Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| crystal structure of 3-hydroxybenzoate hydroxylase from comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site. | the 3-hydroxybenzoate hydroxylase (mhbh) from comamonas testosteroni kh122-3s is a single-component flavoprotein monooxygenase, a member of the glutathione reductase (gr) family. it catalyzes the conversion of 3-hydroxybenzoate to 3,4-dihydroxybenzoate with concomitant requirements for equimolar amounts of nadph and molecular oxygen. the production of dihydroxy-benzenoid derivative by hydroxylation is the first step in the aerobic degradation of various phenolic compounds in soil microorganisms. ... | 2006 | 17045293 |
| characterization of mobr, the 3-hydroxybenzoate-responsive transcriptional regulator for the 3-hydroxybenzoate hydroxylase gene of comamonas testosteroni kh122-3s. | comamonas testosteroni kh122-3s is an aerobic soil bacterium that utilizes 3-hydroxybenzoate as a sole carbon and energy source. in this strain, 3-hydroxybenzoate hydroxylase (moba) acts on the initial step of the degradation to produce 3,4-dihydroxybenzoate, which is subsequently subjected to the meta-cleavage pathway leading to tricarboxylic acid cycle intermediates. gene walking analysis of the upstream region of moba revealed an open reading frame (mobr) that encodes a transcriptional regula ... | 2006 | 17046018 |
| application of smartgene idns software to partial 16s rrna gene sequences for a diverse group of bacteria in a clinical laboratory. | laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. with the emergence of 16s rrna gene sequencing as an identification tool, we evaluated the usefulness of smartgene idns, a 16s rrna sequence database and software program for microbial identification. identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the smartgene and mic ... | 2006 | 17050811 |
| bacterial diversity in aortic aneurysms determined by 16s ribosomal rna gene analysis. | aortic aneurysms are common vascular conditions that cause considerable morbidity and mortality. understanding of the mechanisms involved in the pathogenesis of the condition remains limited. recently, infection has been suggested as possible contributor in the development of the disease. the aim of the present study was to examine aortic aneurysms for the presence of bacterial dna using polymerase chain reaction (pcr) targeting the 16s ribosomal rna (rrna) gene, followed by cloning and sequenci ... | 2006 | 17098542 |
| autoregulator protein phar for biosynthesis of polyhydroxybutyrate [p(3hb)] possibly has two separate domains that bind to the target dna and p(3hb): functional mapping of amino acid residues responsible for dna binding. | phar from paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (phap) and phar itself, both of which are components of polyhydroxyalkanoate (pha) granules (a. maehara, s. taguchi, t. nishiyama, t. yamane, and y. doi, j. bacteriol. 184:3992-4002, 2002). phar is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, pha polyester. in this study, by using a quartz crystal microbalance, we ... | 2007 | 17122335 |
| autoregulator protein phar for biosynthesis of polyhydroxybutyrate [p(3hb)] possibly has two separate domains that bind to the target dna and p(3hb): functional mapping of amino acid residues responsible for dna binding. | phar from paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (phap) and phar itself, both of which are components of polyhydroxyalkanoate (pha) granules (a. maehara, s. taguchi, t. nishiyama, t. yamane, and y. doi, j. bacteriol. 184:3992-4002, 2002). phar is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, pha polyester. in this study, by using a quartz crystal microbalance, we ... | 2007 | 17122335 |
| family shuffling of soil dna to change the regiospecificity of burkholderia xenovorans lb400 biphenyl dioxygenase. | previous work has shown that the c-terminal portion of bpha, especially two amino acid segments designated region iii and region iv, influence the regiospecificity of the biphenyl dioxygenase (bpdo) toward 2,2'-dichlorobiphenyl (2,2'-cb). in this work, we evolved bpdo by shuffling bpha genes amplified from polychlorinated biphenyl-contaminated soil dna. sets of approximately 1-kb dna fragments were amplified with degenerate primers designed to amplify the c-terminal portion of bpha. these fragme ... | 2007 | 17142386 |
| family shuffling of soil dna to change the regiospecificity of burkholderia xenovorans lb400 biphenyl dioxygenase. | previous work has shown that the c-terminal portion of bpha, especially two amino acid segments designated region iii and region iv, influence the regiospecificity of the biphenyl dioxygenase (bpdo) toward 2,2'-dichlorobiphenyl (2,2'-cb). in this work, we evolved bpdo by shuffling bpha genes amplified from polychlorinated biphenyl-contaminated soil dna. sets of approximately 1-kb dna fragments were amplified with degenerate primers designed to amplify the c-terminal portion of bpha. these fragme ... | 2007 | 17142386 |
| transcriptomic analysis reveals a bifurcated terephthalate degradation pathway in rhodococcus sp. strain rha1. | phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. rhodococcus sp. strain rha1 is notable for its ability to degrade a wide range of aromatic compounds. rha1 was previously shown to degrade phthalate (pth) and to have genes putatively encoding terephthalate (tpa) degradation. transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth on pth and that 521 were up-regulated during growth on tpa. distinct ring cleav ... | 2007 | 17142403 |
| transcriptomic analysis reveals a bifurcated terephthalate degradation pathway in rhodococcus sp. strain rha1. | phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. rhodococcus sp. strain rha1 is notable for its ability to degrade a wide range of aromatic compounds. rha1 was previously shown to degrade phthalate (pth) and to have genes putatively encoding terephthalate (tpa) degradation. transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth on pth and that 521 were up-regulated during growth on tpa. distinct ring cleav ... | 2007 | 17142403 |
| biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in rhizobium sp. strain mtp-10005: identification and functional analysis of its gene cluster. | we identified a gene cluster that is involved in the gamma-resorcylate (2,6-dihydroxybenzoate) catabolism of the aerobic bacterium rhizobium sp. strain mtp-10005. the cluster consists of the grardafcbek genes, and graa, grab, grac, and grad were heterologously expressed in escherichia coli. enzymological studies showed that grad, graa, grac, and grab encode the reductase (grad) and oxygenase (graa) components of a resorcinol hydroxylase (ec 1.14.13.x), a maleylacetate reductase (grac) (ec 1.3.1. ... | 2007 | 17158677 |
| biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in rhizobium sp. strain mtp-10005: identification and functional analysis of its gene cluster. | we identified a gene cluster that is involved in the gamma-resorcylate (2,6-dihydroxybenzoate) catabolism of the aerobic bacterium rhizobium sp. strain mtp-10005. the cluster consists of the grardafcbek genes, and graa, grab, grac, and grad were heterologously expressed in escherichia coli. enzymological studies showed that grad, graa, grac, and grab encode the reductase (grad) and oxygenase (graa) components of a resorcinol hydroxylase (ec 1.14.13.x), a maleylacetate reductase (grac) (ec 1.3.1. ... | 2007 | 17158677 |
