| analyses of a polyhydroxyalkanoic acid granule-associated 16-kilodalton protein and its putative regulator in the pha locus of paracoccus denitrificans. | the polyhydroxyalkanoic acid (pha) granule-associated 16-kda protein (ga16 protein) of paracoccus denitrificans was identified, and its corresponding gene was cloned and analyzed at the molecular level. the n-terminal amino acid sequence of ga16 protein revealed that its structural gene is located downstream from the pha synthase gene (phacpd) cloned recently (s. ueda, t. yabutani, a. maehara, and t. yamane, j. bacteriol. 178:774-779, 1996). gene walking around phacpd revealed two new open readi ... | 1999 | 10217786 |
| cloning, expression, and nucleotide sequence of the pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates. | we have cloned and characterized novel oxygenolytic ortho-dehalogenation (ohb) genes from 2-chlorobenzoate (2-cba)- and 2,4-dichlorobenzoate (2,4-dcba)-degrading pseudomonas aeruginosa 142. among 3,700 escherichia coli recombinants, two clones, dh5alphaf'(pod22) and dh5alphaf'(pod33), converted 2-cba to catechol and 2,4-dcba and 2,5-dcba to 4-chlorocatechol. a subclone of pod33, plasmid pe43, containing the 3,687-bp minimized ohb dna region conferred to p. putida pb2440 the ability to grow on 2- ... | 1999 | 10224014 |
| construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls. | cloning and expression of the aromatic ring dehalogenation genes in biphenyl-growing, polychlorinated biphenyl (pcb)-cometabolizing comamonas testosteroni vp44 resulted in recombinant pathways allowing growth on ortho- and para-chlorobiphenyls (cbs) as a sole carbon source. the recombinant variants were constructed by transformation of strain vp44 with plasmids carrying specific genes for dehalogenation of chlorobenzoates (cbas). plasmid pe43 carries the pseudomonas aeruginosa 142 ohb genes codi ... | 1999 | 10224015 |
| prevalence of corynebacterial 16s rrna sequences in patients with bacterial and "nonbacterial" prostatitis. | the etiology of chronic prostatitis syndromes in men is controversial, particularly when positive cultures for established uropathogens are lacking. although identification of bacteria in prostatic fluid has relied on cultivation and microscopy, most microorganisms in the environment, including some human pathogens, are resistant to cultivation. we report here on an rrna-based molecular phylogenetic approach to the identification of bacteria in prostate fluid from prostatitis patients. positive ... | 1999 | 10325338 |
| characterization of the meta-cleavage compound hydrolase gene involved in degradation of the lignin-related biphenyl structure by sphingomonas paucimobilis syk-6. | sphingomonas paucimobilis syk-6 has the ability to transform a lignin-related biphenyl compound, 2,2'-dihydroxy-3,3'-dimethoxy-5, 5'-dicarboxybiphenyl (ddva), to 5-carboxyvanillic acid (5cva) via 2, 2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl (oh-ddva). in the 4.9-kb hindiii fragment containing the oh-ddva meta-cleavage dioxygenase gene (ligz), we found a novel hydrolase gene (ligy) responsible for the conversion of the meta-cleavage compound of oh-ddva to 5cva. incorporation of 18o from h ... | 1999 | 10347082 |
| genetic analysis of a chromosomal region containing vana and vanb, genes required for conversion of either ferulate or vanillate to protocatechuate in acinetobacter. | vana and vanb form an oxygenative demethylase that converts vanillate to protocatechuate in microorganisms. ferulate, an abundant phytochemical, had been shown to be metabolized through a vanillate intermediate in several pseudomonas isolates, and biochemical evidence had indicated that vanillate also is an intermediate in ferulate catabolism by acinetobacter. genetic evidence supporting this conclusion was obtained by characterization of mutant acinetobacter strains blocked in catabolism of bot ... | 1999 | 10348863 |
| cloning and sequencing of a new comamonas testosteroni gene encoding 3 alpha-hydroxysteroid dehydrogenase/carbonyl reductase. | | 1999 | 10352711 |
| uptake of pyocin s3 occurs through the outer membrane ferripyoverdine type ii receptor of pseudomonas aeruginosa. | pyocin s3 was found to kill exclusively pseudomonas aeruginosa isolates producing type ii pyoverdine (exemplified by strain atcc 27853). killing was specifically inhibited by addition of type ii ferripyoverdine. all tn5 mutants resistant to pyocin s3 were defective for pyoverdine-mediated iron uptake and failed to produce an 85-kda iron-repressed outer membrane protein. we conclude that this protein is probably the type ii ferripyoverdine receptor that is used by pyocin s3 to gain entry into the ... | 1999 | 10368165 |
| cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase and cis-1, 2-dihydro-1,2-dihydroxynaphathalene dehydrogenase catalyze dehydrogenation of the same range of substrates. | pseudomonas putida strain g7 cis-1,2-dihydro-1, 2-dihydroxynaphthalene dehydrogenase (nahb) and comamonas testosteroni strain b-356 cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (bphb) were found to be catalytically active towards cis-2,3-dihydro-2,3-dihydroxybiphenyl (specificity factors of 501 and 5850 s-1 mm-1 respectively), cis-1,2-dihydro-1, 2-dihydroxynaphthalene (specificity factors of 204 and 193 s-1 mm-1 respectively) and 3,4-dihydro-3,4-dihydroxy-2,2',5, 5'-tetrachlorobiphenyl (s ... | 1999 | 10381363 |
| ribonucleotide reduction in pseudomonas species: simultaneous presence of active enzymes from different classes. | three separate classes of ribonucleotide reductases exist in nature. they differ widely in protein structure. class i enzymes are found in aerobic bacteria and eukaryotes; class ii enzymes are found in aerobic and anaerobic bacteria; class iii enzymes are found in strict and facultative anaerobic bacteria. usually, but not always, one organism contains only one or two (in facultative anaerobes) classes. surprisingly, the genomic sequence of pseudomonas aeruginosa contains sequences for each of t ... | 1999 | 10383965 |
| substrate and binding specificities of bacterial polyhydroxybutyrate depolymerases. | the substrate specificities of three extracellular polyhydroxybutyrate (phb) depolymerases from alcaligenes faecalis (phaz afa), pseudomonas stutzeri (phaz pst), and comamonas acidovorans (phaz cac), which are grouped into types a and b based on the position of a lipase box sequence in the catalytic domain, were examined for films of 12 different aliphatic polyesters. each of these phb depolymerases used was capable of hydrolyzing poly(3-hydroxybutyrate) (p(3hb)), poly(3-hydroxypropionate) (p(3h ... | 1999 | 10408639 |
| anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on dimethylmalonate. | the microbial capacity to degrade simple organic compounds with quaternary carbon atoms was demonstrated by enrichment and isolation of five denitrifying strains on dimethylmalonate as the sole electron donor and carbon source. quantitative growth experiments showed a complete mineralization of dimethylmalonate. according to phylogenetic analysis of the complete 16s rrna genes, two strains isolated from activated sewage sludge were related to the genus paracoccus within the alpha-proteobacteria ... | 1999 | 10427013 |
| bioconversion of pyrimidine by resting cells of quinoline-degrading bacteria. | nine quinoline-degrading bacterial strains were tested for their ability to hydroxylate pyrimidine. all strains converted pyrimidine to uracil via pyrimidine-4-one in a cometabolic process. quinoline 2-oxidoreductases (quinors) were the catalysts of fortuitous pyrimidine hydroxylation. whereas in most strains the activity of the quinor towards pyrimidine was very low compared to its activity towards quinoline, quinor in crude extracts from comamonas testosteroni 63 showed a specific activity of ... | 1999 | 10427712 |
