,400 bp) carries one large open reading frame (orf) encoding a putative basic protein (with a dde motif conserved among transposases [tnps] of elements belonging to the is256 family) with the highest levels of similarity with the hypothetical tnps of rhodospirillum rubrum and sphingopyxis macrogoltabid ... | 2003 | 14660342 |
| stable long-term indigo production by overexpression of dioxygenase genes using a chromosomal integrated cascade expression circuit. | in our laboratory we have analyzed different factors to maximize the yield in heterologous protein expression for long-term cultivation, by combination of an efficient cascade expression system and stable integration in the bacterial chromosome. in this work, we have explored this system for the production of indigo dye as a model for biotechnological production, by expressing in escherichia coli the thna1a2a3a4 genes from sphingomonas macrogolitabida strain tfa, which encode the components of a ... | 2004 | 15664075 |
| sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family sphingomonadaceae in alpha-4 subclass of the proteobacteria. | strain kw07t, a gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from granules in an up-flow anaerobic sludge blanket (uasb) bioreactor used in the treatment of brewery wastewater. 16s rrna gene sequence analysis revealed that strain kw07t belongs to the alpha-4 subclass of the proteobacteria, and the highest degree of sequence similarity was determined to be to sphingopyxis macrogoltabida ifo 15033t(97.8%). chemotaxonomic data revealed that strain kw07t possesses a quinone s ... | 2005 | 15880090 |
| structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. | the plasmids from 16 sphingomonads which degrade various xenobiotics and polycyclic aromatic compounds were compared with the previously sequenced plasmid pnl1 from sphingomonas aromaticivorans f199. the replicase genes repaaab from plasmid pnl1 were amplified by pcr and used as a gene probe for the identification of plasmids belonging to the same incompatibility group as plasmid pnl1. plasmids were prepared from various sphingomonads and hybridized with the repa gene probe. positive hybridizati ... | 2005 | 15942009 |
| isolation and identification of sphingomonas sp. that yields tert-octylphenol monoethoxylate under aerobic conditions. | topsoil samples were collected from eight golf courses in yamaguchi prefecture, japan, and enrichment cultures were carried out with a basal-salt medium containing 0.2% 4-tert-octylphenol polyethoxylate (oppeo) as sole carbon source. oppeo-degrading activity was detected in one of the samples, from which a strain of oppeo-degrading bacterium was isolated. the isolated bacterium grew on a nutritionally enriched medium (ne medium) containing 0.2% oppeo as sole carbon source, and accumulated 4-tert ... | 2005 | 16041123 |
| isolation of bacteria able to grow on both polyethylene glycol (peg) and polypropylene glycol (ppg) and their peg/ppg dehydrogenases. | two bacterial consortia growing on a random copolymer of ethylene glycol and propylene glycol units were obtained by enrichment cultures from various microbial samples. six major strains included in both consortia were purified and identified as sphingomonads, pseudomonas sp. and stenotrophomonas maltophilia. three of them (sphingobium sp. strain ek-1, sphingopyxis macrogoltabida strain ey-1, and pseudomonas sp. strain pe-2) utilized both peg and polypropylene glycol (ppg) as a sole carbon sourc ... | 2007 | 17043822 |
| structure and conservation of a polyethylene glycol-degradative operon in sphingomonads. | sphingopyxis terrae, and sphingopyxis macrogoltabida strains 103 and 203, can degrade polyethylene glycols (pegs). they differ in the following respects: (i) different substrate specificities (chain length) of assimilable peg, (ii) peg-inducible or constitutive peg-degradative proteins, and (iii) symbiotic or axenic degradation of peg. s. terrae was able to incorporate peg 6000, but strain 103 could not incorporate more than peg 4000, suggesting that the difference in assimilable peg chain lengt ... | 2007 | 17259605 |
| biosynthesis of poly-beta-hydroxyalkanoate by brevundimonas vesicularis lmg p-23615 and sphingopyxis macrogoltabida lmg 17324 using acid-hydrolyzed sawdust as carbon source. | poly-beta-hydroxyalkanoate (pha) is a biodegradable polymer accumulated in intracellular granules by different bacterial species. its physical and chemical properties are similar to those of petroleum-derived plastics. material generated by the acid hydrolysis of wood was evaluated for use in the bacterial synthesis of pha. acid-hydrolyzed sawdust was prepared and adjusted to ph 7. mineral salts with carbon:nitrogen (c:n) proportions of 100:1, 100:3.5, 100:10, 100:30, or 100:50 and trace element ... | 2007 | 17630126 |
