Isolation of Rhodococcus rhodochrous NCIMB13064 derivatives with new biodegradative abilities

Kulakova, Anna N.

doi:10.1016/s0378-1097(96)00414-4

Cited by 9 publications

(9 citation statements)

References 8 publications

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“…I24, the TKN14 NidA and NidB proteins had high amino acid homology to the large and small subunits of naphthalene dioxygenases (NDOs) found in various Rhodococcus species;, i.e., two subspecies (P200 and P400) derived from Rhodococcus rhodochrous NCIMB13064 (DDBJ/EMBL/GenBank accession nos. AY392424 and AY392423) (19,21), Rhodococcus sp. NCIMB12038 (accession no.…”

Section: Resultsmentioning

confidence: 99%

Isolation and Characterization of o -Xylene Oxygenase Genes from Rhodococcus opacus TKN14

Maruyama

Ishikura

Taki

et al. 2005

Appl Environ Microbiol

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o-Xylene is one of the most difficult-to-degrade environmental pollutants. We report here Rhodococcus genes mediating oxygenation in the first step of o-xylene degradation. Rhodococcus opacus TKN14, isolated from soil contaminated with o-xylene, was able to utilize o-xylene as the sole carbon source and to metabolize it to o-methylbenzoic acid. A cosmid library from the genome of this strain was constructed in Escherichia coli. A bioconversion analysis revealed that a cosmid clone incorporating a 15-kb NotI fragment had the ability to convert o-xylene into o-methylbenzyl alcohol. The sequence analysis of this 15-kb region indicated the presence of a gene cluster significantly homologous to the naphthalene-inducible dioxygenase gene clusters (nidABCD) that had been isolated from Rhodococcus sp. strain I24. Complementation studies, using E. coli expressing various combinations of individual open reading frames, revealed that a gene (named nidE) for rubredoxin (Rd) and a novel gene (named nidF) encoding an auxiliary protein, which had no overall homology with any other proteins, were indispensable for the methyl oxidation reaction of o-xylene, in addition to the dioxygenase iron-sulfur protein genes (nidAB). Regardless of the presence of NidF, the enzyme composed of NidABE was found to function as a typical naphthalene dioxygenase for converting naphthalene and various (di)methylnaphthalenes into their corresponding cis-dihydrodiols. All the nidABEF genes were transcriptionally induced in R. opacus TKN14 by the addition of o-xylene to a mineral salt medium. It is very likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by Rhodococcus species as the first key enzyme. o-, m-and p-xylenes, which are included in petroleum, are used as solvents in the production of chemicals and drugs, as thinners for paints and enamels, and as intermediates for the synthesis of numerous chemical compounds. They are therefore widespread environmental contaminants in groundwater and soil (4,11,27). In m-and p-xylenes, numerous bacteria that are able to utilize them as the sole carbon and energy source have been isolated, and details of their catabolic pathways have been well documented. The most elucidated examples are the catabolism of toluene, m-xylene, and p-xylene with the enzymes encoded on a transmissible TOL plasmid (pWW0) from Pseudomonas putida mt-2 (38, 39). Xylene monooxygenase is the first enzyme on this degradation pathway (14, 34). This enzyme consists of two polypeptide subunits encoded by the xylM and xylA genes. XylA, the NADH acceptor reductase component (34), has been characterized as an electron transport protein transferring reducing equivalents from NADH to XylM, which is the hydroxylase component located in the membrane (18). Toluene and m-and p-xylenes are, respectively, metabolized with XylMA to benzyl alcohol and m-and p-methylbenzyl alcohol. These respective alcohols are further metabolized to benzoate and m-and p-toluates via their corresponding aldehydes b...

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Section: Resultsmentioning

confidence: 99%

Isolation and Characterization of o -Xylene Oxygenase Genes from Rhodococcus opacus TKN14

Maruyama

Ishikura

Taki

et al. 2005

Appl Environ Microbiol

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“…Rhodococcus strains NCIMB12038, P200, and P400 have been described previously (16,20). Escherichia coli strain DH5␣ and plasmid vector pBluescript KS(ϩ) were used for the cloning experiments.…”

Section: Methodsmentioning

confidence: 99%

“…Both subunits of the NCIMB12038 NDO showed approximately 30% amino acid identity to the corresponding P. putida NDO subunits, with conservation of the key catalytic residues (19). Rhodococcus strains P200 and P400 were shown to degrade naphthalene via catechol and catechol-2,3-dioxygenase activity and not via the gentisate route (16).…”

mentioning

confidence: 99%

Web-Type Evolution of Rhodococcus Gene Clusters Associated with Utilization of Naphthalene

Kulakov

Chen

Allen

et al. 2005

Appl Environ Microbiol

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Clusters of genes which include determinants for the catalytic subunits of naphthalene dioxygenase (narAa and narAb) were analyzed in naphthalene-degrading Rhodococcus strains. We demonstrated (i) that in the region analyzed homologous gene clusters are separated from each other by nonhomologous DNA, (ii) that there are various degrees of homology between related genes, and (iii) that nar genes are located on plasmids in strains NCIMB12038 and P400 and on a chromosome in P200. These observations suggest that genetic exchange and reshuffling of genetic modules, as well as vertical descent of the genetic information, were the main routes in the evolution of naphthalene degradation in Rhodococcus. These conclusions were supported by studies of transcription patterns in the region analyzed. It was found that the nar region is not organized into a single operon but there are several transcription units which differ in the strains investigated. The narA and narB genes were found to be transcribed as a single unit in all strains analyzed, and their transcription was induced by naphthalene. The putative aldolase gene (narC) was found on the same transcript only in strains P200 and P400. In NCIMB12038 transcription of two more gene clusters was induced by growth on naphthalene. Transcription start sites for narA and narB were found to be different in all of the strains studied. Putative regulatory genes (narR1 and narR2) were transcribed as a single mRNA in naphthalene-induced cells. At the same time, a number of the genes known to be essential for naphthalene catabolism in gram-negative bacteria were not found in the region analyzed.

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“…Although Rhodococcus species utilize naphthalene as their sole carbon and energy source, [82][83][84][85] to the best of our knowledge, the PAH catabolic genes from these have not been characterized until recently. Larkin et al 86) reported the puriˆcation and characteristics of a novel ISP of naphthalene dioxygenase from Rhodococcus sp.…”

Section: )mentioning

confidence: 99%

Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria

Habe

Omori

2003

Bioscience, Biotechnology, and Biochemistry

387

220

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Isolation of Rhodococcus rhodochrous NCIMB13064 derivatives with new biodegradative abilities

Cited by 9 publications

References 8 publications

Isolation and Characterization of o -Xylene Oxygenase Genes from Rhodococcus opacus TKN14

Isolation and Characterization of o -Xylene Oxygenase Genes from Rhodococcus opacus TKN14

Web-Type Evolution of Rhodococcus Gene Clusters Associated with Utilization of Naphthalene

Genetics of Polycyclic Aromatic Hydrocarbon Metabolism in Diverse Aerobic Bacteria

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