Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6

Wei, Li; Shi, Jiandang; Wang, Xuegang; Han, Yong; Tong, Wei; Ma, Lin; Liu, Bin; Cai, Baoli

doi:10.1016/j.gene.2004.03.027

Cited by 95 publications

(65 citation statements)

References 32 publications

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“…2C), and the salB gene product showed the highest similarity to benK (benzoate transporters) transporters of the major facilitator superfamily (64% identity of the deduced amino acid sequence to the benK gene product of Pseudomonas sp. strain ND6 [28]). Transcribed divergently toward salA, an ORF putatively encoding a regulatory protein of the LysR family was identified and termed salR2 (Fig.…”

Section: Resultsmentioning

confidence: 99%

A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate

et al. 2007

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Pseudomonas sp. strain MT1 has recently been reported to degrade 4-and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. Genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. One of the gene clusters characterized (sal) showed a novel gene arrangement, with salA, encoding a salicylate 1-hydroxylase, being clustered with salCD genes, encoding muconate cycloisomerase and catechol 1,2-dioxygenase, respectively, and was expressed during growth on salicylate and chlorosalicylate. A second gene cluster (cat), exhibiting the typical catRBCA arrangement of genes of the catechol branch of the 3-oxoadipate pathway in Pseudomonas strains, was expressed during growth on salicylate. Despite their high sequence similarities with isoenzymes encoded by the cat gene cluster, the catechol 1,2-dioxygenase and muconate cycloisomerase encoded by the sal cluster showed unusual kinetic properties. Enzymes were adapted for turnover of 4-chlorocatechol and 3-chloromuconate; however, 4-methylcatechol and 3-methylmuconate were identified as the preferred substrates. Investigation of the substrate spectrum identified 4-and 5-methylsalicylate as growth substrates, which were effectively converted by enzymes of the sal cluster into 4-methylmuconolactone, followed by isomerization to 3-methylmuconolactone. The function of the sal gene cluster is therefore to channel both chlorosubstituted and methylsubstituted salicylates into a catechol ortho cleavage pathway, followed by dismantling of the formed substituted muconolactones through specific pathways.

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Section: Resultsmentioning

confidence: 99%

A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate

et al. 2007

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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%

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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“…strain NCIB 9816-4 [293,294]: naphthalene + NADH + H + + O 2 Ø (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD + [292]. C2,3O and nahAc genes are commonly found on the same plasmid [228] with C2,3O often present in multiple copies [295,296]. Phillips et al [228] observed a positive correlation between the copy numbers of the two genes and the PAH-mineralization rate, suggesting that plasmid transfer may have been a significant factor influencing the changes in degradation potential.…”

Section: Lateral Gene Transfer In Rhizosphere and Hydrocarbon Degradamentioning

confidence: 99%

Root Exudation: The Ecological Driver of Hydrocarbon Rhizoremediation

2016

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Rhizoremediation is a bioremediation technique whereby microbial degradation of organic contaminants occurs in the rhizosphere. It is considered to be an effective and affordable "green technology" for remediating soils contaminated with petroleum hydrocarbons. Root exudation of a wide variety of compounds (organic, amino and fatty acids, carbohydrates, vitamins, nucleotides, phenolic compounds, polysaccharides and proteins) provide better nutrient uptake for the rhizosphere microbiome. It is thought to be one of the predominant drivers of microbial communities in the rhizosphere and is therefore a potential key factor behind enhanced hydrocarbon biodegradation. Many of the genes responsible for bacterial adaptation in contaminated soil and the plant rhizosphere are carried by conjugative plasmids and transferred among bacteria. Because root exudates can stimulate gene transfer, conjugation in the rhizosphere is higher than in bulk soil. A better understanding of these phenomena could thus inform the development of techniques to manipulate the rhizosphere microbiome in ways that improve hydrocarbon bioremediation.

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Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6

Cited by 95 publications

References 32 publications

A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate

A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate

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

Root Exudation: The Ecological Driver of Hydrocarbon Rhizoremediation

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