| membrane topology of aspartate:alanine antiporter aspt from comamonas testosteroni. | we cloned the aspt gene encoding the l-aspartate:l-alanine antiporter asptct in comamonas testosteroni genomic dna. analysis of the nucleotide sequence revealed that c. testosteroni has an asp operon containing aspt upstream of the l-aspartate 4-decarboxylase gene, and that the gene order of the asp operon of c. testosteroni is the inverse of that of tetragenococcus halophilus. we used proteoliposomes to confirm the transport processes of asptct. to elucidate the two-dimensional structure of asp ... | 2007 | 17158863 |
| regulated polyploidy in halophilic archaea. | polyploidy is common in higher eukaryotes, especially in plants, but it is generally assumed that most prokaryotes contain a single copy of a circular chromosome and are therefore monoploid. we have used two independent methods to determine the genome copy number in halophilic archaea, 1) cell lysis in agarose blocks and southern blot analysis, and 2) real-time quantitative pcr. fast growing h. salinarum cells contain on average about 25 copies of the chromosome in exponential phase, and their p ... | 2006 | 17183724 |
| rational design of novel mutants of fungal 17beta-hydroxysteroid dehydrogenase. | reduction of 17-ketosteroids is a biocatalytic process of economic significance for the production of steroid drugs. this reaction can be catalyzed by different microbial 17beta-hydroxysteroid dehydrogenases (17beta-hsd), like the 17beta-hsd activity of saccharomyces cerevisiae, pichia faranosa and mycobacterium sp., and by purified 3beta,17beta-hsd from pseudomonas testosteroni. in addition to the bacterial 3beta,17beta-hsd the 17beta-hsd of the filamentous fungus cochliobolus lunatus is the on ... | 2007 | 17196285 |
| understanding oligomerization in 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni: an in silico approach and evidence for an active protein. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-hsd/cr) from comamonas testosteroni belongs to the short chain dehydrogenase/reductase (sdr) protein superfamily and catalyzes the oxidoreduction of a variety of steroid substrates, including the steroid antibiotic fusidic acid. the enzyme also mediates the carbonyl reduction of non-steroidal aldehydes and ketones such as a novel insecticide. it is suggested that 3alpha-hsd/cr contributes to the bioremediation of natural and syntheti ... | 2007 | 17258342 |
| a novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with comamonas sp. strain cnb-1. | comamonas sp. strain cnb-1 degrades nitrobenzene and chloronitrobenzene via the intermediates 2-aminomuconate and 2-amino-5-chloromuconate, respectively. deamination of these two compounds results in the release of ammonia, which is used as a source of nitrogen for bacterial growth. in this study, a novel deaminase was purified from comamonas strain cnb-1, and the gene (cnbz) encoding this enzyme was cloned. the n-terminal sequence and peptide fingerprints of this deaminase were determined, and ... | 2007 | 17259310 |
| a gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into mycobacterium tuberculosis survival in macrophages. | rhodococcus sp. strain rha1, a soil bacterium related to mycobacterium tuberculosis, degrades an exceptionally broad range of organic compounds. transcriptomic analysis of cholesterol-grown rha1 revealed a catabolic pathway predicted to proceed via 4-androstene-3,17-dione and 3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (3,4-dhsa). inactivation of each of the hsac, supab, and mce4 genes in rha1 substantiated their roles in cholesterol catabolism. moreover, the hsac(-) mutant accum ... | 2007 | 17264217 |
| influence of cobalt substitution on the activity of iron-type nitrile hydratase: are cobalt type nitrile hydratases regulated by carbon monoxide? | comamonas testosteroni ni1 nitrile hydratase is a fe-type nitrile hydratase whose native and recombinant forms are identical. here, the iron of ni1 nitrile hydratase was replaced by cobalt using a chaperone based escherichia coli expression system. cobalt (coni1) and iron (feni1) enzymes share identical vmax (30 nmol min(-1) mg(-1)) and km (200 microm) toward their substrate and identical ki values for the known competitive inhibitors of feni1. however, nitrophenols used as inhibitors do display ... | 2007 | 17267045 |
| generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls. | recently, a sequence-based approach has been developed for the fast isolation and characterization of class ii aryl-hydroxylating dioxygenase activities (s. kahl and b. hofer, microbiology 149:1475-1481, 2003). it comprises the pcr amplification of segments of alpha subunit genes of unknown sequence that encode the catalytic center and their fusion with sequences of the bpha gene cluster of burkholderia xenovorans lb400. one of the resulting chimeric enzymes, harboring the core segment of a diox ... | 2007 | 17322323 |
| degradation of alkyl methyl ketones by pseudomonas veronii mek700. | pseudomonas veronii mek700 was isolated from a biotrickling filter cleaning 2-butanone-loaded waste air. the strain is able to grow on 2-butanone and 2-hexanol. the genes for degradation of short chain alkyl methyl ketones were identified by transposon mutagenesis using a newly designed transposon, mini-tn5495, and cloned in escherichia coli. dna sequence analysis of a 15-kb fragment revealed three genes involved in methyl ketone degradation. the deduced amino acid sequence of the first gene, me ... | 2007 | 17351032 |
| comamonas odontotermitis sp. nov., isolated from the gut of the termite odontotermes formosanus. | a bacterial strain, designated dant 3-8(t), isolated from the gut of the termite odontotermes formosanus, was investigated by a polyphasic taxonomic approach. the cells were rod-shaped, gram-negative, non-pigmented, non-spore-forming and non-fermentative. phylogenetic analyses using the 16s rrna gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus comamonas, its closest neighbours being comamonas testosteroni ... | 2007 | 17392226 |
| presumed pseudobacteremia outbreak resulting from contamination of proportional disinfectant dispenser. | reported here are the microbiological and epidemiological details of a presumed outbreak of aerobic gram-negative bacilli infections affecting 19 hematological patients, which was traced to contaminated disinfectant. over a 5-month period, the following organisms were isolated from the blood cultures of 19 neutropenic patients: pseudomonas fluorescens (n = 13), achromobacter xylosoxidans (n = 12), comamonas testosteroni (n = 2) or stenotrophomonas maltophilia (n = 1). the affected patients were ... | 2007 | 17393202 |
| characterization of a c-c bond hydrolase from sphingomonas wittichii rw1 with novel specificities towards polychlorinated biphenyl metabolites. | sphingomonas wittichii rw1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. we used inverse pcr to amplify dxnb2, a gene encoding one of three meta-cleavage product (mcp) hydrolases identified in the organism that are homologues of bphd involved in biphenyl catabolism. purified dxnb2 catalyzed the hydrolysis of 8-oh 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (hopda) approximately six times faster than for hopda at saturating substrate concentrations. moreover, the speci ... | 2007 | 17416660 |