| polyethylene glycol (peg)-carboxylate-coa synthetase is involved in peg metabolism in sphingopyxis macrogoltabida strain 103. | sphingopyxis macrogoltabida strain 103 possesses polyethylene-glycol (peg)-inducible pegbcdae operon encoding the genes relevant to peg degradation. peg is converted to peg-carboxylate by pega (peg dehydrogenase) and pegc (peg-aldehyde dehydrogenase). in this study, the recombinant pege (homologous to acyl-coa synthetases) was characterized. pege was an acyl-coa synthetase active for peg-carboxylate and fatty acids. judging from the nature of this kind of protein (located on the cytoplasmic memb ... | 2008 | 17985114 |
| sphingopyxis panaciterrae sp. nov., isolated from soil from ginseng field. | a gram-negative, strictly aerobic, motile bacterial strain, designated gsoil 124t, was isolated from a soil sample taken from a ginseng field in pocheon province (south korea). the isolate contained q-10 as the predominant lipoquinone, plus c18:1 7c and summed feature 4 (c16:1 6c and/or iso- c15:0 2-oh) as the major fatty acids. the g+c content of the genomic dna was 68.1 mol%, and the major polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, and phosphatidyle ... | 2008 | 18600040 |
| sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in south korea. | a gram-negative, aerobic, motile, rod-shaped bacterium (strain gsoil 250(t)) was isolated from soil of a ginseng field in pocheon province (south korea) and was characterized using a polyphasic approach in order to determine its taxonomic position. comparative analysis of 16s rrna gene sequences showed that strain gsoil 250(t) belonged to the family sphingomonadaceae of the class alphaproteobacteria, and was related to sphingopyxis macrogoltabida (98.7 %), sphingopyxis chilensis (98.2 %), sphing ... | 2008 | 18842853 |
| tetralin-induced and thnr-regulated aldehyde dehydrogenase and beta-oxidation genes in sphingomonas macrogolitabida strain tfa. | a new cluster of genes has been found downstream of the previously identified thna2 gene. the gene products are similar to nonacylating aldehyde dehydrogenases (thng) and to proteins representing a complete beta-oxidation pathway (thnh to thnp). thng has a nonacylating nad-dependent pimelic semialdehyde dehydrogenase activity that renders pimelic acid a seven-carbon dicarboxylic acid. for further metabolism via beta-oxidation, pimelic acid could be acylated by a constitutive acyl coenzyme a (acy ... | 2010 | 19897762 |
| sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. | a gram-negative, rod-shaped, motile bacterium was isolated from the soil of a ginseng field in daejeon, south korea, and characterized in order to determine its taxonomic position. phylogenetic analysis based on 16s rrna gene sequence analysis revealed that strain dcy34(t) belonged to the family sphingomonadaceae, and the highest degree of sequence similarity was found with sphingopyxis witflariensis w-50(t) (97.1 %), sphingopyxis ginsengisoli gsoil 250(t) (97.0 %), sphingopyxis chilensis s37(t) ... | 2010 | 19933588 |
| thny is a ferredoxin reductase-like iron-sulfur flavoprotein that has evolved to function as a regulator of tetralin biodegradation gene expression. | previous genetic studies in sphingomonas macrogolitabida strain tfa have established that expression of genes involved in tetralin biodegradation (thn genes) requires the function of the lysr type activator thnr and also thny. sequence comparison indicated that thny is homologous to bacterial oxygenase-coupled nad(p)h-dependent ferredoxin reductases. however, thny showed substitutions in highly conserved positions of the pyridine nucleotide binding domain of these ferredoxin reductases. thny exp ... | 2010 | 21068394 |
| molecular and biochemical characterization of the tetralin degradation pathway in rhodococcus sp. strain tfb. | the tetralin biodegradation pathway in rhodococcus sp. strain tfb, a gram-positive bacterium resistant to genetic manipulation, was characterized using a proteomic approach. relative protein expression in cell free extracts from tetralin- and glucose-grown cells was compared using the 2d-dige technique. identification of proteins specifically expressed in tetralin-grown cells was used to characterize a complete set of genes involved in tetralin degradation by reverse genetics. we propose a tetra ... | 2009 | 21261920 |
