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Eiji Masai - One of the best experts on this subject based on the ideXlab platform.
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functional characterization of a catabolic plasmid from Polychlorinated Biphenyl degrading rhodococcus sp strain rha1
Journal of Bacteriology, 2004Co-Authors: Rene L Warren, William W L Hsiao, Hisashi Kudo, Matt Myhre, Manisha Dosanjh, Anca Petrescu, Hiroyuki Kobayashi, Satoru Shimizu, Keisuke Miyauchi, Eiji MasaiAbstract:Rhodococcus sp. strain RHA1, a potent Polychlorinated-Biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative “genomic islands” (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.
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characterization of Biphenyl catabolic genes of gram positive Polychlorinated Biphenyl degrader rhodococcus sp strain rha1
Applied and Environmental Microbiology, 1995Co-Authors: Eiji Masai, Akihiro Yamada, J M Healy, Takashi Hatta, Kazuhide Kimbara, Masao Fukuda, Keiji YanoAbstract:Rhodococcus sp. strain RHA1 is a gram-positive Polychlorinated Biphenyl (PCB) degrader which can degrade 10 ppm of PCB48 (equivalent to Aroclor1248), including tri-, tetra-, and pentachloroBiphenyls, in a few days. We isolated the 7.6-kb EcoRI-BamHI fragment carrying the Biphenyl catabolic genes of RHA1 and determined their nucleotide sequence. On the basis of deduced amino acid sequence homology, we identified six bph genes, bphA1A2A3A4, bphB, and bphC, that are responsible for the initial three steps of Biphenyl degradation. The order of bph genes in RHA1 is bphA1A2A3A4-bphC-bphB. This gene order differs from that of other PCB degraders reported previously. The amino acid sequences deduced from the RHA1 bph genes have a higher degree of homology with the tod genes from Pseudomonas putida F1 (49 to 79%) than with the bph genes of Pseudomonas sp. strains KF707 and KKS102 (30 to 65%). In Escherichia coli, bphA gene activity was not observed even when expression vectors were used. The activities of bphB and bphC, however, were confirmed by observing the transformation of Biphenyl to a meta-cleavage compound with the aid of benzene dioxygenase activity that complemented the bphA gene activity (S. Irie, S. Doi, T. Yorifuji, M. Takagi, and K. Yano, J. Bacteriol. 169:5174-5179, 1987). The expected products of the cloned bph genes, except bphA3, were observed in E. coli in an in vitro transcription-translation system. Insertion mutations of bphA1 and bphC of Rhodococcus sp. strain RHA1 were constructed by gene replacement with cloned gene fragments.(ABSTRACT TRUNCATED AT 250 WORDS)
R J Nostrom - One of the best experts on this subject based on the ideXlab platform.
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immunoquantitation of cytochromes p450 1a and p450 2b and comparison with chlorinated hydrocarbon levels in archivedd polar bear liver samples
Chemosphere, 1997Co-Authors: Stelvio M Bandiera, S M Torok, R J Letcher, R J NostromAbstract:The present study examined the utility of an immunoblot method for quantitation of cytochrome P450 isozymes in archived liver samples as a bioassay of exposure to halogenated hydrocarbons. Hepatic microsomes were prepared from 44 archived polar bear (Ursus maritimus) liver homogenates that had been stored at approximately −40°C for 9–10 years and analyzed on blots probed with antibodies to rat cytochromes P450 1A1 and P450 2B1. The results revealed a positive correlation between cytochrome P450 1A and total Polychlorinated Biphenyl (PCB) levels in the archived liver samples, suggesting that cytochrome P450 1A was induced in polar bears by environmental exposure to PCBs.
James M Tiedje - One of the best experts on this subject based on the ideXlab platform.