| a tale of two oxidation states: bacterial colonization of arsenic-rich environments. | microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. although this metalloid is ubiquitous on earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. in-depth exploration of the genome of the beta ... | 2007 | 17432936 |
| [study on the structure and function of a stable methane-oxidizing mixed microbial consortium]. | from an agricultural sample taken in chongqing, a stable methane-oxidizing mixed microbial consortium was established by enrichment culture with methane as a sole source of carbon and energy. the mixed consortium showed high capability of phenol degradation and 1,2-epoxypropane production from propene. more than 99% of phenol at an initial concentration of 600mg/l could be degraded by the mixed microbial consortium after 11 h of cultivation. the productivity of 1, 2-epoxypropane could be increas ... | 2007 | 17436634 |
| a polyomic approach to elucidate the fluoranthene-degradative pathway in mycobacterium vanbaalenii pyr-1. | mycobacterium vanbaalenii pyr-1 is capable of degrading a wide range of high-molecular-weight polycyclic aromatic hydrocarbons (pahs), including fluoranthene. we used a combination of metabolomic, genomic, and proteomic technologies to investigate fluoranthene degradation in this strain. thirty-seven fluoranthene metabolites including potential isomers were isolated from the culture medium and analyzed by high-performance liquid chromatography, gas chromatography-mass spectrometry, and uv-visibl ... | 2007 | 17449607 |
| evaluation of the colorimetric vitek 2 card for identification of gram-negative nonfermentative rods: comparison to 16s rrna gene sequencing. | ninety strains of a collection of well-identified clinical isolates of gram-negative nonfermentative rods collected over a period of 5 years were evaluated using the new colorimetric vitek 2 card. the vitek 2 colorimetric system identified 53 (59%) of the isolates to the species level and 9 (10%) to the genus level; 28 (31%) isolates were misidentified. an algorithm combining the colorimetric vitek 2 card and 16s rrna gene sequencing for adequate identification of gram-negative nonfermentative r ... | 2007 | 17507509 |
| characterization of biphenyl dioxygenase of pandoraea pnomenusa b-356 as a potent polychlorinated biphenyl-degrading enzyme. | biphenyl dioxygenase (bpdo) catalyzes the aerobic transformation of biphenyl and various polychlorinated biphenyls (pcbs). in three different assays, bpdo(b356) from pandoraea pnomenusa b-356 was a more potent pcb-degrading enzyme than bpdo(lb400) from burkholderia xenovorans lb400 (75% amino acid sequence identity), transforming nine congeners in the following order of preference: 2,3',4-trichloro approximately 2,3,4'-trichloro > 3,3'-dichloro > 2,4,4'-trichloro > 4,4'-dichloro approximately 2, ... | 2007 | 17526697 |
| nucleotide sequence of plasmid pcnb1 from comamonas strain cnb-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation. | the nucleotide sequence of a new plasmid pcnb1 from comamonas sp. strain cnb-1 that degrades 4-chloronitrobenzene (4cnb) was determined. pcnb1 belongs to the incp-1beta group and is 91,181 bp in length. a total of 95 open reading frames appear to be involved in (i) the replication, maintenance, and transfer of pcnb1; (ii) resistance to arsenate and chromate; and (iii) the degradation of 4cnb. the 4cnb degradative genes and arsenate resistance genes were located on an extraordinarily large transp ... | 2007 | 17526790 |
| molecular characterization of class 3 integrons from delftia spp. | two environmental strains, delftia acidovorans c17 and delftia tsuruhatensis a90, were found to carry class 3 integrons, which have seldom been reported and then only from pathogens in which they are associated with antibiotic resistance genes. the delftia integrons comprised a highly conserved class 3 integrase gene, upstream and oppositely oriented from a set of three or four gene cassettes that encoded unidentified functions. the a90 integron had one more gene cassette than the c17 integron, ... | 2007 | 17573473 |
| protein subunit interfaces: heterodimers versus homodimers. | protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ... | 2005 | 17597849 |
| a survey of orphan enzyme activities. | using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an enzyme commission number. here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. the survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases ... | 2007 | 17623104 |
| 4-sulfomuconolactone hydrolases from hydrogenophaga intermedia s1 and agrobacterium radiobacter s2. | the 4-carboxymethylen-4-sulfo-but-2-en-olide (4-sulfomuconolactone) hydrolases from hydrogenophaga intermedia strain s1 and agrobacterium radiobacter strain s2 are part of a modified protocatechuate pathway responsible for the degradation of 4-sulfocatechol. in both strains, the hydrolase-encoding genes occur downstream of those encoding the enzymes that catalyze the lactonization of 3-sulfomuconate. the deduced amino acid sequences of the 4-sulfomuconolactone hydrolases demonstrated the highest ... | 2007 | 17660282 |
| biochemical and genetic investigation of initial reactions in aerobic degradation of the bile acid cholate in pseudomonas sp. strain chol1. | bile acids are surface-active steroid compounds with toxic effects for bacteria. recently, the isolation and characterization of a bacterium, pseudomonas sp. strain chol1, growing with bile acids as the carbon and energy source was reported. in this study, initial reactions of the aerobic degradation pathway for the bile acid cholate were investigated on the biochemical and genetic level in strain chol1. these reactions comprised a-ring oxidation, activation with coenzyme a (coa), and beta-oxida ... | 2007 | 17693490 |
| human wild-type alanine:glyoxylate aminotransferase and its naturally occurring g82e variant: functional properties and physiological implications. | human hepatic peroxisomal agt (alanine:glyoxylate aminotransferase) is a plp (pyridoxal 5'-phosphate)-dependent enzyme whose deficiency causes primary hyperoxaluria type i, a rare autosomal recessive disorder. to acquire experimental evidence for the physiological function of agt, the k(eq),(overall) of the reaction, the steady-state kinetic parameters of the forward and reverse reactions, and the pre-steady-state kinetics of the half-reactions of the plp form of agt with l-alanine or glycine an ... | 2007 | 17696873 |
| ligand specificity of mobr, a transcriptional regulator for the 3-hydroxybenzoate hydroxylase gene of comamonas testosteroni kh122-3s. | mobr from comamonas testosteroni kh122-3s is a member of the marr family of transcriptional regulators and functions as a repressor for the moba gene that encodes a 3-hydroxybenzoate 4-hydroxylase. 3-hydroxybenzoate binds to mobr as a ligand, resulting in an efficient induction of moba. various 3-hydroxybenzoate analogues were examined for their inducibilities using the moba::lacz transcriptional fusion system. beta-galactosidase was induced by the addition of 2,3-dihydroxybenzoate or 3,5-dihydr ... | 2007 | 17707338 |