| characterization of a cryptic plasmid, psm103mini, from polyethylene-glycol degrading sphingopyxis macrogoltabida strain 103. | a cryptic plasmid, psm103mini, was found in polyethylene-glycol degrading bacterium sphingopyxis macrogoltabida, strain 103. the plasmid was 4,328-bp long and its gc content was 57.5%. it contained four open reading frames, but only two of them showed significant similarity to reported proteins. orf3 and orf4 were assumed to encode resolvase and replication protein (repa) respectively. downstream of orf4 we found complex repeat sequences. these together with orf3 and 4 were necessary and suffici ... | 2011 | 21307601 |
| sphingopyxis italica sp. nov., isolated from roman catacombs. | a gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain sc13e-s71(t), was isolated from tuff, volcanic rock, where the roman catacombs of saint callixtus in rome, italy, was excavated. analysis of 16s rrna gene sequences revealed that strain sc13e-s71(t) belongs to the genus sphingopyxis, and that it shows the greatest sequence similarity with sphingopyxis chilensis dsm 14889(t) (98.72 %), sphingopyxis taejonensis dsm 15583(t) (98.65 %), sphingopyxis ginsengisoli lmg 23390(t) (98.16 ... | 2012 | 23264504 |
| polyvinyl alcohol and polyethylene glycol form polymer bodies in the periplasm of sphingomonads that are able to assimilate them. | scanning electron microscopy (sem) shows remarkable morphological surface changes in sphingopyxis sp. 113p3 cells grown in polyvinyl alcohol (pva) but not in luria-bertani medium (lb) (hu et al. in arch microbiol 188: 235-241, 2007). however, transmission electron microscopy showed no surface changes in pva-grown cells and revealed the presence of polymer bodies in the periplasm of pva-grown cells, which were not observed in lb-grown cells. the presence of polymer bodies was supported by low-vac ... | 2012 | 23263333 |
| complete genome sequence of sphingopyxis macrogoltabida strain 203n (nbrc 111659), a polyethylene glycol degrader. | we determined the complete genome sequence of sphingopyxis macrogoltabida strain 203n, a polyethylene glycol degrader. because the pacbio assembly (285× coverage) seemed to be full of nucleotide-level mismatches, the newbler assembly of miseq mate-pair and paired-end data was used for finishing and the pacbio assembly was used as a reference. the pacbio assembly carried 414 nucleotide mismatches over 5,953,153 bases of the 203n genome. | 2016 | 27284142 |
| complete genome sequence of sphingopyxis macrogoltabida type strain nbrc 15033, originally isolated as a polyethylene glycol degrader. | sphingopyxis macrogoltabida strain 203, the type strain of the species, grew on polyethylene glycol (peg) and has been deposited to the stock culture at the biological resource center, national institute of technology and evaluation (nite), under the number nbrc 15033. here, we report the complete genome sequence of strain nbrc 15033. unfortunately, genes for peg degradation were missing. | 2015 | 26659674 |
| complete genome sequence of polypropylene glycol- and polyethylene glycol-degrading sphingopyxis macrogoltabida strain ey-1. | strain ey-1 was isolated from a microbial consortium growing on a random polymer of ethylene oxide and propylene oxide. strain ey-1 grew on polyethylene glycol and polypropylene glycol and identified as sphingopyxis macrogoltabida. here, we report the complete genome sequence of sphingopyxis macrogoltabida ey-1. the genome of strain ey-1 is comprised of a 4.76-mb circular chromosome, and five plasmids. the whole finishing was conducted in silico, with aids of computational tools genofinisher and ... | 2015 | 26634754 |
| involvement of poly(3-hydroxybutyrate) synthesis in catabolite repression of tetralin biodegradation genes in sphingomonas macrogolitabida strain tfa. | the tetralin biodegradation genes of sphingomonas macrogolitabida strain tfa are repressed by catabolite. insertion mutants in which thn genes are transcribed in the presence of a preferential carbon source and tetralin, bear the insertion in phac, encoding a poly(3-hydroxybutyrate) (phb) synthase, a key enzyme in phb synthesis. mutant complementation with phac genes from either ralstonia euthropha or tfa restored phb accumulation and the wild-type regulatory pattern of thn genes, thus indicatin ... | 2011 | 23761344 |
