title: The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family.
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.
authors: 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.
authors: Xiaobin
authors: X
authors: Li
authors: Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho Moscow, ID, USA.
authors: Eva M
authors: EM
authors: Top
authors: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China.
authors: Yafei
authors: Y
authors: Wang
authors: Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho Moscow, ID, USA.
authors: Celeste J
authors: CJ
authors: Brown
authors: 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.
authors: Fei
authors: F
authors: Yao
authors: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China.
authors: Shan
authors: S
authors: Yang
authors: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China.
authors: Yong
authors: Y
authors: Jiang
authors: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China.
authors: Hui
authors: H
authors: Li
keywords: PromA plasmid family; broad-host-range plasmid; comparative genomic analysis; complete sequence; plasmid backbone regions
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