| host-plant selectivity of rhizobacteria in a crop/weed model system. | belowground microorganisms are known to influence plants' performance by altering the soil environment. plant pathogens such as cyanide-producing strains of the rhizobacterium pseudomonas may show strong host-plant selectivity. we analyzed interactions between different host plants and pseudomonas strains and tested if these can be linked to the cyanide sensitivity of host plants, the cyanide production of bacterial strains or the plant identity from which strains had been isolated. eight strain ... | 2007 | 17786217 |
| comparative transcriptome analysis of methylibium petroleiphilum pm1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. | high-density whole-genome cdna microarrays were used to investigate substrate-dependent gene expression of methylibium petroleiphilum pm1, one of the best-characterized aerobic methyl tert-butyl ether (mtbe)-degrading bacteria. differential gene expression profiling was conducted with pm1 grown on mtbe and ethanol as sole carbon sources. based on microarray high scores and protein similarity analysis, an mtbe regulon located on the megaplasmid was identified for further investigation. putative f ... | 2007 | 17890343 |
| mechanism of proton transfer in the 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni catalyzes the oxidation of androsterone with nad(+) to form androstanedione and nadh with a concomitant releasing of protons to bulk solvent. to probe the proton transfer during the enzyme reaction, we used mutagenesis, chemical rescue, and kinetic isotope effects to investigate the release of protons. the kinetic isotope effects of (d)v and (d(2)o)v for wild-type enzyme are 1 and 2.1 at pl 10.4 (where l represent ... | 2007 | 17893142 |
| comamonas testosteroni bacteremia in a patient with perforated acute appendicitis. short communication. | comamonas testosteroni is an uncommon isolate in the clinical laboratory as a human pathogen. c. testosteroni most commonly emerges in abdominal pathologies especially in perforated appendicitis. in turkey we report first time a case of bacteremia due to this organism, in a 22-year-old man with perforated acute appendicitis. the organism was shown to be susceptible to routine antibiotics so it was easily eliminated even after having caused a bacteremia. | 2007 | 17896478 |
| convergent evolution of a new arsenic binding site in the arsr/smtb family of metalloregulators. | acidithiobacillus ferrooxidans has an arsenic resistance operon that is controlled by an as(iii)-responsive transcriptional repressor, afarsr, a member of the arsr/smtb family of metalloregulators. afarsr lacks the as(iii) binding site of the arsrs from plasmid r773 and escherichia coli, which have a cys(32)-val-cys(34)-asp-leu-cys(37) sequence in the dna binding site. in contrast, it has three cysteine residues, cys(95), cys(96), and cys(102), that are not present in the r773 and e. coli arsrs. ... | 2007 | 17897948 |
| purification and characterization of a three-component salicylate 1-hydroxylase from sphingomonas sp. strain chy-1. | in the bacterial degradation of polycyclic aromatic hydrocarbons (pahs), salicylate hydroxylases catalyze essential reactions at the junction between the so-called upper and lower catabolic pathways. unlike the salicylate 1-hydroxylase from pseudomonads, which is a well-characterized flavoprotein, the enzyme found in sphingomonads appears to be a three-component fe-s protein complex, which so far has not been characterized. here, the salicylate 1-hydroxylase from sphingomonas sp. strain chy-1 wa ... | 2007 | 17905882 |
| evolution and functional characterization of the rh50 gene from the ammonia-oxidizing bacterium nitrosomonas europaea. | the family of ammonia and ammonium channel proteins comprises the amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous rh proteins (rh50 and rh30) that have been described thus far only in eukaryotes. the existence of an rh50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium nitrosomonas europaea. here we have used a phylogenetic approach to study the evolution of the n. europaea r ... | 2007 | 17921289 |
| cholest-4-en-3-one-delta 1-dehydrogenase, a flavoprotein catalyzing the second step in anoxic cholesterol metabolism. | the anoxic metabolism of cholesterol was studied in the denitrifying bacterium sterolibacterium denitrificans, which was grown with cholesterol and nitrate. cholest-4-en-3-one was identified before as the product of cholesterol dehydrogenase/isomerase, the first enzyme of the pathway. the postulated second enzyme, cholest-4-en-3-one-delta(1)-dehydrogenase, was partially purified, and its n-terminal amino acid sequence and tryptic peptide sequences were determined. based on this information, the ... | 2008 | 17993555 |
| cholest-4-en-3-one-delta 1-dehydrogenase, a flavoprotein catalyzing the second step in anoxic cholesterol metabolism. | the anoxic metabolism of cholesterol was studied in the denitrifying bacterium sterolibacterium denitrificans, which was grown with cholesterol and nitrate. cholest-4-en-3-one was identified before as the product of cholesterol dehydrogenase/isomerase, the first enzyme of the pathway. the postulated second enzyme, cholest-4-en-3-one-delta(1)-dehydrogenase, was partially purified, and its n-terminal amino acid sequence and tryptic peptide sequences were determined. based on this information, the ... | 2008 | 17993555 |
| the fto (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. | genetic variants in the fto (fat mass and obesity associated) gene have been associated with an increased risk of obesity. however, the function of its protein product has not been experimentally studied and previously reported sequence similarity analyses suggested the absence of homologs in existing protein databases. here, we present the first detailed computational analysis of the sequence and predicted structure of the protein encoded by fto. | 2007 | 17996046 |
| expression, purification, crystallization and initial crystallographic characterization of the p-hydroxybenzoate hydroxylase from corynebacterium glutamicum. | p-hydroxybenzoate hydroxylase (phbh) is an fad-dependent monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate (pohb) to 3,4-dihydroxybenzoate in an nadph-dependent reaction and plays an important role in the biodegradation of aromatic compounds. phbh from corynebacterium glutamicum was crystallized using the hanging-drop vapour-diffusion method in the presence of nah(2)po(4) and k(2)hpo(4) as precipitants. x-ray diffraction data were collected to a maximum resolution of 2.5 a on a ... | 2007 | 18007046 |
| establishment and characterization of dual-species biofilms formed from a 3,5-dinitrobenzoic-degrading strain and bacteria with high biofilm-forming capabilities. | in this study, the possibility of establishing a dual-species biofilm from a bacterium with a high biofilm-forming capability and a 3,5-dinitrobenzoic acid (3,5-dnba)-degrading bacterium, comamonas testosteroni a3, was investigated. our results showed that the combinations of strain a3 with each of five strains with a high biofilm-forming capability (pseudomonas sp. m8, pseudomonas putida m9, bacillus cereus m19, pseudomonas plecoglossicida m21 and aeromonas hydrophila m22) presented different l ... | 2008 | 18034834 |
| study of anoxic and oxic cholesterol metabolism by sterolibacterium denitrificans. | the initial enzymes and genes involved in the anoxic metabolism of cholesterol were studied in the denitrifying bacterium sterolibacterium denitrificans chol-1s(t). the second enzyme of the proposed pathway, cholest-4-en-3-one-delta1-dehydrogenase (acmb), was partially purified. based on amino acid sequence analysis, a gene probe was derived to screen a cosmid library of chromosomal dna for the acmb gene. a positive clone comprising a 43-kbp dna insert was sequenced. in addition to the acmb gene ... | 2008 | 18039763 |