| heterologous expression and characterization of the purified oxygenase component of rhodococcus globerulus p6 biphenyl dioxygenase and of chimeras derived from it. | in this work, we have purified the his-tagged oxygenase (ht-oxygenase) component of rhodococcus globerulus p6 biphenyl dioxygenase. the alpha or beta subunit of p6 oxygenase was exchanged with the corresponding subunit of pseudomonas sp. strain lb400 or of comamonas testosteroni b-356 to create new chimeras that were purified ht-proteins and designated ht-alpha(p6)beta(p6), ht-alpha(p6)beta(lb400), ht-alpha(p6)beta(b-356), ht-alpha(lb400)beta(p6), and ht-alpha(b-356)beta(p6). ht-alpha(p6)beta(p6 ... | 1999 | 10438748 |
| microbial degradation of nitrobenzene and mono-nitrophenol by bacteria enriched from municipal activated sludge. | using a mixture of three mono nitrophenols as sole carbon, nitrogen and energy sources, mixed cultures were enriched from municipal activated sludge to degrade both nitrophenols and nitrobenzene. bacterial growth and degradation rate could be increased by supplementing the medium with 0.1% ye. microorganisms were isolated from the nitrophenols enrichment, and they were identified as strains of comamonas testosteroni and acidovorax delafieldii. these strains showed broad degradation ability towar ... | 1999 | 10446720 |
| development of rrna-based pcr assays for identification of burkholderia cepacia complex isolates recovered from cystic fibrosis patients. | pcr assays targeting rrna genes were developed to identify species (genomovars) within the burkholderia cepacia complex. each assay was tested with 177 bacterial isolates that also underwent taxonomic analysis by whole-cell protein profile. these isolates were from clinical and environmental sources and included 107 b. cepacia complex strains, 23 burkholderia gladioli strains, 20 ralstonia pickettii strains, 10 pseudomonas aeruginosa strains, 8 stenotrophomonas maltophilia strains, and 9 isolate ... | 1999 | 10488171 |
| mechanistic insights from the three-dimensional structure of 3-oxo-delta(5)-steroid isomerase. | 3-oxo-delta(5)-steroid isomerase (ksi) catalyzes the isomerization of beta,gamma-unsaturated 3-oxosteroids to their conjugated isomers through the formation of an intermediate dienolate. the three-dimensional structure of the enzyme from pseudomonas testosteroni was solved by multidimensional heteronuclear magnetic resonance spectroscopy. this protein, a 28-kda symmetric dimer, exhibits a three-dimensional fold with the two independently folded monomers packed together via extensive hydrophobic ... | 1999 | 10496971 |
| adaptation of comamonas testosteroni ta441 to utilization of phenol by spontaneous mutation of the gene for a trans-acting factor. | comamonas testosteroni ta441 adapts to utilization of phenol upon incubation with phenol as the major carbon source. strain ta441 has a cluster of genes (aphklmnopqb) encoding the catabolic enzymes phenol hydroxylase and catechol 2,3-dioxygenase, and a divergently transcribed regulatory gene (aphr), but these genes are silent until adaptation occurs. we found another regulatory gene (aphs) downstream of aphr. aphs belongs to the gntr family of transcriptional regulators. all adapted strains were ... | 1999 | 10510228 |
| a cole1-compatible expression vector for the production of his-tagged fusion proteins. | plasmid pdb31 is a cole1-compatible expression vector based on the p15a origin of replication. it is designed to express his-tagged fusion proteins in cells co-hosting a compatible expression vector. it was constructed by assembling the operator/promoter region plus the 6xhis and the multiple cloning site of pqe31 (qiagen) with the p15a origin of replication plus kanr of pgp1-2. the plasmid was found to be stable in escherichia coli strains bl21 and dh11s. it was used to produce and purify the f ... | 1999 | 10510716 |
| genetic organization and characteristics of the 3-(3-hydroxyphenyl)propionic acid degradation pathway of comamonas testosteroni ta441. | comamonas testosteroni ta441 degrades 3-(3-hydroxyphenyl)propionate (3hpp) via the meta pathway. a gene cluster required for degradation of 3hpp was cloned from strain ta441 and sequenced. the genes encoding six catabolic enzymes, a flavin-type hydroxylase (mhpa), extradiol dioxygenase (mhpb), 2-keto-4-pentenoate hydratase (mhpd), acetaldehyde dehydrogenase (acylating) (mhpf), 4-hydroxy-2-ketovalerate aldolase (mhpe) and the meta cleavage compound hydrolase (mhpc), were found in this cluster, en ... | 1999 | 10537203 |
| endotoxins and igg antibodies as indicators of occupational exposure to the microbial contaminants of metal-working fluids. | the aim of this study was to evaluate workers' exposure to microbes and bacterial endotoxins during the use of metal-working fluids (mwf). | 1999 | 10541909 |
| thermicanus aegyptius gen. nov., sp. nov., isolated from oxic soil, a fermentative microaerophile that grows commensally with the thermophilic acetogen moorella thermoacetica. | a thermophilic, fermentative microaerophile (et-5b) and a thermophilic acetogen (et-5a) were coisolated from oxic soil obtained from egypt. the 16s rrna gene sequence of et-5a was 99.8% similar to that of the classic acetogen moorella thermoacetica. further analyses confirmed that et-5a was a new strain of m. thermoacetica. for et-5b, the nearest 16s rrna gene sequence similarity value to known genera was approximately 88%. et-5b was found to be a motile rod with a genomic g+c content of 50.3 mo ... | 1999 | 10543831 |
| crystal structure of delta(5)-3-ketosteroid isomerase from pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization. | delta(5)-3-ketosteroid isomerase from pseudomonas testosteroni has been intensively studied as a prototype to understand an enzyme-catalyzed allylic isomerization. asp(38) (pk(a) approximately 4.7) was identified as the general base abstracting the steroid c4beta proton (pk(a) approximately 12.7) to form a dienolate intermediate. a key and common enigmatic issue involved in the proton abstraction is the question of how the energy required for the unfavorable proton transfer can be provided at th ... | 1999 | 10551849 |
| characterization of a high-affinity phenol hydroxylase from comamonas testosteroni r5 by gene cloning, and expression in pseudomonas aeruginosa pao1c. | comamonas testosteroni strain r5 is a phenol-degrading bacterium which expresses a phenol-oxygenating activity that is characterized by low ks (the apparent half-saturation constant in haldane's equation) and low k(si) (the apparent inhibition constant) values. we have now cloned the gene cluster encoding a phenol hydroxylase (phcklmnop) and its cognate regulator (phcr) from strain r5. transformation of pseudomonas aeruginosa pao1c (phenol catechol+) with pror502, a derivative of pro1614 contain ... | 1999 | 10589844 |
| hbpr, a new member of the xylr/dmpr subclass within the ntrc family of bacterial transcriptional activators, regulates expression of 2-hydroxybiphenyl metabolism in pseudomonas azelaica hbp1. | the regulation of 2-hydroxybiphenyl and 2,2'-dihydroxybiphenyl degradation in pseudomonas azelaica is mediated by the regulatory gene, hbpr. the hbpr gene encodes a 63-kda protein belonging to the ntrc family of prokaryotic transcriptional activators and having the highest homology to members of the xylr/dmpr subclass. disruption of the hbpr gene in p. azelaica and complementation in trans showed that the hbpr protein was the key regulator for 2-hydroxybiphenyl metabolism. induction experiments ... | 2000 | 10629187 |