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dna stable isotope probing integrated with metagenomics for retrieval of Biphenyl dioxygenase genes from Polychlorinated Biphenyl contaminated river sediment
Applied and Environmental Microbiology, 2009Co-Authors: John F Quensen, Joonhong Park, Jorge L M Rodrigues, Laurie Seliger, Tamara V Tsoi, Gerben J Zylstra, James M TiedjeAbstract:Stable isotope probing with [ 13 C]Biphenyl was used to explore the genetic properties of indigenous bacteria able to grow on Biphenyl in PCB-contaminated River Raisin sediment. A bacterial 16S rRNA gene clone library generated from [ 13 C]DNA after a 14-day incubation with [ 13 C]Biphenyl revealed the dominant organisms to be members of the genera Achromobacter and Pseudomonas . A library built from PCR amplification of genes for aromatic-ring-hydroxylating dioxygenases from the [ 13 C]DNA fraction revealed two sequence groups similar to bphA (encoding Biphenyl dioxygenase) of Comamonas testosteroni strain B-356 and of Rhodococcus sp. RHA1. A library of 1,568 cosmid clones was produced from the [ 13 C]DNA fraction. A 31.8-kb cosmid clone, detected by aromatic dioxygenase primers, contained genes of Biphenyl dioxygenase subunits bphAE , while the rest of the clone9s sequence was similar to that of an unknown member of the Gammaproteobacteria . A discrepancy in G+C content near the bphAE genes implies their recent acquisition, possibly by horizontal transfer. The Biphenyl dioxygenase from the cosmid clone oxidized Biphenyl and unsubstituted and para -only-substituted rings of Polychlorinated Biphenyl (PCB) congeners. A DNA-stable isotope probing-based cosmid library enabled the retrieval of functional genes from an uncultivated organism capable of PCB metabolism and suggest dispersed dioxygenase gene organization in nature.
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classification of the Biphenyl and Polychlorinated Biphenyl degrading strain lb400t and relatives as burkholderia xenovorans sp nov
International Journal of Systematic and Evolutionary Microbiology, 2004Co-Authors: Johan Goris, John F Quensen, James M Tiedje, Jesus Caballeromellado, Joonhong Park, Enevold Falsen, Peter VandammeAbstract:Strain LB400T is the best-studied Polychlorinated Biphenyl (PCB) degrader. This organism has previously been allocated in the genus Burkholderia, since its 16S rRNA gene sequence shows 98·6 % sequence similarity to the type strains of Burkholderia graminis and Burkholderia terricola. A polyphasic study was undertaken to clarify the actual taxonomic position of this biotechnologically important organism and of two strains, one recovered from a blood culture vial and one from a coffee plant rhizosphere, both of which resembled strain LB400T in their whole-cell protein patterns. DNA–DNA hybridization experiments revealed that the three strains represented a single novel species, for which the name Burkholderia xenovorans sp. nov. is proposed. Strains of this novel species can be differentiated phenotypically from nearly all other Burkholderia species by their inability to assimilate l-arabinose. The whole-cell fatty acid profile of B. xenovorans strains is consistent with their classification in the genus Burkholderia, with 18 : 1ω7c, 16 : 1ω7c, 16 : 0, 14 : 0 3OH, 16 : 0 3OH, 17 : 0 cyclo and 14 : 0 being the most abundant fatty acids. The G+C content of the species varies between 62·4 and 62·9 mol%. The type strain of B. xenovorans is LB400T (=LMG 21463T=CCUG 46959T=NRRL B-18064T).