| study of anoxic and oxic cholesterol metabolism by sterolibacterium denitrificans. | the initial enzymes and genes involved in the anoxic metabolism of cholesterol were studied in the denitrifying bacterium sterolibacterium denitrificans chol-1s(t). the second enzyme of the proposed pathway, cholest-4-en-3-one-delta1-dehydrogenase (acmb), was partially purified. based on amino acid sequence analysis, a gene probe was derived to screen a cosmid library of chromosomal dna for the acmb gene. a positive clone comprising a 43-kbp dna insert was sequenced. in addition to the acmb gene ... | 2008 | 18039763 |
| distinct roles for two cyp226 family cytochromes p450 in abietane diterpenoid catabolism by burkholderia xenovorans lb400. | the 80-kb dit cluster of burkholderia xenovorans lb400 encodes the catabolism of abietane diterpenoids. this cluster includes ditq and ditu, predicted to encode cytochromes p450 (p450s) belonging to the poorly characterized cyp226a subfamily. using proteomics, we identified 16 dit-encoded proteins that were significantly more abundant in lb400 cells grown on dehydroabietic acid (dha) or abietic acid (aba) than in succinate-grown cells. a key difference in the catabolism of dha and aba lies in th ... | 2008 | 18156276 |
| distinct roles for two cyp226 family cytochromes p450 in abietane diterpenoid catabolism by burkholderia xenovorans lb400. | the 80-kb dit cluster of burkholderia xenovorans lb400 encodes the catabolism of abietane diterpenoids. this cluster includes ditq and ditu, predicted to encode cytochromes p450 (p450s) belonging to the poorly characterized cyp226a subfamily. using proteomics, we identified 16 dit-encoded proteins that were significantly more abundant in lb400 cells grown on dehydroabietic acid (dha) or abietic acid (aba) than in succinate-grown cells. a key difference in the catabolism of dha and aba lies in th ... | 2008 | 18156276 |
| contributions of a disulfide bond to the structure, stability, and dimerization of human igg1 antibody ch3 domain. | recombinant human monoclonal antibodies have become important protein-based therapeutics for the treatment of various diseases. the antibody structure is complex, consisting of beta-sheet rich domains stabilized by multiple disulfide bridges. the dimerization of the c(h)3 domain in the constant region of the heavy chain plays a pivotal role in the assembly of an antibody. this domain contains a single buried, highly conserved disulfide bond. this disulfide bond was not required for dimerization, ... | 2008 | 18156469 |
| comamonas composti sp. nov., isolated from food waste compost. | a bacterial strain designated yy287(t), isolated from food waste compost, was investigated by polyphasic taxonomic approach. the cells were rod-shaped, gram-negative, non-pigmented, non-spore-forming and non-fermentative. phylogenetic analyses using the 16s rrna gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus comamonas; its closest neighbours were the type strains comamonas testosteroni dsm 50244(t) (96.5 ... | 2008 | 18175717 |
| social bacteria and asocial eukaryotes. | 2008 | 18199122 | |
| degradation of 4-fluorophenol by arthrobacter sp. strain if1. | a gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-fp) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. the organism, designated strain if1, was identified as a member of the genus arthrobacter on the basis of 16s ribosomal rna gene sequence analysis. arthrobacter strain if1 was able to mineralize 4-fp up to concentrations of 5 mm in batch culture. stoichiometric release of fluor ... | 2008 | 18228015 |
| different bacterial strategies to degrade taurocholate. | aerobic enrichment cultures with taurocholate or alkanesulfonates as sole sources of carbon and energy for growth were successful and yielded nine bacterial isolates, all of which utilized taurocholate. growth was complex and involved not only many, usually transient, excretion products but also sorption of taurocholate and cholate to cells. three metabolic strategies to dissimilate taurocholate were elucidated, all of which involved bile salt hydrolase cleaving taurocholate to cholate and tauri ... | 2008 | 18320171 |
| novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of patagonia. | polycyclic aromatic hydrocarbons (pahs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. our knowledge of pah-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. in this work, genes coding catabolic enzymes from pah-biodegradation pathways were characterized in coastal sediments of patagonia with different levels ... | 2008 | 18366740 |
| crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism. | the crystal structures of two ternary complexes of human spermine synthase (ec 2.5.1.22), one with 5'-methylthioadenosine and spermidine and the other with 5'-methylthioadenosine and spermine, have been solved. they show that the enzyme is a dimer of two identical subunits. each monomer has three domains: a c-terminal domain, which contains the active site and is similar in structure to spermidine synthase; a central domain made up of four beta-strands; and an n-terminal domain with remarkable s ... | 2008 | 18367445 |
| architecture and spatial organization in a triple-species bacterial biofilm synergistically degrading the phenylurea herbicide linuron. | members of a triple-species 3-(3,4-dichlorophenyl)-1-methoxy-1-methyl urea (linuron)-mineralizing consortium, i.e. the linuron- and 3,4-dichloroaniline-degrading variovorax sp. wdl1, the 3,4-dichloroaniline-degrading comamonas testosteroni wdl7 and the n,o-dimethylhydroxylamine-degrading hyphomicrobium sulfonivorans wdl6, were cultivated as mono- or multi-species biofilms in flow cells irrigated with selective or nonselective media, and examined with confocal laser scanning microscopy. in contra ... | 2008 | 18373685 |
| a new classification system for bacterial rieske non-heme iron aromatic ring-hydroxylating oxygenases. | rieske non-heme iron aromatic ring-hydroxylating oxygenases (rhos) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many rhos have been discovered, which do not belong to any group in the previous classification. here, we present a scheme for classification of rhos reflecting new sequence information and interactio ... | 2008 | 18387195 |
| the binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase. | the usage by enzymes of specific binding pathways for gaseous substrates or products is debated. the crystal structure of the redox enzyme cholesterol oxidase, determined at sub-angstrom resolution, revealed a hydrophobic tunnel that may serve as a binding pathway for oxygen and hydrogen peroxide. this tunnel is formed by a cascade of conformational rearrangements and connects the active site with the exterior surface of the protein. to elucidate the relationship between this tunnel and gas bind ... | 2008 | 18410129 |
