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The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family.

Li X, Top EM, Wang Y, Brown CJ, Yao F, Yang S, Jiang Y, Li H - Front Microbiol (2015)

Bottom Line: Nevertheless, phylogenetic divergence was found in specific gene products.Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged.Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China ; College of Resources and Environment, University of Chinese Academy of Sciences Beijing, China.

ABSTRACT
A self-transmissible broad-host-range (BHR) plasmid pSFA231 was isolated from petroleum-contaminated sediment in Shen-fu wastewater irrigation zone, China, using the triparental mating exogenous plasmid capture method. Based on its complete sequence the plasmid has a size of 41.5 kb and codes for 50 putative open reading frames (orfs), 29 of which represent genes involved in replication, partitioning and transfer functions of the plasmid. Phylogenetic analysis grouped pSFA231 into the newly defined PromA plasmid family, which currently includes five members. Further comparative genomic analysis shows that pSFA231 shares the common backbone regions with the other PromA plasmids, i.e., genes involved in replication, maintenance and control, and conjugative transfer. Nevertheless, phylogenetic divergence was found in specific gene products. We propose to divide the PromA group into two subgroups, PromA-α (pMRAD02, pSB102) and PromA-β (pMOL98, pIPO2T, pSFA231, pTer331), based on the splits network analysis of the RepA protein. Interestingly, a cluster of hypothetical orfs located between parA and traA of pSFA231 shows high similarity with the corresponding regions on pMOL98, pIPO2T, and pTer331, suggesting these hypothetical orfs may represent "essential" plasmid backbone genes for the PromA-β subgroup. Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged. Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.

No MeSH data available.


Related in: MedlinePlus

Alignment of the pSFA231 replicative origin region with the putative oriV regions of pMOL98. DnaA refers to DnaA boxes, IHF refers to putative Integration Host Factor binding sites.
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Figure 3: Alignment of the pSFA231 replicative origin region with the putative oriV regions of pMOL98. DnaA refers to DnaA boxes, IHF refers to putative Integration Host Factor binding sites.

Mentions: Comparison of the oriV region of plasmid pSFA231 and its closest homolog, pMOL98, further verified that the replication module of pSFA231 was similar to PromA plasmids. Like other members of the PromA family, pSFA231 was characterized as θ-type mode of replication, with an oriV-like region being located at 5.1 kb downstream of the repA gene. Within this region, we identified four putative iterons (RepA binding site), which are identical to the iteron sequences from pMOL98. Furthermore, a putative DnaA-binding site, a potential integration host factor (IHF) site and an AT-rich (86.67%) region were also found in this region (Figure 3).


The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family.

Li X, Top EM, Wang Y, Brown CJ, Yao F, Yang S, Jiang Y, Li H - Front Microbiol (2015)

Alignment of the pSFA231 replicative origin region with the putative oriV regions of pMOL98. DnaA refers to DnaA boxes, IHF refers to putative Integration Host Factor binding sites.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4290620&req=5

Figure 3: Alignment of the pSFA231 replicative origin region with the putative oriV regions of pMOL98. DnaA refers to DnaA boxes, IHF refers to putative Integration Host Factor binding sites.
Mentions: Comparison of the oriV region of plasmid pSFA231 and its closest homolog, pMOL98, further verified that the replication module of pSFA231 was similar to PromA plasmids. Like other members of the PromA family, pSFA231 was characterized as θ-type mode of replication, with an oriV-like region being located at 5.1 kb downstream of the repA gene. Within this region, we identified four putative iterons (RepA binding site), which are identical to the iteron sequences from pMOL98. Furthermore, a putative DnaA-binding site, a potential integration host factor (IHF) site and an AT-rich (86.67%) region were also found in this region (Figure 3).

Bottom Line: Nevertheless, phylogenetic divergence was found in specific gene products.Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged.Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China ; College of Resources and Environment, University of Chinese Academy of Sciences Beijing, China.

ABSTRACT
A self-transmissible broad-host-range (BHR) plasmid pSFA231 was isolated from petroleum-contaminated sediment in Shen-fu wastewater irrigation zone, China, using the triparental mating exogenous plasmid capture method. Based on its complete sequence the plasmid has a size of 41.5 kb and codes for 50 putative open reading frames (orfs), 29 of which represent genes involved in replication, partitioning and transfer functions of the plasmid. Phylogenetic analysis grouped pSFA231 into the newly defined PromA plasmid family, which currently includes five members. Further comparative genomic analysis shows that pSFA231 shares the common backbone regions with the other PromA plasmids, i.e., genes involved in replication, maintenance and control, and conjugative transfer. Nevertheless, phylogenetic divergence was found in specific gene products. We propose to divide the PromA group into two subgroups, PromA-α (pMRAD02, pSB102) and PromA-β (pMOL98, pIPO2T, pSFA231, pTer331), based on the splits network analysis of the RepA protein. Interestingly, a cluster of hypothetical orfs located between parA and traA of pSFA231 shows high similarity with the corresponding regions on pMOL98, pIPO2T, and pTer331, suggesting these hypothetical orfs may represent "essential" plasmid backbone genes for the PromA-β subgroup. Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged. Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.

No MeSH data available.


Related in: MedlinePlus