| a study on the prevalence of gram-negative bacteria in bulk tank milk. | bulk tank milk from 131 dairy herds in eastern south dakota and western minnesota were examined for coliforms and noncoliform bacteria. coliforms were detected in 62.3% of bulk tank milk samples. counts ranged from 0 to 4.7 log10 cfu/ml. the mean count was 3.4 log10 cfu/ml. gram-negative noncoliform bacteria were observed in 76.3% of bulk tank milk. counts ranged from 0 to 6.2 log10 cfu/ml. the mean count was 4.8 log10 cfu/ml. a total of 234 isolates from bulk tank milk were examined to species ... | 1999 | 10629809 |
| identification and characterization of the nitrobenzene catabolic plasmids pnb1 and pnb2 in pseudomonas putida hs12. | pseudomonas putida hs12, which is able to grow on nitrobenzene, was found to carry two plasmids, pnb1 and pnb2. the activity assay experiments of wild-type hs12(pnb1 and pnb2), a spontaneous mutant hs121(pnb2), and a cured derivative hs124(pnb1) demonstrated that the catabolic genes coding for the nitrobenzene-degrading enzymes, designated nbz, are located on two plasmids, pnb1 and pnb2. the genes nbza, nbzc, nbzd, and nbze, encoding nitrobenzene nitroreductase, 2-aminophenol 1,6-dioxygenase, 2- ... | 2000 | 10633088 |
| functional analysis of the small component of the 4-hydroxyphenylacetate 3-monooxygenase of escherichia coli w: a prototype of a new flavin:nad(p)h reductase subfamily. | escherichia coli w uses the aromatic compound 4-hydroxyphenylacetate (4-hpa) as a sole source of carbon and energy for growth. the monooxygenase which converts 4-hpa into 3,4-dihydroxyphenylacetate, the first intermediate of the pathway, consists of two components, hpab (58.7 kda) and hpac (18.6 kda), encoded by the hpab and hpac genes, respectively, that form a single transcription unit. overproduction of the small hpac component in e. coli k-12 cells has facilitated the purification of the pro ... | 2000 | 10633095 |
| substrate range and genetic analysis of acinetobacter vanillate demethylase. | an acinetobacter sp. genetic screen was used to probe structure-function relationships in vanillate demethylase, a two-component monooxygenase. mutants with null, leaky, and heat-sensitive phenotypes were isolated. missense mutations tended to be clustered in specific regions, most of which make known contributions to catalytic activity. the vanillate analogs m-anisate, m-toluate, and 4-hydroxy-3,5-dimethylbenzoate are substrates of the enzyme and weakly inhibit the metabolism of vanillate by wi ... | 2000 | 10671462 |
| substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. | the three-component naphthalene dioxygenase (ndo) enzyme system carries out the first step in the aerobic degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the three-dimensional structure of ndo revealed that several of the amino acids at the active site of the oxygenase are hydrophobic, which is consistent with the enzyme's preference for aromatic hydrocarbon substrates. although ndo catalyzes cis-dihydroxylation of a wide range of substrates, it is highly regio- and enantiosele ... | 2000 | 10692370 |
| catalytic activity of the d38a mutant of 3-oxo-delta 5-steroid isomerase: recruitment of aspartate-99 as the base. | 3-oxo-delta(5)-steroid isomerase (ksi) from comamonas (pseudomonas) testosteroni catalyzes the isomerization of beta,gamma-unsaturated 3-oxosteroids to their conjugated isomers through an intermediate dienolate. residue asp-38 (pk(a) 4.57) acts as a base to abstract a proton from c-4 of the substrate to form an intermediate dienolate, which is then reprotonated on c-6. both tyr-14 (pk(a) 11.6) and asp-99 (pk(a) >/= 9.5) function as hydrogen-bond donors to o-3 of the steroid, helping to stabilize ... | 2000 | 10727228 |
| a novel phenanthrene dioxygenase from nocardioides sp. strain kp7: expression in escherichia coli. | nocardioides sp. strain kp7 grows on phenanthrene but not on naphthalene. this organism degrades phenanthrene via 1-hydroxy-2-naphthoate, o-phthalate, and protocatechuate. the genes responsible for the degradation of phenanthrene to o-phthalate (phd) were found by southern hybridization to reside on the chromosome. a 10.6-kb dna fragment containing eight phd genes was cloned and sequenced. the phda, phdb, phdc, and phdd genes, which encode the alpha and beta subunits of the oxygenase component, ... | 2000 | 10735855 |
| isolation and characterization of a new denitrifying spirillum capable of anaerobic degradation of phenol. | two kinds of phenol-degrading denitrifying bacteria, azoarcus sp. strain cc-11 and spiral bacterial strain cc-26, were isolated from the same enrichment culture after 1 and 3 years of incubation, respectively. both strains required ferrous ions for growth, but strain cc-26 grew better than strain cc-11 grew under iron-limited conditions, which may have resulted in the observed change in the phenol-degrading bacteria during the enrichment process. strain cc-26 grew on phenol, benzoate, and other ... | 2000 | 10742201 |
| poly(3-hydroxyvalerate) depolymerase of pseudomonas lemoignei. | pseudomonas lemoignei is equipped with at least five polyhydroxyalkanoate (pha) depolymerase structural genes (phaz1 to phaz5) which enable the bacterium to utilize extracellular poly(3-hydroxybutyrate) (phb), poly(3-hydroxyvalerate) (phv), and related polyesters consisting of short-chain-length hxdroxyalkanoates (pha(scl)) as the sole sources of carbon and energy. four genes (phaz1, phaz2, phaz3, and phaz5) encode phb depolymerases c, b, d, and a, respectively. it was speculated that the remain ... | 2000 | 10742216 |
| steady-state kinetic characterization and crystallization of a polychlorinated biphenyl-transforming dioxygenase. | the oxygenase component of biphenyl dioxygenase (bpdo) from comamonas testosteroni b-356 dihydroxylates biphenyl and some polychlorinated biphenyls (pcbs), thereby initiating their degradation. overexpressed, anaerobically purified bpdo had a specific activity of 4.9 units/mg, and its oxygenase component appeared to contain a full complement of fe(2)s(2) center and catalytic iron. oxygenase crystals in space group r3 were obtained under anaerobic conditions using polyethylene glycol as the preci ... | 2000 | 10777527 |
| quantification of phnac and nahac in contaminated new zealand soils by competitive pcr. | unculturable polycyclic aromatic hydrocarbon (pah)-degrading bacteria are a significant reservoir of the microbial potential to catabolize low-molecular-weight pahs. the population of these bacteria is larger than the population of nah-like bacteria that are the dominant organisms in culture-based studies. we used the recently described phn genes of burkholderia sp. strain rp007, which feature only rarely in culture-based studies, as an alternative genotype for naphthalene and phenanthrene degra ... | 2000 | 10788344 |
| isolation of adherent polycyclic aromatic hydrocarbon (pah)-degrading bacteria using pah-sorbing carriers. | two different procedures were compared to isolate polycyclic aromatic hydrocarbon (pah)-utilizing bacteria from pah-contaminated soil and sludge samples, i.e., (i) shaken enrichment cultures in liquid mineral medium in which pahs were supplied as crystals and (ii) a new method in which pah degraders were enriched on and recovered from hydrophobic membranes containing sorbed pahs. both techniques were successful, but selected from the same source different bacterial strains able to grow on pahs a ... | 2000 | 10788347 |
| targeted disruption of the kstd gene encoding a 3-ketosteroid delta(1)-dehydrogenase isoenzyme of rhodococcus erythropolis strain sq1. | microbial phytosterol degradation is accompanied by the formation of steroid pathway intermediates, which are potential precursors in the synthesis of bioactive steroids. degradation of these steroid intermediates is initiated by delta(1)-dehydrogenation of the steroid ring structure. characterization of a 2.9-kb dna fragment of rhodococcus erythropolis sq1 revealed an open reading frame (kstd) showing similarity with known 3-ketosteroid delta(1)-dehydrogenase genes. heterologous expression of k ... | 2000 | 10788377 |
