The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the β-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria

Habe, Hiroshi; Chung, Jane; Ishida, Ayako; Kasuga, Kano; Ide, Kazuki; Takemura, Tamiko; Nojiri, Hideaki; Yamane, Hisakazu; Omori, Toshio

doi:10.1099/mic.0.28215-0

Cited by 33 publications

(18 citation statements)

References 46 publications

(52 reference statements)

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“…After the RT reaction, quantitative real-time PCR with SYBR GREEN PCR Master Mix (Applied Biosystems, Foster City, CA) was performed using the synthesized cDNA as a template on the ABI7700 sequence detection system (Applied Biosystems). The copy number of each mRNA was determined by a standard curve using a series of known concentrations of the target sequence according to the method of Habe et al (10). For normalization, 16S rRNA of KA1 was used as an internal standard.…”

Section: Methodsmentioning

confidence: 99%

Plasmid pCAR3 Contains Multiple Gene Sets Involved in the Conversion of Carbazole to Anthranilate

Urata

Uchimura

Noguchi

et al. 2006

Appl Environ Microbiol

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The carbazole degradative car-I gene cluster (carAaIBaIBbICIAcI) of Sphingomonas sp. strain KA1 is located on the 254-kb circular plasmid pCAR3. Carbazole conversion to anthranilate is catalyzed by carbazole 1,9a-dioxygenase (CARDO; CarAaIAcI), meta-cleavage enzyme (CarBaIBbI), and hydrolase (CarCI). CARDO is a three-component dioxygenase, and CarAaI and CarAcI are its terminal oxygenase and ferredoxin components. The car-I gene cluster lacks the gene encoding the ferredoxin reductase component of CARDO. In the present study, based on the draft sequence of pCAR3, we found multiple carbazole degradation genes dispersed in four loci on pCAR3, including a second copy of the car gene cluster (carAaIIBaIIBbIICIIAcII) and the ferredoxin/reductase genes fdxI-fdrI and fdrII. Biotransformation experiments showed that FdrI (or FdrII) could drive the electron transfer chain from NAD(P)H to CarAaI (or CarAaII) with the aid of ferredoxin (CarAcI, CarAcII, or FdxI). Because this electron transfer chain showed phylogenetic relatedness to that consisting of putidaredoxin and putidaredoxin reductase of the P450cam monooxygenase system of Pseudomonas putida, CARDO systems of KA1 can be classified in the class IIA Rieske non-heme iron oxygenase system. Reverse transcription-PCR (RT-PCR) and quantitative RT-PCR analyses revealed that two car gene clusters constituted operons, and their expression was induced when KA1 was exposed to carbazole, although the fdxI-fdrI and fdrII genes were expressed constitutively. Both terminal oxygenases of KA1 showed roughly the same substrate specificity as that from the well-characterized carbazole degrader Pseudomonas resinovorans CA10, although slight differences were observed.

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Section: Methodsmentioning

confidence: 99%

Plasmid pCAR3 Contains Multiple Gene Sets Involved in the Conversion of Carbazole to Anthranilate

Urata

Uchimura

Noguchi

et al. 2006

Appl Environ Microbiol

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“…In DBF63, the DFDO is thought to be composed of a multicomponent system with a terminal oxygenase, ferredoxin, and ferredoxin reductase, although the specific ferredoxin reductase has not been identified in the DBF63 genome (60). The dbf genes are localized on a linear plasmid pDBF1 in DBF63 clustered with other fluorene-catabolic (fln) genes, phthalate-catabolic (pht) genes, and protocatechuate-catabolic (pca) genes, and their products can convert fluorene into tricarboxylic acid cycle intermediates (22,23,25). From the pCAR3 sequence, we found a gene encoding a candidate ferredoxin component of the DFDO; the product of ORF243 showed 33% identity with CumA3 identified in P. fluorescens IP01 (24), and it had a putative Rieske-type [2Fe-2S] binding motif (data not shown).…”

Section: Downloaded Frommentioning

confidence: 99%

“…Third, the gene products might function as degrading enzymes for other compounds not used in the present study. As for phthalate and protocatechuate, one of the intermediate compounds of dibenzofuran or fluorene (22,23,25,42), both strains KA1 and Anthranilate…”

