Molecular classification of IncP-9 naphthalene degradation plasmids

Izmalkova, T. Yu.; Mavrodi, Dmitri V.; Sokolov, S. L.; Кошелева, И. А.; Smalla, Kornelia; Thomas, Christopher M.; Boronin, A. M.

doi:10.1016/j.plasmid.2005.12.004

Cited by 32 publications

(22 citation statements)

References 21 publications

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“…IncP-9 plasmids are important vehicles for the dissemination of genes coding for enzymes involved in the degradation of polycyclic aromatic hydrocarbons (PAH) and are very often found in environments polluted with oil [23] (Flocco et al , unpublished).…”

Section: Discussionmentioning

confidence: 99%

Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats

et al. 2014

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IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are “hot spots” of plasmids potentially carrying catabolic genes.

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Section: Discussionmentioning

confidence: 99%

Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats

et al. 2014

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“…The bacterial host range of IncP-9 plasmids determined by us is also restricted only to the genus Pseudomonas . Although the genus Pseudomonas is one of the most ubiquitous bacterial genera known so far [24], IncP-9 plasmids have been isolated only from a few species— P. putida, P. fluorescens, P. aeruginosa and P. aureofaciens [3,6]. Our study extended the bacterial host species range of the IncP-9 family, revealing IncP-9 plasmids in P. stutzeri and P. migulae as well.…”

Section: Resultsmentioning

confidence: 59%

“…These components were chosen because the catabolic pathways for the degradation of these chemicals are often encoded by plasmids [2,3,6,15]. The bacterial strains obtained from nonselective R2A media were taken for further analysis only if they tested positive on mentioned selective media.…”

Section: Resultsmentioning

confidence: 99%

“…The degradation of naturally occurring pollutants is mediated mostly by IncP-2, IncP-7 and IncP-9 catabolic plasmids, but the detoxification of xenobiotics, i.e. , man-made chemical compounds is often encoded by IncP-1 representatives [1,3,4]. It has been shown also that the resistance to antibiotics in Pseudomonas species is associated with the IncP-9 plasmids [5,6].…”

Section: Introductionmentioning

confidence: 99%

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Occurrence of Plasmids in the Aromatic Degrading Bacterioplankton of the Baltic Sea

Jutkina

Heinaru

Vedler

et al. 2011

Genes

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Plasmids are mobile genetic elements that provide their hosts with many beneficial traits including in some cases the ability to degrade different aromatic compounds. To fulfill the knowledge gap regarding catabolic plasmids of the Baltic Sea water, a total of 209 biodegrading bacterial strains were isolated and screened for the presence of these mobile genetic elements. We found that both large and small plasmids are common in the cultivable Baltic Sea bacterioplankton and are particularly prevalent among bacterial genera Pseudomonas and Acinetobacter. Out of 61 plasmid-containing strains (29% of all isolates), 34 strains were found to carry large plasmids, which could be associated with the biodegradative capabilities of the host bacterial strains. Focusing on the diversity of IncP-9 plasmids, self-transmissible m-toluate (TOL) and salicylate (SAL) plasmids were detected. Sequencing the repA gene of IncP-9 carrying isolates revealed a high diversity within IncP-9 plasmid family, as well as extended the assumed bacterial host species range of the IncP-9 representatives. This study is the first insight into the genetic pool of the IncP-9 catabolic plasmids in the Baltic Sea bacterioplankton.

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“…This is supported by (i) our finding that Tn4657 has the replication machinery of IncP-7 plasmid, and (ii) a recent report of a NAH plasmid having both IncP-7 and − 9 replication machineries. 51 The plausible genetic exchange might be greatly facilitated by the movement of other catabolic transposons such as Tn4651 and Tn4653 on pWW0, 15 Tn4655 on NAH7, 16 and a putative transposon Tn4660 on pWW53. More sequence information on other IncP-7 plasmids as well as other TOL and NAH plasmids, together with the functional analysis of their backbone regions, will give us additional clues to understand the relationships between the catabolic genes and the two Inc groups as well as molecular mechanisms for the acquisition and the shuffling of catabolic gene clusters.…”

Section: Discussionmentioning

confidence: 99%

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

Garruto

Sota

et al. 2007

Journal of Molecular Biology

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Molecular classification of IncP-9 naphthalene degradation plasmids

Cited by 32 publications

References 21 publications

Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats

Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats

Occurrence of Plasmids in the Aromatic Degrading Bacterioplankton of the Baltic Sea

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

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