| coexistence of two different o demethylation systems in lignin metabolism by sphingomonas paucimobilis syk-6: cloning and sequencing of the lignin biphenyl-specific o-demethylase (ligx) gene. | sphingomonas paucimobilis syk-6 can grow on several dimeric model compounds of lignin as a carbon and energy source. it has o demethylation systems on three kinds of substrates: 5, 5'-dehydrodivanillic acid (ddva), syringate, and vanillate. we previously reported the cloning of a gene involved in the tetrahydrofolate-dependent o demethylation of syringate and vanillate. in the study reported here, we cloned the gene responsible for ddva o demethylation. using nitrosoguanidine mutagenesis, a muta ... | 2000 | 10788391 |
| cloning and expression of ntnd, encoding a novel nad(p)(+)-independent 4-nitrobenzyl alcohol dehydrogenase from pseudomonas sp. strain tw3. | pseudomonas sp. strain tw3 is able to metabolize 4-nitrotoluene to 4-nitrobenzoate and toluene to benzoate aerobically via a route analogous to the upper pathway of the tol plasmids. we report the cloning and characterization of a benzyl alcohol dehydrogenase gene (ntnd) which encodes the enzyme for the catabolism of 4-nitrobenzyl alcohol and benzyl alcohol to 4-nitrobenzaldehyde and benzaldehyde, respectively. the gene is located downstream of the previously reported ntn gene cluster. ntnd bear ... | 2000 | 10809692 |
| active site residues of cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase from comamonas testosteroni strain b-356. | cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (bphb) from comamonas testosteroni strain b-356 is the second enzyme of the biphenyl/polychlorinated biphenyl degradation pathway. based on the crystal structure of a related bphb, three conserved residues, ser142, tyr155, and lys159, have been suggested to function as a "catalytic triad" as for other members of the short-chain alcohol dehydrogenase/reductase (sdr) family. in this study, substitution of each triad residue was examined in bphb. ... | 2000 | 10819967 |
| functional expression, purification, and characterization of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni. | 3alpha-hydroxysteroid dehydrogenase (3alpha-hsd) catalyzes the oxidoreduction at carbon 3 of steroid hormones and is postulated to initiate the complete mineralization of the steroid nucleus to co(2) and h(2)o in comamonas testosteroni. by this activity, 3alpha-hsd provides the basis for c. testosteroni to grow on steroids as sole carbon and energy source. 3alpha-hsd was cloned and overexpressed in e. coli and purified to homogeneity by an affinity chromatography system as his-tagged protein. th ... | 2000 | 10833462 |
| genetic investigation of the catabolic pathway for degradation of abietane diterpenoids by pseudomonas abietaniphila bkme-9. | we have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by pseudomonas abietaniphila bkme-9. the dit gene cluster is located on a 16.7-kb dna fragment containing 13 complete open reading frames (orfs) and 1 partial orf. the genes dita1a2a3 encode the alpha and beta subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8, 13-abietadien acid. the dioxygenase mutant ... | 2000 | 10850995 |
| degradation of anaerobic reductive dechlorination products of aroclor 1242 by four aerobic bacteria. | we studied the aerobic degradation of eight pcb congeners which comprise from 70 to 85% of the anaerobic dechlorination products from aroclor 1242, including 2-, 4-, 2,4-, 2,6-, 2,2'-, 2,4'-, 2,2', 4-, and 2,4,4'-chlorobiphenyl (cb), and the biodegradation of their mixtures designed to simulate anaerobic dechlorination profiles m and c. strains comamonas testosteroni vp44 and rhodococcus erythreus ny05 preferentially oxidized a para-substituted ring, while rhodococcus sp. rha1, similar to well k ... | 1999 | 10870552 |
| bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading comamonas testosteroni strain, i2gfp. | a strain identified as comamonas testosteroni i2 was isolated from activated sludge and found to be able to mineralize 3-chloroaniline (3-ca). during the mineralization, a yellow intermediate accumulated temporarily, due to the distal meta-cleavage of chlorocatechol. this strain was tested for its ability to clean wastewater containing 3-ca upon inoculation into activated sludge. to monitor its survival, the strain was chromosomally marked with the gfp gene and designated i2gfp. after inoculatio ... | 2000 | 10877785 |
| influence of chlorine substituents on rates of oxidation of chlorinated biphenyls by the biphenyl dioxygenase of burkholderia sp. strain lb400. | biphenyl dioxygenase from burkholderia (pseudomonas) sp. strain lb400 catalyzes the first reaction of a pathway for the degradation of biphenyl and a broad range of chlorinated biphenyls (cbs). the effect of chlorine substituents on catalysis was determined by measuring the specific activity of the enzyme with biphenyl and 18 congeners. the catalytic oxygenase component was purified and incubated with individual cbs in the presence of electron transport proteins and cofactors that were required ... | 2000 | 10877788 |
| a new klebsiella planticola strain (cd-1) grows anaerobically at high cadmium concentrations and precipitates cadmium sulfide. | heavy metal resistance by bacteria is a topic of much importance to the bioremediation of contaminated soils and sediments. we report here the isolation of a highly cadmium-resistant klebsiella planticola strain, cd-1, from reducing salt marsh sediments. the strain grows in up to 15 mm cdcl(2) under a wide range of nacl concentrations and at acidic or neutral ph. in growth medium amended with thiosulfate, it precipitated significant amounts of cadmium sulfide (cds), as confirmed by x-absorption ... | 2000 | 10877810 |
| arrangement and regulation of the genes for meta-pathway enzymes required for degradation of phenol in comamonas testosteroni ta441. | comamonas testosteroni ta441 degrades phenol by a meta-cleavage pathway after the occurrence of a spontaneous mutation that derepresses the aphklmnopqb operon encoding phenol hydroxylase and catechol 2,3-dioxygenase, the enzymes for the initial two steps of the degradation pathway. a gene cluster, aphcefghji, encoding the meta-pathway enzymes for degradation of 2-hydroxymuconic semialdehyde (hms) to tca cycle intermediates was found downstream of the aphk operon. the upstream operon and the down ... | 2000 | 10878134 |
| the serotype of type ia and iii group b streptococci is determined by the polymerase gene within the polycistronic capsule operon. | streptococcus agalactiae is a primary cause of neonatal morbidity and mortality. essential to the virulence of this pathogen is the production of a type-specific capsular polysaccharide (cps) that enables the bacteria to evade host immune defenses. the identification, cloning, sequencing, and functional characterization of seven genes involved in type iii capsule production have been previously reported. here, we describe the cloning and sequencing of nine additional adjacent genes, cps(iii)fghi ... | 2000 | 10913080 |
| steroid-inducible transcription of the 3beta/17beta-hydroxysteroid dehydrogenase gene (3beta/17beta-hsd) in comamonas testosteroni. | the expression of the comamonas testosteroni gene, encoding 3beta/17beta-hydroxysteroid dehydrogenase enzyme (3beta/17beta-hsd), was analyzed at the transcriptional level. northern blot analysis detected a 1 kb transcript in bacterial cells grown in minimum media supplemented with casamino acids and testosterone. also this transcript was observed when cells were grown in presence of 1-dehydrotestosterone, androstenedione and 1,4-androstadien-3, 17dione, but not in presence of acetate, citrate, c ... | 2000 | 10925214 |