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dechlorination of four commercial Polychlorinated Biphenyl mixtures aroclors by anaerobic microorganisms from sediments
Applied and Environmental Microbiology, 1990Co-Authors: John F Quensen, Stephen A Boyd, James M TiedjeAbstract:The rate, extent, and pattern of dechlorination of four Aroclors by inocula prepared from two Polychlorinated Biphenyl (PCB)-contaminated sediments were compared. The four mixtures used, Aroclors 1242, 1248, 1254, and 1260, average approximately three, four, five, and six chlorines, respectively, per Biphenyl molecule. All four Aroclors were dechlorinated with the loss of meta plus para chlorines ranging from 15 to 85%. Microorganisms from an Aroclor 1242-contaminated site in the upper Hudson River dechlorinated Aroclor 1242 to a greater extent than did microorganisms from Aroclor 1260-contaminated sediments from Silver Lake, Mass. The Silver Lake inoculum dechlorinated Aroclor 1260 more rapidly than the Hudson River inoculum did and showed a preferential removal of meta chlorines. For each inoculum the rate and extent of dechlorination tended to decrease as the degree of chlorination of the Aroclor increased, especially for Aroclor 1260. The maximal observed dechlorination rates were 0.3, 0.3, and 0.2 μg-atoms of Cl removed per g of sediment per week for Aroclors 1242, 1248, and 1254, respectively. The maximal observed dechlorination rates for Hudson River and Silver Lake organisms for Aroclor 1260 were 0.04 and 0.21 μg-atoms of Cl removed per g of sediment per week, respectively. The dechlorination patterns obtained suggested that the Hudson River microorganisms were more capable than the Silver Lake organisms of removing the last para chlorine. These results suggest that there are different PCB-dechlorinating microorganisms at different sites, with characteristic specificities for PCB dechlorination.
Keiji Yano - One of the best experts on this subject based on the ideXlab platform.
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characterization of Biphenyl catabolic genes of gram positive Polychlorinated Biphenyl degrader rhodococcus sp strain rha1
Applied and Environmental Microbiology, 1995Co-Authors: Eiji Masai, Akihiro Yamada, J M Healy, Takashi Hatta, Kazuhide Kimbara, Masao Fukuda, Keiji YanoAbstract:Rhodococcus sp. strain RHA1 is a gram-positive Polychlorinated Biphenyl (PCB) degrader which can degrade 10 ppm of PCB48 (equivalent to Aroclor1248), including tri-, tetra-, and pentachloroBiphenyls, in a few days. We isolated the 7.6-kb EcoRI-BamHI fragment carrying the Biphenyl catabolic genes of RHA1 and determined their nucleotide sequence. On the basis of deduced amino acid sequence homology, we identified six bph genes, bphA1A2A3A4, bphB, and bphC, that are responsible for the initial three steps of Biphenyl degradation. The order of bph genes in RHA1 is bphA1A2A3A4-bphC-bphB. This gene order differs from that of other PCB degraders reported previously. The amino acid sequences deduced from the RHA1 bph genes have a higher degree of homology with the tod genes from Pseudomonas putida F1 (49 to 79%) than with the bph genes of Pseudomonas sp. strains KF707 and KKS102 (30 to 65%). In Escherichia coli, bphA gene activity was not observed even when expression vectors were used. The activities of bphB and bphC, however, were confirmed by observing the transformation of Biphenyl to a meta-cleavage compound with the aid of benzene dioxygenase activity that complemented the bphA gene activity (S. Irie, S. Doi, T. Yorifuji, M. Takagi, and K. Yano, J. Bacteriol. 169:5174-5179, 1987). The expected products of the cloned bph genes, except bphA3, were observed in E. coli in an in vitro transcription-translation system. Insertion mutations of bphA1 and bphC of Rhodococcus sp. strain RHA1 were constructed by gene replacement with cloned gene fragments.(ABSTRACT TRUNCATED AT 250 WORDS)
Stelvio M Bandiera - One of the best experts on this subject based on the ideXlab platform.
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immunoquantitation of cytochromes p450 1a and p450 2b and comparison with chlorinated hydrocarbon levels in archivedd polar bear liver samples
Chemosphere, 1997Co-Authors: Stelvio M Bandiera, S M Torok, R J Letcher, R J NostromAbstract:The present study examined the utility of an immunoblot method for quantitation of cytochrome P450 isozymes in archived liver samples as a bioassay of exposure to halogenated hydrocarbons. Hepatic microsomes were prepared from 44 archived polar bear (Ursus maritimus) liver homogenates that had been stored at approximately −40°C for 9–10 years and analyzed on blots probed with antibodies to rat cytochromes P450 1A1 and P450 2B1. The results revealed a positive correlation between cytochrome P450 1A and total Polychlorinated Biphenyl (PCB) levels in the archived liver samples, suggesting that cytochrome P450 1A was induced in polar bears by environmental exposure to PCBs.