| co-ordinated regulation of two divergent promoters through higher-order complex formation by the lysr-type regulator thnr. | the genes required for tetralin biodegradation by sphingomonas macrogolitabida strain tfa are clustered in two divergent and closely linked operons. thnr, a lysr-type regulator, activates transcription from each operon in response to tetralin. the regulatory thnr gene is co-transcribed with the catabolic genes thnc, thna3 and thna4, resulting in positive autoregulation. thnr binds with different affinity to two primary binding sites, designated b and c, in the intervening region between the two ... | 2009 | 19682246 |
| involvement of peg-carboxylate dehydrogenase and glutathione s-transferase in peg metabolism by sphingopyxis macrogoltabida strain 103. | sphingopyxis terrae and the sphingopyxis macrogoltabida strains 103 and 203 are able to degrade polyethylene glycol (peg). they possess the peg operon, which is responsible for the conversion of peg to peg-carboxylate-coenzyme a (coa). the upstream (3.0 kb) and downstream (6.5 kb) regions of the operon in strain 103 were cloned and sequenced. the structure was well conserved between s. macrogoltabida strain 203 and s. terrae, except that two sets of transposases are absent in strain 203. the dow ... | 2008 | 18719904 |
| dual regulation of a polyethylene glycol degradative operon by arac-type and galr-type regulators in sphingopyxis macrogoltabida strain 103. | the genes for polyethylene glycol (peg) catabolism (pegb, c, d, a and e) in sphingopyxis macrogoltabida strain 103 were shown to form a peg-inducible operon. the pegr gene, encoding an arac-type regulator in the downstream area of the operon, is transcribed in the reverse direction. the transcription start sites of the operon were mapped, and three putative sigma(70)-type promoter sites were identified in the pegb, pega and pegr promoters. a promoter activity assay showed that the pegb promoter ... | 2006 | 17005983 |
| a novel nicotinoprotein aldehyde dehydrogenase involved in polyethylene glycol degradation. | a gene (pegc) encoding aldehyde dehydrogenase (aldh) was located 3.4 kb upstream of a gene encoding polyethylene glycol (peg) dehydrogenase (pega) in sphingomonas macrogoltabidus strain 103. aldh was expressed in escherichia coli and purified on a ni-nitrilotriacetic acid agarose column. the recombinant enzyme was a homotetramer consisting of four 46.1-kda subunits. the alignment of the putative amino acid sequence of the cloned enzyme showed high similarity with a group of nad(p)-dependent aldh ... | 2005 | 15726348 |
| regulation of tetralin biodegradation and identification of genes essential for expression of thn operons. | the tetralin biodegradation genes of sphingomonas macrogolitabida strain tfa are clustered in two closely linked and divergent operons. to analyze expression of both operons under different growth conditions, transcriptional and translational gene fusions of the first genes of each operon to lacz have been constructed in plasmids unable to replicate in sphingomonas and integrated by recombination into the genome of strain tfa. expression analysis indicated that the transcription of both genes is ... | 2004 | 15342579 |
| identification of a serine hydrolase which cleaves the alicyclic ring of tetralin. | a gene designated thnd, which is required for biodegradation of the organic solvent tetralin by sphingomonas macrogoltabidus strain tfa, has been identified. sequence comparison analysis indicated that thnd codes for a carbon-carbon bond serine hydrolase showing highest similarity to hydrolases involved in biodegradation of biphenyl. an insertion mutant defective in thnd accumulates the ring fission product which results from the extradiol cleavage of the aromatic ring of dihydroxytetralin. the ... | 2000 | 10986248 |
| genetic analysis of biodegradation of tetralin by a sphingomonas strain. | a strain designated tfa which very efficiently utilizes tetralin has been isolated from the rhine river. the strain has been identified as sphingomonas macrogoltabidus, based on 16s rdna sequence similarity. genetic analysis of tetralin biodegradation has been performed by insertion mutagenesis and by physical analysis and analysis of complementation between the mutants. the genes involved in tetralin utilization are clustered in a region of 9 kb, comprising at least five genes grouped in two di ... | 1999 | 10103288 |