| genetic analysis of a gene cluster for cyclohexanol oxidation in acinetobacter sp. strain se19 by in vitro transposition. | biological oxidation of cyclic alcohols normally results in formation of the corresponding dicarboxylic acids, which are further metabolized and enter the central carbon metabolism in the cell. we isolated an acinetobacter sp. from an industrial wastewater bioreactor that utilized cyclohexanol as a sole carbon source. a cosmid library was constructed from acinetobacter sp. strain se19, and oxidation of cyclohexanol to adipic acid was demonstrated in recombinant escherichia coli carrying a se19 d ... | 2000 | 10940013 |
| starvation improves survival of bacteria introduced into activated sludge. | a phenol-degrading bacterium, ralstonia eutropha e2, was grown in luria-bertani (lb) medium or in an inorganic medium (called mp) supplemented with phenol and harvested at the late-exponential-growth phase. phenol-acclimated activated sludge was inoculated with the e2 cells immediately after harvest or after starvation in mp for 2 or 7 days. the densities of the e2 populations in the activated sludge were then monitored by quantitative pcr. the e2 cells grown on phenol and starved for 2 days (p- ... | 2000 | 10966407 |
| the crystal structure of 3alpha -hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family. | the crystal structure of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni (3alpha-hsdh) as well as the structure of its binary complex with nad(+) have been solved at 1.68-a and 1.95-a resolution, respectively. the enzyme is a member of the short chain dehydrogenase/reductase (sdr) family. accordingly, the active center and the conformation of the bound nucleotide cofactor closely resemble those of other sdrs. the crystal structure reveals one homodimer per asym ... | 2000 | 11007791 |
| equilibrium and kinetic analysis of folding of ketosteroid isomerase from comamonas testosteroni. | equilibrium and kinetic analyses have been carried out to elucidate the folding mechanism of homodimeric ketosteroid isomerase (ksi) from comamonas testosteroni. the folding of ksi was reversible since the activity as well as the fluorescence and cd spectra was almost completely recovered after refolding. the equilibrium unfolding transitions monitored by fluorescence and cd measurements were almost coincident with each other, and the transition midpoint increased with increasing protein concent ... | 2000 | 11041875 |
| benr, a xyls homologue, regulates three different pathways of aromatic acid degradation in pseudomonas putida. | pseudomonas putida converts benzoate to catechol using two enzymes that are encoded on the chromosome and whose expression is induced by benzoate. benzoate also binds to the regulator xyls to induce expression of the tol (toluene degradation) plasmid-encoded meta pathway operon for benzoate and methylbenzoate degradation. finally, benzoate represses the ability of p. putida to transport 4-hydroxybenzoate (4-hba) by preventing transcription of pcak, the gene encoding the 4-hba permease. here we i ... | 2000 | 11053377 |
| monitoring bacterial transport by stable isotope enrichment of cells. | understanding the transport and behavior of bacteria in the environment has broad implications in diverse areas, ranging from agriculture to groundwater quality, risk assessment, and bioremediation. the ability to reliably track and enumerate specific bacterial populations in the context of native communities and environments is key to developing this understanding. we report a novel bacterial tracking approach, based on altering the stable carbon isotope value (delta(13)c) of bacterial cells, w ... | 2000 | 11055946 |
| genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in sphingomonas paucimobilis syk-6. | protocatechuate (pca) is the key intermediate metabolite in the lignin degradation pathway of sphingomonas paucimobilis syk-6 and is metabolized to pyruvate and oxaloacetate via the pca 4,5-cleavage pathway. we characterized the 4-carboxy-2-hydroxymuconate-6-semialdehyde (chms) dehydrogenase gene (ligc). chms is the 4,5-cleavage product of pca and is converted into 2-pyrone-4,6-dicarboxylate (pdc) by ligc. we found that ligc was located 295 bp downstream of ligb, which encodes the large subunit ... | 2000 | 11073908 |
| transcriptional organization and dynamic expression of the hbpcad genes, which encode the first three enzymes for 2-hydroxybiphenyl degradation in pseudomonas azelaica hbp1. | pseudomonas azelaica hbp1 degrades the toxic substance 2-hydroxybiphenyl (2-hbp) by means of three enzymes that are encoded by structural genes hbpc, hbpa, and hbpd. these three genes form a small noncontiguous cluster. their expression is activated by the product of regulatory gene hbpr, which is located directly upstream of the hbpcad genes. the hbpr protein is a transcription activator and belongs to the so-called xylr/dmpr subclass within the ntrc family of transcriptional activators. transc ... | 2001 | 11114926 |
| characterization of fungal 17beta-hydroxysteroid dehydrogenases. | to promote understanding of the evolution of the steroid hormone signalling and hydroxysteroid dehydrogenases (hsds), comparative characterization of fungal 17beta-hsds was performed. constitutive 17beta-hsd activity was determined in cytosols of the fungi: cochliobolus lunatus, pleospora herbarum, fusarium lini, trichoderma viride, mucor spinosus, rhizopus nigricans and pleurotus ostreatus. the reaction equilibrium in all species except p. ostreatus was shifted towards reduction. the preferenti ... | 2000 | 11126752 |
| occurrence of tn4371-related mobile elements and sequences in (chloro)biphenyl-degrading bacteria. | tn4371, a 55-kb transposable element involved in the degradation and biphenyl or 4-chlorobiphenyl identified in ralstonia eutropha a5, displays a modular structure including a phage-like integrase gene (int), a pseudomonas-like (chloro)biphenyl catabolic gene cluster (bph), and rp4- and ti-plasmid-like transfer genes (trb) (c. merlin, d. springael, and a. toussaint, plasmid 41:40-54, 1999). southern blot hybridization was used to examine the presence of different regions of tn4371 in a collectio ... | 2001 | 11133426 |
| role of the dmpr-mediated regulatory circuit in bacterial biodegradation properties in methylphenol-amended soils. | pathway substrates and some structural analogues directly activate the regulatory protein dmpr to promote transcription of the dmp operon genes encoding the (methyl)phenol degradative pathway of pseudomonas sp. strain cf600. while a wide range of phenols can activate dmpr, the location and nature of substituents on the basic phenolic ring can limit the level of activation and thus utilization of some compounds as assessed by growth on plates. here we address the role of the aromatic effector res ... | 2001 | 11133441 |
| analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of pcr-amplified 16s rrna as well as dna fragments coding for 16s rrna. | the effect of developing chrysanthemum roots on the presence and activity of bacterial populations in the rhizosphere was examined by using culture-independent methods. nucleic acids were extracted from rhizosphere soil samples associated with the bases of roots or root tips of plants harvested at different stages of development. pcr and reverse transcriptase (rt) pcr were used to amplify 16s ribosomal dna (rdna) and 16s rrna, respectively, and the products were subjected to denaturing gradient ... | 2001 | 11133442 |