Section: Downloaded Frommentioning

confidence: 99%

The Sphingomonas Plasmid pCAR3 Is Involved in Complete Mineralization of Carbazole

et al. 2007

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We determined the complete 254,797-bp nucleotide sequence of the plasmid pCAR3, a carbazole-degradative plasmid from Sphingomonas sp. strain KA1. A region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pNL1 isolated from the aromatic-degrading Novosphingobium aromaticivorans strain F199. The presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. Although pCAR3 is thought to carry clustered genes for conjugative transfer, a filter-mating assay between KA1 and a pCAR3-cured strain (KA1W) was unsuccessful, indicating that pCAR3 might be deficient in conjugative transfer. Several degradative genes were found on pCAR3, including two kinds of carbazole-degradative gene clusters (car-I and car-II), and genes for electron transfer components of initial oxygenase for carbazole (fdxI, fdrI, and fdrII). Putative genes were identified for the degradation of anthranilate (and), catechol (cat), 2-hydroxypenta-2,4-dienoate (carDFE), dibenzofuran/fluorene (dbf/fln), protocatechuate (lig), and phthalate (oph). It appears that pCAR3 may carry clustered genes (car-I, car-II, fdxI, fdrI, fdrII, and, and cat) for the degradation of carbazole into tricarboxylic acid cycle intermediates; KA1W completely lost the ability to grow on carbazole, and the carbazole-degradative genes listed above were all expressed when KA1 was grown on carbazole. Reverse transcription-PCR analysis also revealed that the transcription of car-I, car-II, and cat genes was induced by carbazole or its metabolic intermediate. Southern hybridization analyses with probes prepared from car-I, car-II, repA, parA, traI, and traD genes indicated that several Sphingomonas carbazole degraders have DNA regions similar to parts of pCAR3.

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“…In this case, studies have shown that the function of a gene can often be deduced from the gene organization or arrangement (14,15,52,55). We analyzed the genomic contexts to search missing ORFs for which functional evidence is lacking.…”

Section: Pyrene Induction Experimentmentioning

confidence: 99%

Complete and Integrated Pyrene Degradation Pathway in Mycobacterium vanbaalenii PYR-1 Based on Systems Biology

Kim

Kweon

Jones³

et al. 2007

J Bacteriol

253

188

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Mycobacterium vanbaalenii PYR-1 was the first bacterium isolated by virtue of its ability to metabolize the high-molecular-weight polycyclic aromatic hydrocarbon (PAH) pyrene. We used metabolic, genomic, and proteomic approaches in this investigation to construct a complete and integrated pyrene degradation pathway for M. vanbaalenii PYR-1. Genome sequence analyses identified genes involved in the pyrene degradation pathway that we have proposed for this bacterium. To identify proteins involved in the degradation, we conducted a proteome analysis of cells exposed to pyrene using one-dimensional gel electrophoresis in combination with liquid chromatography-tandem mass spectrometry. Database searching performed with the M. vanbaalenii PYR-1 genome resulted in identification of 1,028 proteins with a protein false discovery rate of <1%. Based on both genomic and proteomic data, we identified 27 enzymes necessary for constructing a complete pathway for pyrene degradation. Our analyses indicate that this bacterium degrades pyrene to central intermediates through o-phthalate and the ␤-ketoadipate pathway. Proteomic analysis also revealed that 18 enzymes in the pathway were upregulated more than twofold, as indicated by peptide counting when the organism was grown with pyrene; three copies of the terminal subunits of ring-hydroxylating oxygenase (NidAB2, MvanDraft_0817/0818, and PhtAaAb), dihydrodiol dehydrogenase (MvanDraft_0815), and ring cleavage dioxygenase (MvanDraft_3242) were detected only in pyrene-grown cells. The results presented here provide a comprehensive picture of pyrene metabolism in M. vanbaalenii PYR-1 and a useful framework for understanding cellular processes involved in PAH degradation.

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The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the β-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria

Cited by 33 publications

References 46 publications

Plasmid pCAR3 Contains Multiple Gene Sets Involved in the Conversion of Carbazole to Anthranilate

Plasmid pCAR3 Contains Multiple Gene Sets Involved in the Conversion of Carbazole to Anthranilate

The Sphingomonas Plasmid pCAR3 Is Involved in Complete Mineralization of Carbazole

Complete and Integrated Pyrene Degradation Pathway in Mycobacterium vanbaalenii PYR-1 Based on Systems Biology

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