Complete Sequence Determination Combined with Analysis of Transposition/Site-specific Recombination Events to Explain Genetic Organization of IncP-7 TOL Plasmid pWW53 and Related Mobile Genetic Elements

Yano, Hirokazu; Garruto, Christine E.; Sota, Masahiro; Ohtsubo, Yoshiyuki; Nagata, Yasunobu; Zylstra, Gerben J.; Williams, Peter A.; Tsuda, Masashi

doi:10.1016/j.jmb.2007.02.098

Cited by 42 publications

(32 citation statements)

References 60 publications

(51 reference statements)

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“…been published: the carbazole (nitrogen-containing aromatic heterocyclic organic compound)-degradative plasmid pCAR1 (56,107), the naphthalene-degradative plasmid pND6-1 (55), and the toluene/xylene-degradative plasmids pWW53 and pDK1 (128,129). pCAR1 and pCAR2 were previously identified as pCAR1.1 and pCAR1.2 due to a single nucleotide substitution.…”

Section: Behavior Of the Narrow Host Range Incp-7 Plasmids In The Envmentioning

confidence: 99%

“…However, we consider them to be identical and so refer to them as pCAR1 (56,90,91,92,106). Like pWW0, class II transposons are located within pCAR1, pDK1, and pWW53, indicating that degradative genes on these plasmids can transpose into other replicons in the host cell (56,91,118,128,129). Of the sequenced IncP-7 plasmids, pCAR1 and pDK1 possess functional conjugative transfer systems, whereas the others may have lost these genes (55,128).…”

Section: Behavior Of the Narrow Host Range Incp-7 Plasmids In The Envmentioning

confidence: 99%

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The Behavior and Significance of Degradative Plasmids Belonging to Inc Groups in <i>Pseudomonas</i> within Natural Environments and Microcosms

et al. 2010

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Over the past few decades, degradative plasmids have been isolated from bacteria capable of degrading a variety of both natural and man-made compounds. Degradative plasmids belonging to three incompatibility (Inc) groups in Pseudomonas (IncP-1, P-7, and P-9) have been well studied in terms of their replication, maintenance, and capacity for conjugative transfer. The host ranges of these plasmids are determined by replication or conjugative transfer systems. The host range of IncP-1 is broad, that of IncP-9 is intermediate, and that of IncP-7 is narrow. To understand the behavior of these plasmids and their hosts in various environments, the survivability of inocula, stability or transferability, and efficiency of biodegradation in environments and microcosms have been monitored. The biodegradation and plasmid transfer in various environments have been observed for all three groups, although the kinds of transconjugants differed with the Inc groups. In some cases, the deletion and amplification of catabolic genes acted to reduce the production of toxic catabolic intermediates, or to increase the activity on a particular catabolic pathway. The combination of degradative genes, the plasmid backbone of each Inc group, and the host of the plasmids is key to the degraders adapting to various hosts or to heterogeneous environments.

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Section: Behavior Of the Narrow Host Range Incp-7 Plasmids In The Envmentioning

confidence: 99%

Section: Behavior Of the Narrow Host Range Incp-7 Plasmids In The Envmentioning

confidence: 99%

The Behavior and Significance of Degradative Plasmids Belonging to Inc Groups in <i>Pseudomonas</i> within Natural Environments and Microcosms

et al. 2010

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“…Plasmid encodes 3-chlorocatechol meta-cleavage pathway dehydrogenase integrated in proteobacterial meta-cleavage pathways (Yano et al, 2007). Analysis of cell extracts of E. coli (pXPQ) confirmed mhpF to encode an acetaldehyde dehydrogenase, as evidenced by an activity of 350 units (g protein)…”

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confidence: 99%

Degradation of chloroaromatics by Pseudomonas putida GJ31: assembled route for chlorobenzene degradation encoded by clusters on plasmid pKW1 and the chromosome

et al. 2009

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Pseudomonas putida GJ31 has been reported to grow on chlorobenzene using a meta-cleavage pathway with chlorocatechol 2,3-dioxygenase (CbzE) as a key enzyme. The CbzE-encoding gene was found to be localized on the 180 kb plasmid pKW1 in a cbzTEXGS cluster, which is flanked by transposases and encodes only a partial (chloro)catechol meta-cleavage pathway comprising ferredoxin reductase, chlorocatechol 2,3-dioxygenase, an unknown protein, 2-hydroxymuconic semialdehyde dehydrogenase and glutathione S-transferase. Downstream of cbzTEXGS are located cbzJ, encoding a novel type of 2-hydroxypent-2,4-dienoate hydratase, and a transposon region highly similar to Tn5501. Upstream of cbzTEXGS, traNEOFG transfer genes were found. The search for gene clusters possibly completing the (chloro)catechol metabolic pathway of GJ31 revealed the presence of two additional catabolic gene clusters on pKW1. The mhpRBCDFETP cluster encodes enzymes for the dissimilation of 2,3-dihydroxyphenylpropionate in a novel arrangement characterized by the absence of a gene encoding 3-(3-hydroxyphenyl)propionate monooxygenase and the presence of a GntR-type regulator, whereas the nahINLOMKJ cluster encodes part of the naphthalene metabolic pathway. Transcription studies supported their possible involvement in chlorobenzene degradation. The upper pathway cluster, comprising genes encoding a chlorobenzene dioxygenase and a chlorobenzene dihydrodiol dehydrogenase, was localized on the chromosome. A high level of transcription in response to chlorobenzene revealed it to be crucial for chlorobenzene degradation. The chlorobenzene degradation pathway in strain GJ31 is thus a mosaic encoded by four gene clusters.