| nag genes of ralstonia (formerly pseudomonas) sp. strain u2 encoding enzymes for gentisate catabolism. | ralstonia sp. strain u2 metabolizes naphthalene via gentisate to central metabolites. we have cloned and sequenced a 21.6-kb region spanning the nag genes. upstream of the pathway genes are nagy, homologous to chemotaxis proteins, and nagr, a regulatory gene of the lysr family. divergently transcribed from nagr are the genes for conversion of naphthalene to gentisate (nagaaghabacadbfcqed) (s. l. fuenmayor, m. wild, a. l. boyes, and p. a. williams, j. bacteriol. 180:2522-2530, 1998), which except ... | 2001 | 11133965 |
| regulation of the steroid-inducible 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase gene in comamonas testosteroni. | the comamonas testosteroni 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase gene (hsda) codes for an adaptive enzyme in the degradation of steroid compounds. however, no information was available on the molecular regulation of steroid-inducible genes nor on the mechanism of steroid signaling in procaryotes. we, therefore, investigated the cis- and trans-acting elements of hsda expression to infer the mechanism of its molecular regulation by steroids. the gene was localized on a 5.257-kilob ... | 2001 | 11139589 |
| catalytic and molecular properties of the quinohemoprotein tetrahydrofurfuryl alcohol dehydrogenase from ralstonia eutropha strain bo. | the quinohemoprotein tetrahydrofurfuryl alcohol dehydrogenase (thfa-dh) from ralstonia eutropha strain bo was investigated for its catalytic properties. the apparent k(cat)/k(m) and k(i) values for several substrates were determined using ferricyanide as an artificial electron acceptor. the highest catalytic efficiency was obtained with n-pentanol exhibiting a k(cat)/k(m) value of 788 x 10(4) m(-1) s(-1). the enzyme showed substrate inhibition kinetics for most of the alcohols and aldehydes inve ... | 2001 | 11222593 |
| genetic diversity among 3-chloroaniline- and aniline-degrading strains of the comamonadaceae. | we examined the diversity of the plasmids and of the gene tdnq, involved in the oxidative deamination of aniline, in five bacterial strains that are able to metabolize both aniline and 3-chloroaniline (3-ca). three strains have been described and identified previously, i.e., comamonas testosteroni i2 and delftia acidovorans ca28 and bn3.1. strains lme1 and b8c were isolated in this study from linuron-treated soil and from a wastewater treatment plant, respectively, and were both identified as d. ... | 2001 | 11229899 |
| an inducible 1-butanol dehydrogenase, a quinohaemoprotein, is involved in the oxidation of butane by "pseudomonas butanovora". | butane-grown "pseudomonas butanovora" expressed two soluble alcohol dehydrogenases (adhs), an nad(+)-dependent secondary adh and an nad(+)-independent primary adh. two additional nad(+)-dependent secondary adhs could be detected when cells were grown on 2-butanol and lactate. the inducible nad(+)-independent 1-butanol dehydrogenase (bdh) of butane-grown cells was primarily responsible for 1-butanol oxidation in the butane metabolism pathway. bdh was purified to near homogeneity and identified as ... | 2001 | 11238982 |
| altering catalytic properties of 3-chlorocatechol-oxidizing extradiol dioxygenase from sphingomonas xenophaga bn6 by random mutagenesis. | the 2,3-dihydroxybiphenyl 1,2-dioxygenase from sphingomonas xenophaga strain bn6 (bphc1) oxidizes 3-chlorocatechol by a rather unique distal ring cleavage mechanism. in an effort to improve the efficiency of this reaction, bphc1 was randomly mutated by error-prone pcr. mutants which showed increased activities for 3-chlorocatechol were obtained, and the mutant forms of the enzyme were shown to contain two or three amino acid substitutions. variant enzymes containing single substitutions were con ... | 2001 | 11244073 |
| roles of dimerization in folding and stability of ketosteroid isomerase from pseudomonas putida biotype b. | equilibrium and kinetic analyses have been performed to elucidate the roles of dimerization in folding and stability of ksi from pseudomonas putida biotype b. folding was reversible in secondary and tertiary structures as well as in activity. equilibrium unfolding transition, as monitored by fluorescence and ellipticity measurements, could be modeled by a two-state mechanism without thermodynamically stable intermediates. consistent with the two-state model, one dimensional (1d) nmr spectra and ... | 2001 | 11274465 |
| map of the incp1beta plasmid ptsa encoding the widespread genes (tsa) for p-toluenesulfonate degradation in comamonas testosteroni t-2. | the catabolic incp1beta plasmid ptsa from comamonas testosteroni t-2 was mapped by subtractive analysis of restriction digests, by sequencing outwards from the tsa operon (toluenesulfonate degradation), and by generating overlapping, long-distance-pcr amplification products. the plasmid was estimated to comprise 72 +/- 4 kb. the tsa region was found to be a composite transposon flanked by two is1071 elements. a cryptic tsa operon was also present in the tsa transposon. those backbone genes and r ... | 2001 | 11282598 |
| identification of methyl halide-utilizing genes in the methyl bromide-utilizing bacterial strain imb-1 suggests a high degree of conservation of methyl halide-specific genes in gram-negative bacteria. | strain imb-1, an aerobic methylotrophic member of the alpha subgroup of the proteobacteria, can grow with methyl bromide as a sole carbon and energy source. a single cmu gene cluster was identified in imb-1 that contained six open reading frames: cmuc, cmua, orf146, paae, huti, and partial metf. cmua from imb-1 has high sequence homology to the methyltransferase cmua from methylobacterium chloromethanicum and hyphomicrobium chloromethanicum and contains a c-terminal corrinoid-binding motif and a ... | 2001 | 11282657 |
| 15n nmr relaxation studies of backbone dynamics in free and steroid-bound delta 5-3-ketosteroid isomerase from pseudomonas testosteroni. | the backbone dynamics of delta(5)-3-ketosteroid isomerase (ksi) from pseudomonas testosteroni has been studied in free enzyme and its complex with a steroid ligand, 19-nortestosterone hemisuccinate (19-nths), by (15)n relaxation measurements. the relaxation data were analyzed using the model-free formalism to extract the model-free parameters (s(2), tau(e), and r(ex)) and the overall rotational correlation time (tau(m)). the rotational correlation times were 19.23 +/- 0.08 and 17.08 +/- 0.07 ns ... | 2001 | 11300777 |
| folding mechanism of ketosteroid isomerase from comamonas testosteroni. | ketosteroid isomerase (ksi) from comamonas testosteroni is a homodimeric enzyme with 125 amino acids in each monomer catalyzing the allylic isomerization reaction at rates comparable to the diffusion limit. kinetic analysis of ksi refolding has been carried out to understand its folding mechanism. the refolding process as monitored by fluorescence change revealed that the process consists of three steps with a unimolecular fast, a bimolecular intermediate, and most likely unimolecular slow phase ... | 2001 | 11305917 |
| 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni: biological significance, three-dimensional structure and gene regulation. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-hsd/cr) catalyses the oxidoreduction at carbon 3 of steroid hormones and is postulated to initiate the complete mineralisation of the steroid nucleus to co(2) and h(2)o in comamonas testosteroni. the enzyme was found to be functional towards a variety of steroid substrates, including the steroid antibiotic fusidic acid. the enzyme also catalyses the carbonyl reduction of non-steroidal aldehydes and ketones such as a novel insecticide ... | 2001 | 11306088 |
| a model on the regulation of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase expression in comamonas testosteroni. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-hsd/cr) from comamonas testosteroni is a key enzyme involved in the degradation of steroids and xenobiotic carbonyl compounds. the enzyme has recently been cloned and characterized by our group. a strong induction of enzyme activity is observed in the presence of steroids like testosterone. in the present investigation, two repressor proteins (rep1 and rep2) containing 78 and 420 amino acids, respectively, were found to regulate 3alp ... | 2001 | 11306089 |
