Diversity of 2,3-dihydroxybiphenyl dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1

Sakai, Masayuki; Masai, Eiji; Asami, Hiroki; Sugiyama, Katsumi; Kimbara, Kazuhide; Fukuda, Masao

doi:10.1016/s1389-1723(02)80078-0

Cited by 48 publications

(29 citation statements)

References 15 publications

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“…11,12) In contrast, Rhodococcus sp. RHA1 and R. globerulus P6 have six (bphC1 to bphC5 and etbC) 13) and three y To whom correspondence should be addressed. Fax: +81-48-462-4672; E-mail: ktaguchi@riken.jp Abbreviations: PCB, polychlorinated biphenyl; 23DHBP, 2,3-dihydroxybiphenyl; HOPDA, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (bphC1 to bphC3) 2) bphC genes respectively.…”

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confidence: 99%

Polychlorinated Biphenyl/Biphenyl Degrading Gene Clusters inRhodococcussp. K37, HA99, and TA431 Are Different from Well-KnownbphGene Clusters of Rhodococci

Taguchi¹,

Motoyama²,

Iida³

et al. 2007

Bioscience, Biotechnology, and Biochemistry

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Four kinds of polychlorinated biphenyl (PCB)-degrading Rhodococcus sp. (TA421, TA431, HA99, and K37) have been isolated from termite ecosystem and under alkaline condition. The bph gene cluster involved in the degradation of PCB/biphenyl has been analyzed in strain TA421. This gene cluster was highly homologous to bph gene clusters in R. globerulus P6 and Rhodococcus sp. RHA1. In this study, we cloned and analyzed the bph gene cluster essential to PCB/biphenyl degradation from R. rhodochrous K37. The order of the genes and the sequence were different in K37 than in P6, RHA1, and TA421. The bphC8 K37 gene was more homologous to the meta-cleavage enzyme involved in phenanthrene metabolism than bphC genes involved in biphenyl metabolism. Two other Rhodococcus strains (HA99 and TA431) had PCB/biphenyl degradation gene clusters similar to that in K37. These findings suggest that these bph gene clusters evolved separately from the well-known bph gene clusters of PCB/biphenyl degraders.

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Polychlorinated Biphenyl/Biphenyl Degrading Gene Clusters inRhodococcussp. K37, HA99, and TA431 Are Different from Well-KnownbphGene Clusters of Rhodococci

Taguchi¹,

Motoyama²,

Iida³

et al. 2007

Bioscience, Biotechnology, and Biochemistry

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“…strain RHA1, which has a great capacity to degrade highly chlorinated PCBs. 6) Multiple biphenyl/PCB degradation genes were found in RHA1, which includes aromatic ring hydroxylation dioxygenases, 7) ring-cleavage dioxygenases, 8) and ringcleavage compound hydrolases. 9) Expression of these multiple biphenyl degradation genes is induced simultaneously in the presence of aromatic compounds including biphenyl and ethylbenzene.…”

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Biphenyl-inducible Promoters in a Polychlorinated Biphenyl-degrading Bacterium,Rhodococcussp. RHA1

Takeda

Hara

Sakai

et al. 2004

Bioscience, Biotechnology, and Biochemistry

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“…For each of these four steps, RHA1 appears to possess multiple isozymes, which may help explain the strain's superior PCB-transforming capabilities. Thus, the strain contains at least three bph-type ring-hydroxylating dioxygenases (33) and at least seven different bph-type ring cleavage enzymes (51). It is unclear which of these isozymes is involved in the catabolism of biphenyl or closely related compounds and how these different activities are regulated.…”

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Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading Rhodococcus sp. Strain RHA1

Warren¹,

Hsiao

Kudo

et al. 2004

J Bacteriol

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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.Rhodococcus is a widely occurring genus of aerobic, nonmotile soil bacteria that are closely related to three other genera of GC-rich actinomycetes: Gordonia, Nocardia, and Mycobacterium. Rhodococci degrade an extraordinarily wide variety of organic substrates and thus play an important role in the global C cycle. The unusual armamentarium of enzymatic activities involved in these processes has been exploited in applications ranging from commodity chemical production to the desulfurization of fossil fuels (6). Consequently, the metabolic capabilities of rhodococci are of interest to the pharmaceutical, environmental, chemical, and energy sectors.Rhodococcus sp. strain RHA1 is characterized by its exceptional ability to transform polychlorinated biphenyls (PCBs) (53), a particularly widespread and persistent class of environmental pollutants. It is generally thought that in aerobic bacteria, PCBs are cometabolized by the bph pathway, which is responsible for the aerobic degradation of biphenyl (23). The upper bph pathway consists of four enzymatic activities that together transform biphenyl to benzoate and 2-hydroxypenta-2,4-dienoate. For each of these four steps, RHA1 appears to possess multiple isozymes, which may help explain the strain's superior PCB-transforming capabilities. Thus, the strain contains at least three bph-type ring-hydroxylating di...

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Diversity of 2,3-dihydroxybiphenyl dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1

Cited by 48 publications

References 15 publications

Polychlorinated Biphenyl/Biphenyl Degrading Gene Clusters inRhodococcussp. K37, HA99, and TA431 Are Different from Well-KnownbphGene Clusters of Rhodococci

Polychlorinated Biphenyl/Biphenyl Degrading Gene Clusters inRhodococcussp. K37, HA99, and TA431 Are Different from Well-KnownbphGene Clusters of Rhodococci

Biphenyl-inducible Promoters in a Polychlorinated Biphenyl-degrading Bacterium,Rhodococcussp. RHA1

Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading Rhodococcus sp. Strain RHA1

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