| examination and expansion of the substrate range of m-hydroxybenzoate hydroxylase. | the gene encoding m-hydroxybenzoate hydroxylase (moba) was cloned from comamonas testosteroni gz39. moba converts m-hydroxybenzoate and to a lesser extent p-hydroxybenzoate to protocatechuate. to explore the structural and functional relationships in phenolic acid monooxygenases, moba was subjected to in vitro mutagenesis by error-prone pcr and the mutant mobas were screened for their ability to oxidize phenol or 3-aminophenol. a mutant moba with a single v257a substitution was able to transform ... | 2008 | 18417078 |
| testosterone-inducible regulator is a kinase that drives steroid sensing and metabolism in comamonas testosteroni. | the mechanism of gene regulation by steroids in bacteria is still a mystery. we use steroid-inducible 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-hsd/cr) as a reporter system to study steroid signaling in comamonas testosteroni. in previous investigations we cloned and characterized the 3alpha-hsd/cr-encoding gene, hsda. in addition, we identified two negative regulator genes (repa and repb) in the vicinity of hsda, the protein products which repress hsda expression on the lev ... | 2008 | 18424443 |
| biphenyl dioxygenase from an arctic isolate is not cold adapted. | biphenyl dioxygenase from the psychrotolerant bacterium pseudomonas sp. strain cam-1 (bpdo(cam-1)) was purified and found to have an apparent k(cat) for biphenyl of 1.1 +/- 0.1 s(-1) (mean +/- standard deviation) at 4 degrees c. in contrast, bpdo(lb400) from the mesophile burkholderia xenovorans lb400 had no detectable activity at this temperature. at 57 degrees c, the half-life of the bpdo(cam-1) oxygenase was less than half that of the bpdo(lb400) oxygenase. nevertheless, bpdo(cam-1) appears t ... | 2008 | 18424535 |
| 15n nmr relaxation studies of y14f mutant of ketosteroid isomerase: the influence of mutation on backbone mobility. | the backbone dynamics of y14f mutant of delta(5)-3-ketosteroid isomerase (ksi) from comamonas testosteroni has been studied in free enzyme and its complex with a steroid analogue, 19-nortestosterone hemisuccinate (19-nths), by 15n nmr relaxation measurements. model-free analysis of the relaxation data showed that the single-point mutation induced a substantial decrease in the order parameters (s2) in free y14f ksi, indicating that the backbone structures of y14f ksi became significantly mobile b ... | 2008 | 18424811 |
| protocol to determine accurate absorption coefficients for iron-containing transferrins. | an accurate protein concentration is an essential component of most biochemical experiments. the simplest method to determine a protein concentration is by measuring the a(280) using an absorption coefficient (epsilon) and applying the beer-lambert law. for some metalloproteins (including all transferrin family members), difficulties arise because metal binding contributes to the a(280) in a nonlinear manner. the edelhoch method is based on the assumption that the epsilon of a denatured protein ... | 2008 | 18471984 |
| crystal structure and mutagenic analysis of gdosp, a gentisate 1,2-dioxygenase from silicibacter pomeroyi. | dioxygenases catalyze dioxygen incorporation into various organic compounds and play a key role in the complex degradation pathway of mono- and polycyclic aromatic and hetero-aromatic compounds. here we report the crystal structure of gentisate 1,2-dioxygenase from silicibacter pomeroyi (gdosp) at a 2.8 a resolution. the enzyme possessed a conserved three-dimensional structure of the bicupin family, forming a homotetramerization. however, each subunit of gdosp unusually contained two ferrous cen ... | 2008 | 18505738 |
| identification of genes involved in inversion of stereochemistry of a c-12 hydroxyl group in the catabolism of cholic acid by comamonas testosteroni ta441. | comamonas testosteroni ta441 degrades steroids such as testosterone via aromatization of the a ring, followed by meta-cleavage of the ring. in the dna region upstream of the meta-cleavage enzyme gene tesb, two genes required during cholic acid degradation for the inversion of an alpha-oriented hydroxyl group on c-12 were identified. a dehydrogenase, stea, converts 7 alpha,12 alpha-dihydroxyandrosta-1,4-diene-3,17-dione to 7 alpha-hydroxyandrosta-1,4-diene-3,12,17-trione, and a hydrogenase, steb, ... | 2008 | 18539741 |
| crystal structure of a carbonyl reductase from candida parapsilosis with anti-prelog stereospecificity. | a novel short-chain (s)-1-phenyl-1,2-ethanediol dehydrogenase (scr) from candida parapsilosis exhibits coenzyme specificity for nadph over nadh. it catalyzes an anti-prelog type reaction to reduce 2-hydroxyacetophenone into (s)-1-phenyl-1,2-ethanediol. the coding gene was overexpressed in escherichia coli and the purified protein was crystallized. the crystal structure of the apo-form was solved to 2.7 a resolution. this protein forms a homo-tetramer with a broken 2-2-2 symmetry. the overall fol ... | 2008 | 18566346 |
| comamonas testosteroni meningitis in a homeless man. | we report a case of meningitis caused by comamonas testosteroni in a 54-year-old, alcoholic, homeless man. he, as a pedestrian, was struck by a car and suffered multiple fractures of the facial bones including the left frontal sinus. over the course of 2-week hospitalization, he was clinically diagnosed with multiple cerebral and cerebellar infarcts resulting in altered mental status. he was pronounced dead 15 days after the injury. at the time of autopsy, diffuse purulent meningitis was found o ... | 2008 | 18637874 |
| high crystallizability under air-exclusion conditions of the full-length lysr-type transcriptional regulator tsar from comamonas testosteroni t-2 and data-set analysis for a miras structure-solution approach. | the full-length lysr-type transcriptional regulator tsar from comamonas testosteroni t-2 was heterologously overexpressed in escherichia coli, purified and stabilized under conditions that favoured its rapid crystallization using the microbatch-under-oil technique. the purified protein was highly crystallizable and two different crystal forms were readily obtained. however, only monoclinic crystals gave diffraction beyond 2 a and there was a slight variation in unit-cell parameters between cryst ... | 2008 | 18678953 |
| cloning the bacterial bphc gene into nicotiana tabacum to improve the efficiency of pcb phytoremediation. | the aim of this work is to increase the efficiency of the biodegradation of polychlorinated biphenyls (pcbs) by the introduction of bacterial genes into the plant genome. for this purpose, we selected the bphc gene encoding 2,3-dihydroxybiphenyl-1,2-dioxygenase from pseudomonas testosteroni b-356 to be cloned into tobacco plants. the dihydroxybiphenyldioxygenase enzyme is the third enzyme in the biphenyl degradation pathway, and its unique function is the cleavage of biphenyl. three different co ... | 2009 | 18683252 |
| expression of a fused fpg gene in e. coli and engineering a strain comamonas testosteroni zd4-1-fpg for environmental application. | a fused fpg gene composed of phe b and gfp gene, which encoded catechol 2,3-dioxygenase (c23o) and green fluorescence protein (gfp), respectively, was expressed in e. coli to investigate its functional intactness. the expression results showed that c23o activity was detected in the induced bacterial cells and the e. coli cells containing the fusion protein emitted green fluorescence under epifluorescence microscopy, indicating that the fused fpg gene expressed correctly in e. coli. after express ... | 2008 | 18780218 |