| endotoxic properties of lipid a from comamonas testosteroni. | the lipid a from comamonas testosteroni has been isolated and its complete chemical structure determined [iida, t., haishima, y., tanaka, a., nishijima, k., saito, s. & tanamoto, k. (1996). eur j biochem 237, 468-475]. in this work, the relationship between its chemical structure and biological activity was studied. the lipid a was highly homogeneous chemically and was characterized by the relatively short chain length (c(10)) of the 3-hydroxy fatty acid components directly bound to the glucosam ... | 2001 | 11320112 |
| diversity in kinetics of trichloroethylene-degrading activities exhibited by phenol-degrading bacteria. | whole-cell kinetics of phenol- and trichloroethylene (tce)-degrading activities expressed by 13 phenol-degrading bacteria were analyzed. the ks (apparent affinity constant in haldane's equation) values for tce were unexpectedly diverse, ranging from 11 microm to over 800 microm. the vmax/ks values for phenol were three orders of magnitude higher than the values for tce in all bacteria analyzed, suggesting that these bacteria preferentially degrade phenol rather than tce. a positive correlation b ... | 2001 | 11330722 |
| isolation and characterization of two aerobic bacterial strains that completely degrade ethyl tert-butyl ether (etbe). | two bacterial strains, e1 and e2, isolated from gasoline-polluted soil completely degraded ethyl tert-butyl ether (etbe), as the sole source of carbon and energy, at specific rates of about 80 mg g(-1) and 58 mg g(-1) of cell protein day(-1), respectively. on the basis of morphological and phenotypic characteristics, strain e1 was tentatively identified as comamonas testosteroni and strain e2 as belonging to centre for disease control group a-5. the inhibitory effect of metyrapone on the degrada ... | 2001 | 11341318 |
| dehalogenation, denitration, dehydroxylation, and angular attack on substituted biphenyls and related compounds by a biphenyl dioxygenase. | the attack by the bph-encoded biphenyl dioxygenase of burkholderia sp. strain lb400 on a number of symmetrical ortho-substituted biphenyls or quasi ortho-substituted biphenyl analogues has been investigated. 2,2'-difluoro-, 2,2'-dibromo-, 2,2'-dinitro-, and 2,2'-dihydroxybiphenyl were accepted as substrates. dioxygenation of all of these compounds showed a strong preference for the semisubstituted pair of vicinal ortho and meta carbons, leading to the formation of 2'-substituted 2,3-dihydroxybip ... | 2001 | 11371517 |
| genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader pseudomonas sp. strain ca10. | the nucleotide sequences of the 27,939-bp-long upstream and 9,448-bp-long downstream regions of the caraaaababbcac(orf7)ad genes of carbazole-degrading pseudomonas sp. strain ca10 were determined. thirty-two open reading frames (orfs) were identified, and the car gene cluster was consequently revealed to consist of 10 genes (caraaaababbcacaddfe) encoding the enzymes for the three-step conversion of carbazole to anthranilate and the degradation of 2-hydroxypenta-2,4-dienoate. the high identities ... | 2001 | 11371531 |
| plasmid-encoded phthalate catabolic pathway in arthrobacter keyseri 12b. | several 2-substituted benzoates (including 2-trifluoromethyl-, 2-chloro-, 2-bromo-, 2-iodo-, 2-nitro-, 2-methoxy-, and 2-acetyl-benzoates) were converted by phthalate-grown arthrobacter keyseri (formerly micrococcus sp.) 12b to the corresponding 2-substituted 3,4-dihydroxybenzoates (protocatechuates). because these products lack a carboxyl group at the 2 position, they were not substrates for the next enzyme of the phthalate catabolic pathway, 3,4-dihydroxyphthalate 2-decarboxylase, and accumula ... | 2001 | 11371533 |
| induction of bpha, encoding biphenyl dioxygenase, in two polychlorinated biphenyl-degrading bacteria, psychrotolerant pseudomonas strain cam-1 and mesophilic burkholderia strain lb400. | we investigated induction of biphenyl dioxygenase in the psychrotolerant polychlorinated biphenyl (pcb) degrader pseudomonas strain cam-1 and in the mesophilic pcb degrader burkholderia strain lb400. using a counterselectable gene replacement vector, we inserted a lacz-gm(r) fusion cassette between chromosomal genes encoding the large subunit (bpha) and small subunit (bphe) of biphenyl dioxygenase in cam-1 and lb400, generating cam-10 and lb400-1, respectively. potential inducers of bpha were ad ... | 2001 | 11375179 |
| isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria associated with the rhizosphere of salt marsh plants. | polycyclic aromatic hydrocarbon (pah)-degrading bacteria were isolated from contaminated estuarine sediment and salt marsh rhizosphere by enrichment using either naphthalene, phenanthrene, or biphenyl as the sole source of carbon and energy. pasteurization of samples prior to enrichment resulted in isolation of gram-positive, spore-forming bacteria. the isolates were characterized using a variety of phenotypic, morphologic, and molecular properties. identification of the isolates based on their ... | 2001 | 11375181 |
| phcs represses gratuitous expression of phenol-metabolizing enzymes in comamonas testosteroni r5. | we identified an open reading frame, designated phcs, downstream of the transcriptional activator gene (phcr) for the expression of multicomponent phenol hydroxylase (mph) in comamonas testosteroni r5. the deduced product of phcs was homologous to aphs of c. testosteroni ta441, which belongs to the gntr family of transcriptional regulators. the transformation of pseudomonas aeruginosa pao1c (phenol negative, catechol positive) with pror502 containing phcr and the mph genes conferred the ability ... | 2001 | 11418563 |
| identification and functional characterization of cbar, a marr-like modulator of the cbaabc-encoded chlorobenzoate catabolism pathway. | in comamonas testosteroni br60 (formerly alcaligenes sp. strain br60), catabolism of the pollutant 3-chlorobenzoate (3cba) is initiated by enzymes encoded by cbaabc, an operon found on composite transposon tn5271 of plasmid pbrc60. the cbaabc gene product cbaabc converts 3cba to protocatechuate (pca) and 5-cl-pca, which are then metabolized by the chromosomal pca meta (extradiol) ring fission pathway. in this study, cbaa was found to possess a sigma(70) type promoter. o(2) uptake experiments wit ... | 2001 | 11472929 |
| molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from mycobacterium sp. strain pyr-1. | mycobacterium sp. strain pyr-1 degrades high-molecular-weight polycyclic hydrocarbons (pahs) primarily through the introduction of both atoms of molecular oxygen by a dioxygenase. to clone the dioxygenase genes involved in pah degradation, two-dimensional (2d) gel electrophoresis of pah-induced proteins from cultures of mycobacterium sp. strain pyr-1 was used to detect proteins that increased after phenanthrene, dibenzothiophene, and pyrene exposure. comparison of proteins from induced and unind ... | 2001 | 11472934 |
| methane oxidation and the competition for oxygen in the rice rhizosphere. | a mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. in flooded rice paddies these methanotrophs compete for available o(2) with other types of bacteria. soil incubation studies and most-probable-number (mpn) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. mpn counts of methanotrophs showed large ... | 2001 | 11472935 |