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“…Several catabolic plasmids within members of the genus Pseudomonas have been identified and have been classified mostly into incompatibility groups IncP-1, IncP-2, IncP-7, and IncP-9. Recently, the complete genome sequences of several IncP-1, IncP-7, and IncP-9 catabolic plasmids were determined (16,28,44,45,47,76,77,83,86,93). The 199,035-bp catabolic plasmid pCAR1 was originally discovered in Pseudomonas resinovorans CA10, which is able to utilize carbazole as its sole source of carbon, nitrogen, and energy (53, 56), and was the first IncP-7 plasmid to be completely sequenced (45).…”

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confidence: 99%

Transcriptome Analysis ofPseudomonas putidaKT2440 Harboring the Completely Sequenced IncP-7 Plasmid pCAR1

et al. 2007

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The IncP-7 plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon transfer to the recipient strain P. putida KT2440. We designed a customized whole-genome oligonucleotide microarray to study the coordinated expression of pCAR1 and the chromosome in the transconjugant strain KT2440(pCAR1). First, the transcriptome of KT2440(pCAR1) during growth with carbazole as the sole carbon source was compared to that during growth with succinate. The carbazole catabolic car and ant operons were induced, along with the chromosomal cat and pca genes involved in the catechol branch of the ␤-ketoadipate pathway. Additionally, the regulatory gene antR encoding the AraC/XylS family transcriptional activator specific for car and ant operons was upregulated. The characterization of the antR promoter revealed that antR is transcribed from an RpoN-dependent promoter, suggesting that the successful expression of the carbazole catabolic operons depends on whether the chromosome contains the specific RpoN-dependent activator. Next, to analyze whether the horizontal transfer of a plasmid alters the transcription network of its host chromosome, we compared the chromosomal transcriptomes of KT2440(pCAR1) and KT2440 under the same growth conditions. Only subtle changes were caused by the transfer of pCAR1, except for the significant induction of the hypothetical gene PP3700, designated parI, which encodes a putative ParA-like ATPase with an N-terminal Xre-type DNA-binding motif. Further transcriptional analyses showed that the parI promoter was positively regulated by ParI itself and the pCAR1-encoded protein ParA.Many catabolic plasmids can be transferred horizontally between different bacteria and play an important role in the distribution of the ability to degrade and utilize recalcitrant chemical compounds (15,90). Several catabolic plasmids within members of the genus Pseudomonas have been identified and have been classified mostly into incompatibility groups IncP-1, IncP-2, IncP-7, and IncP-9. Recently, the complete genome sequences of several IncP-1, IncP-7, and IncP-9 catabolic plasmids were determined (16,28,44,45,47,76,77,83,86,93). The 199,035-bp catabolic plasmid pCAR1 was originally discovered in Pseudomonas resinovorans CA10, which is able to utilize carbazole as its sole source of carbon, nitrogen, and energy (53, 56), and was the first IncP-7 plasmid to be completely sequenced (45). pCAR1 carries the car and ant operons, which encode the upper and meta pathway enzymes and the anthranilate 1,2-dioxygenase, respectively (see Fig. 1A). The operons are transcribed from two identical anthranilate-inducible promoters, P ant , under the control of the AraC/XylS family activator AntR (85), and the constitutive promoter P carAa also originates the transcription of the car operon (50). Carbazole catabolism begins with the upper pathway to yield anthranilate and 2-hydroxypenta-2,4-dienoate, and then 2-hydroxypenta-2,4-dienoate is mineralized into pyruvate and acetyl coenzyme A (acetylCoA) by the met...

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Complete Sequence Determination Combined with Analysis of Transposition/Site-specific Recombination Events to Explain Genetic Organization of IncP-7 TOL Plasmid pWW53 and Related Mobile Genetic Elements

Cited by 42 publications

References 60 publications

The Behavior and Significance of Degradative Plasmids Belonging to Inc Groups in <i>Pseudomonas</i> within Natural Environments and Microcosms

The Behavior and Significance of Degradative Plasmids Belonging to Inc Groups in <i>Pseudomonas</i> within Natural Environments and Microcosms

Degradation of chloroaromatics by Pseudomonas putida GJ31: assembled route for chlorobenzene degradation encoded by clusters on plasmid pKW1 and the chromosome

Transcriptome Analysis ofPseudomonas putidaKT2440 Harboring the Completely Sequenced IncP-7 Plasmid pCAR1

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