| regulation of testosterone degradation in comamonas testosteroni. | recently, we have identified a gene encoding a luxr-type factor, teir (testosterone-inducible regulator), which positively regulates steroid degradation in comamonas testosteroni. herein, we demonstrate that teir interacts in vivo with steroid catabolic gene promoters. the presence of testosterone induces a significant teir protein increase at the early logarithmic phase of growth. interestingly, it is not until the early stationary phase where the activation of a steroid-inducible gene promoter ... | 2008 | 18852046 |
| antibacterial activity of some plant extracts used in folk medicine. | in the present work, selected plants were screened for their potential antibacterial activity. for evaluating antibacterial activity, both aqueous and organic solvent methanol was used. the plants screened were ocimum sanctum, jatropha gossypifolia, boerhavia diffusa, azadirachta indica, solidago virgaurea, and commelina benghalensis. the antibacterial activity was assessed against six bacterial strains--pseudomonas testosteroni, staphylococcus epidermidis, klebsiella pneumoniae, bacillus subtil ... | 2007 | 18928141 |
| analyzing the catalytic mechanism of the fe-type nitrile hydratase from comamonas testosteroni ni1. | in order to gain insight into the catalytic mechanism of fe-type nitrile hydratases (nhase), the ph and temperature dependence of the kinetic parameters k cat, k m, and k cat/ k m along with the solvent isotope effect were examined for the fe-type nhase from comamonas testosteroni ni1 ( ctnhase). ctnhase was found to exhibit a bell-shaped curve for plots of relative activity vs ph over ph values 4-10 for the hydration of acrylonitrile and was found to display maximal activity at ph approximately ... | 2008 | 18942853 |
| mutational analysis of the stability of the h2a and h2b histone monomers. | the eukaryotic histone heterodimer h2a-h2b folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. it is unclear whether there is partial folding of the isolated monomers before association. to address the possible contributions of structure in the monomers to the rapid association, we characterized h2a and h2b monomers in the absence of their heterodimeric partner. by far-uv circular dichroism, the h2a and h2b ... | 2008 | 18976667 |
| cis- and trans-regulatory elements of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase as biosensor system for steroid determination in the environment. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni is a key enzyme in the degradation of steroids in the environment. the encoding gene, hsda, is expressed only at very low levels in the absence of steroids, but undergoes a several fold induction in the presence of steroid substrates. in previous investigations, we have elucidated the mechanism of hsda regulation that involves several activators and repressors. in the present study, the hsda gene was replaced by t ... | 2009 | 19000658 |
| medium- and short-chain dehydrogenase/reductase gene and protein families : the sdr superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. | short-chain dehydrogenases/reductases (sdrs) constitute a large family of nad(p)(h)-dependent oxidoreductases, sharing sequence motifs and displaying similar mechanisms. sdr enzymes have critical roles in lipid, amino acid, carbohydrate, cofactor, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. sequence identities are low, and the most conserved feature is an alpha/beta folding pattern with a central beta sheet flanked by 2 - 3 alpha-helices from each side, thus a classi ... | 2008 | 19011750 |
| isolation of the phe-operon from g. stearothermophilus comprising the phenol degradative meta-pathway genes and a novel transcriptional regulator. | geobacillus stearothermophilus is able to utilize phenol as a sole carbon source. a dna fragment encoding a phenol hydroxylase catalyzing the first step in the meta-pathway has been isolated previously. based on these findings a pcr-based dna walk was performed initially to isolate a catechol 2,3-dioxygenase for biosensoric applications but was continued to elucidate the organisation of the genes encoding the proteins for the metabolization of phenol. | 2008 | 19014555 |
| 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase as a tool for isolation and characterization of a new marine steroid degrading bacterial strain. | steroid contamination of sea water is an ever growing problem and impacts population dynamics of all kinds of sea animals. we have long experience with the soil bacterium comamonas testosteroni which is able to catabolize a variety of steroids and polycyclic aromatic hydrocarbons, and which might be used in the bioremediation of contaminated soil. for our studies, we use 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3 alpha-hsd/cr) as an indicator system, since it is a key enzyme in ad ... | 2009 | 19026617 |
| microbial iron redox cycling in a circumneutral-ph groundwater seep. | the potential for microbially mediated redox cycling of iron (fe) in a circumneutral-ph groundwater seep in north central alabama was studied. incubation of freshly collected seep material under anoxic conditions with acetate-lactate or h(2) as an electron donor revealed the potential for rapid fe(iii) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). fe(iii) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). culture-based ... | 2009 | 19047399 |
| [microbial community structure of beer wastewater treatment plants analyzed by pcr-dgge technique]. | the microbial community structure of beer wastewater treatment plants with hydrolyze-acidification and sbr process was studied by pcr amplification and denaturing gradient gel electrophoresis (dgge) based 16s rdna. activated sludge samples were collected from both hydrolyze-acidification tank and sbr tank at different depth and disposal period. the total dna was extracted and the 16s rdna was amplified by universal primer. the microbial community structure was analyzed by denaturing gradient gel ... | 2008 | 19143400 |
| structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from streptococcus suis: crystal structures of the substrate-free and quaternary complex enzymes. | gluconate 5-dehydrogenase (ga5dh) is an nadp(h)-dependent enzyme that catalyzes a reversible oxidoreduction reaction between d-gluconate and 5-keto-d-gluconate, thereby regulating the flux of this important carbon and energy source in bacteria. despite the considerable amount of physiological and biochemical knowledge of ga5dh, there is little physical or structural information available for this enzyme. to this end, we herein report the crystal structures of ga5dh from pathogenic streptococcus ... | 2009 | 19177572 |
| thiosulfate oxidation by comamonas sp. s23 isolated from a sulfur spring. | a bacterial isolate s23 capable of oxidizing thiosulfate was isolated from a sulfur spring. strain s23 is gram-negative, aerobic, and motile. the g + c content of dna is 61.4 mol%. the fatty acid composition and phylogenetic analysis of the 16s rrna gene sequence of strain s23 showed that it is related to the members of the genus comamonas, and most closely related to comamonas testosteroni (99.9% sequence similarity). the isolate s23 exhibited thiosulfate oxidation under a mixotrophic growth co ... | 2009 | 19189181 |