| transformation of 2,2'-bimorphine to the novel compounds 10-alpha-s-monohydroxy-2,2'-bimorphine and 10,10'-alpha,alpha'-s,s'-dihydroxy-2,2'-bimorphine by cylindrocarpon didymum. | whole-cell suspensions of cylindrocarpon didymum were observed to transform 2,2'-bimorphine to the compounds 10-alpha-s-monohydroxy-2,2'-bimorphine and 10,10'-alpha,alpha'-s,s'-dihydroxy-2,2'-bimorphine. mass spectrometry and (1)h nuclear magnetic resonance spectroscopy confirmed the identities of these new morphine alkaloids. | 2001 | 11472953 |
| new inhibitors of iron-containing nitrile hydratases. | there is growing evidence in the literature emphasizing the significance of the post-translational modification of cysteine thiols to sulfenic acids (soh), which have been found in a number of proteins. crystallographic and mass spectrometric evidence has shown the presence of this group in an inactive form of the industrially important enzyme nitrile hydratase (nhase). this oxidized cysteine is unique in that it forms part of the coordination sphere of the low-spin iron iii at the active site o ... | 2001 | 11481039 |
| comamonas testosteroni br6020 possesses a single genetic locus for extradiol cleavage of protocatechuate. | a key intermediate for biodegradation of various distinct aromatic growth substrates in comamonas testosteroni is protocatechuate (pca), which is metabolized by the 4,5-extradiol (meta) ring fission pathway. a locus harbouring genes from c. testosteroni br6020 was cloned, dubbed pmd, which encodes the enzymes that degrade pca. the identity of pmdab, encoding respectively the alpha- and beta-subunit of the pca ring-cleavage enzyme, was confirmed by n-terminal sequencing and molecular mass determi ... | 2001 | 11495993 |
| central venous catheter-related infection due to comamonas testosteroni in a woman with breast cancer. | a 75-y-old woman with breast cancer presented with bacteremia due to comamonas testosteroni. evolution was favorable following adapted antimicrobial therapy and removal of a central venous catheter. this germ seems to be a rare pathogen; as reported in the literature, it is mostly encountered in patients with predisposing factors. | 2001 | 11525361 |
| laboratory evolution of toluene dioxygenase to accept 4-picoline as a substrate. | we are using directed evolution to extend the range of dioxygenase-catalyzed biotransformations to include substrates that are either poorly accepted or not accepted at all by the naturally occurring enzymes. here we report on the oxidation of a heterocyclic substrate, 4-picoline, by toluene dioxygenase (tdo) and improvement of the enzyme's activity by laboratory evolution. the biotransformation of 4-picoline proceeds at only approximately 4.5% of the rate of the natural reaction on toluene. ran ... | 2001 | 11525981 |
| complete nucleotide sequence and organization of the atrazine catabolic plasmid padp-1 from pseudomonas sp. strain adp. | the complete 108,845-nucleotide sequence of catabolic plasmid padp-1 from pseudomonas sp. strain adp was determined. plasmid padp-1 was previously shown to encode atza, atzb, and atzc, which catalyze the sequential hydrolytic removal of s-triazine ring substituents from the herbicide atrazine to yield cyanuric acid. computational analyses indicated that padp-1 encodes 104 putative open reading frames (orfs), which are predicted to function in catabolism, transposition, and plasmid maintenance, t ... | 2001 | 11544232 |
| cloning, nucleotide sequencing, and functional analysis of a novel, mobile cluster of biodegradation genes from pseudomonas aeruginosa strain jb2. | we have identified in pseudomonas aeruginosa strain jb2 a novel cluster of mobile genes encoding degradation of hydroxy- and halo-aromatic compounds. nineteen open reading frames were located and, based on sequence similarities, were putatively identified as encoding a ring hydroxylating oxygenase (hybabcd), an atp-binding cassette-type transporter, an extradiol ring-cleavage dioxygenase, transcriptional regulatory proteins, enzymes mediating chlorocatechol degradation, and transposition functio ... | 2001 | 11571162 |
| group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation. | the sequences of the largest subunit of bacterial multicomponent phenol hydroxylases (lmphs) were compared. it was found that lmphs formed three phylogenetic groups, i, ii, and iii, corresponding to three previously reported kinetic groups, low-k(s) (the half-saturation constant in haldane's equation for trichloroethylene [tce]), moderate-k(s), and high-k(s) groups. consensus sequences and specific amino acid residues for each group of lmph were found, which facilitated the design of universal a ... | 2001 | 11571171 |
| genetic and functional analysis of the tbc operons for catabolism of alkyl- and chloroaromatic compounds in burkholderia sp. strain js150. | burkholderia sp. strain js150 is able to metabolize a wide range of alkyl-and chloroaromatic hydrocarbons through multiple, apparently redundant catabolic pathways. previous research has shown that strain js150 is able to synthesize enzymes for multiple upper pathways as well as multiple lower pathways to accommodate variously substituted catechols that result from degradation of complex mixtures of monoaromatic compounds. we report here the genetic organization and functional characterization o ... | 2001 | 11571188 |
| cloning and characterization of benzoate catabolic genes in the gram-positive polychlorinated biphenyl degrader rhodococcus sp. strain rha1. | benzoate catabolism is thought to play a key role in aerobic bacterial degradation of biphenyl and polychlorinated biphenyls (pcbs). benzoate catabolic genes were cloned from a pcb degrader, rhodococcus sp. strain rha1, by using pcr amplification and temporal temperature gradient electrophoresis separation. a nucleotide sequence determination revealed that the deduced amino acid sequences encoded by the rha1 benzoate catabolic genes, benabcdk, exhibit 33 to 65% identity with those of acinetobact ... | 2001 | 11673430 |
| crystallization of quinohaemoprotein alcohol dehydrogenase from comamonas testosteroni: crystals with unique optical properties. | quinohaemoprotein alcohol dehydrogenase from comamonas testosteroni is a functional electron-transfer protein containing both a haem c and a pyrroloquinoline quinone cofactor. the enzyme has been crystallized at 277 k using polyethylene glycol 6000 as precipitant. the crystals belong to space group c2, with unit-cell parameters a = 98.1, b = 74.3, c = 92.2 a, beta = 105.9 degrees. a native data set with a resolution of 2.44 a resolution has been collected. the approximate orientation of the haem ... | 2001 | 11679760 |
| membrane-associated quinoprotein formaldehyde dehydrogenase from methylococcus capsulatus bath. | a membrane-associated, dye-linked formaldehyde dehydrogenase (dl-faldh) was isolated from the obligate methylotroph methylococcus capsulatus bath. the enzyme was the major formaldehyde-oxidizing enzyme in cells cultured in high (above 1 micromol of cu per mg of cell protein) copper medium and expressing the membrane-associated methane monooxygenase. soluble nad(p)(+)-linked formaldehyde oxidation was the major activity in cells cultured in low-copper medium and expressing the soluble methane mon ... | 2001 | 11698372 |
| direct ring fission of salicylate by a salicylate 1,2-dioxygenase activity from pseudaminobacter salicylatoxidans. | in cell extracts of pseudaminobacter salicylatoxidans strain bn12, an enzymatic activity was detected which converted salicylate in an oxygen-dependent but nad(p)h-independent reaction to a product with an absorbance maximum at 283 nm. this metabolite was isolated, purified, and identified by mass spectrometry and (1)h and (13)c nuclear magnetic resonance spectroscopy as 2-oxohepta-3,5-dienedioic acid. this metabolite could be formed only by direct ring fission of salicylate by a 1,2-dioxygenase ... | 2001 | 11698383 |