| post-operative endophthalmitis due to an unusual pathogen, comamonas testosteroni. | here, we describe the first report of post-operative endophthalmitis due to comamonas testosteroni in an elderly diabetic patient after complicated cataract surgery. the isolate was identified by using mini api strips. the patient was successfully treated with intravitreal ceftazidime and oral ciprofloxacin. | 2009 | 19208890 |
| principles of bone marrow transplantation (bmt): providing optimal veterinary and husbandry care to irradiated mice in bmt studies. | bone marrow transplantation (bmt) is the treatment of choice for many leukemias, solid tumors, and metabolic diseases. the field of bone marrow research is highly dependent on in vivo experimentation, because in vitro techniques do not mimic these complicated in vivo systems. therefore, understanding the medical and husbandry care needs of these transiently immunodeficient bone marrow recipient animals is crucial for researchers, veterinary and animal care personnel. here we discuss the principl ... | 2009 | 19245745 |
| bioaugmentation of activated sludge towards 3-chloroaniline removal with a mixed bacterial population carrying a degradative plasmid. | a bioaugmentation approach combining several strategies was applied to achieve degradation of 3-chloroaniline (3ca) in semicontinuous activated sludge reactors. in a first step, a 3ca-degrading comamonas testosteroni strain carrying the degradative plasmid pnb2 was added to a biofilm reactor, and complete 3ca degradation together with spread of the plasmid within the indigenous biofilm population was achieved. a second set of reactors was then bioaugmented with either a suspension of biofilm cel ... | 2009 | 19268574 |
| population growth of a rhabditid nematode on plant growth promoting bacteria from potato tubers and rhizosphere soil. | nine bacterial isolates from the rhizosphere and(or) tubers of potato (solanum tuberosum cv. kennebec) at a field site on prince edward island were assessed as food sources for a bacteria-feeding nematode species tentatively identified as diplogaster lheritieri. this species was the most common rhabditid nematode recovered from soil around potato roots at the same site. in laboratory feeding trials, an isolate of comamonas testosteroni recovered from soil was an excellent food source for d. lher ... | 1996 | 19277195 |
| structure of the plp degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from mesorhizobium loti maff303099 and its mechanistic implications. | a vitamin b(6) degradative pathway has recently been identified and characterized in mesorhizobium loti maff303099. one of the enzymes on this pathway, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (mhpco), is a flavin-dependent enzyme and catalyzes the oxidative ring-opening of 2-methyl-3-hydroxypyridine-5-carboxylic acid to form e-2-(acetamino-methylene)succinate. the gene for this enzyme has been cloned, and the corresponding protein has been overexpressed in escherichia coli and pur ... | 2009 | 19317437 |
| chaperone-fusion expression plasmid vectors for improved solubility of recombinant proteins in escherichia coli. | the enteric bacterium escherichia coli is the most extensively used prokaryotic organism for production of proteins of therapeutic or commercial interest. however, it is common that heterologous over-expressed recombinant proteins fail to properly fold resulting in formation of insoluble aggregates known as inclusion bodies. complex systems have been developed that employ simultaneous over-expression of chaperone proteins to aid proper folding and solubility during bacterial expression. here we ... | 2009 | 19328840 |
| configurational entropy in protein-peptide binding: computational study of tsg101 ubiquitin e2 variant domain with an hiv-derived ptap nonapeptide. | configurational entropy is thought to influence biomolecular processes, but there are still many open questions about this quantity, including its magnitude, its relationship to molecular structure, and the importance of correlation. the mutual information expansion (mie) provides a novel and systematic approach to extracting configurational entropy changes due to correlated motions from molecular simulations. we present the first application of the mie method to protein-ligand binding using mul ... | 2009 | 19362095 |
| pseudomonas aeruginosa pao1 preferentially grows as aggregates in liquid batch cultures and disperses upon starvation. | in both natural and artificial environments, bacteria predominantly grow in biofilms, and bacteria often disperse from biofilms as freely suspended single-cells. in the present study, the formation and dispersal of planktonic cellular aggregates, or 'suspended biofilms', by pseudomonas aeruginosa in liquid batch cultures were closely examined, and compared to biofilm formation on a matrix of polyester (pe) fibers as solid surface in batch cultures. plankton samples were analyzed by laser-diffrac ... | 2009 | 19436737 |
| bacterial degradation of aromatic compounds. | aromatic compounds are among the most prevalent and persistent pollutants in the environment. petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (pahs) and heterocyclic aromatics. aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. this review focuses on bacterial degradation pathways o ... | 2009 | 19440284 |
| fido, a novel ampylation domain common to fic, doc, and avrb. | the vibrio parahaemolyticus type iii secreted effector vops contains a fic domain that covalently modifies rho gtpase threonine with amp to inhibit downstream signaling events in host cells. the vops fic domain includes a conserved sequence motif (hpfx[d/e]gn[g/k]r) that contributes to ampylation. fic domains are found in a variety of species, including bacteria, a few archaea, and metazoan eukaryotes. | 2009 | 19503829 |
| role of s114 in the nadh-induced conformational change and catalysis of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase reversibly catalyzes the oxidation of androsterone with nad(+) to form androstanedione and nadh. in this study, we characterize the role of the conserved residue s114 in cofactor binding and catalysis, using site-directed mutagenesis, steady-state kinetics, fluorescence quenching and anisotropy measurements. the catalytic efficiency of v/k(nadh)et for wild-type and s114a is 1.5 x10(7) and 3.8 x 10(3) m(-1) s(-1), respectively, suggesting tha ... | 2009 | 19520191 |
| igr genes and mycobacterium tuberculosis cholesterol metabolism. | recently, cholesterol was identified as a physiologically important nutrient for mycobacterium tuberculosis survival in chronically infected mice. however, it remained unclear precisely when cholesterol is available to the bacterium and what additional bacterial functions are required for its metabolism. here, we show that the igr locus, which we previously found to be essential for intracellular growth and virulence of m. tuberculosis, is required for cholesterol metabolism. while igr-deficient ... | 2009 | 19542286 |
| glycosylation of fluorophenols by plant cell cultures. | fluoroaromatic compounds are used as agrochemicals and released into environment as pollutants. glycosylation of 2-, 3-, and 4-fluorophenols using plant cell cultures of nicotiana tabacum was investigated to elucidate their potential to metabolize these compounds. cultured n. tabacum cells converted 2-fluorophenol into its beta-glucoside (60%) and beta-gentiobioside (10%). 4-fluorophenol was also glycosylated to its beta-glucoside (32%) and beta-gentiobioside (6%) by n. tabacum cells. on the oth ... | 2009 | 19564930 |