title: Comparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics.
abstract: Comamonas plasmids play important roles in shaping the phenotypes of their hosts and the adaptation of these hosts to changing environments, and understanding the evolutionary strategy of these plasmids is thus of great concern. In this study, the sequence of the 119-kb 3,5-dibromo-4-hydroxybenzonitrile-catabolizing plasmid pBHB from Comamonas sp. strain 7D-2 was studied and compared with those of three other Comamonas haloaromatic catabolic plasmids. Incompatibility group determination based on a phylogenetic analysis of 24 backbone gene proteins, as well as TrfA, revealed that these four plasmids all belong to the IncP-1β subgroup. Comparison of the four plasmids revealed a conserved backbone region and diverse genetic-load regions. The four plasmids share a core genome consisting of 40 genes (>50% similarities) and contain 12 to 50 unique genes each, most of which are xenobiotic-catabolic genes. Two functional reductive dehalogenase gene clusters are specifically located on pBHB, showing distinctive evolution of pBHB for haloaromatics. The higher catabolic ability of the bhbA2B2 cluster than the bhbAB cluster may be due to the transcription levels and the character of the dehalogenase gene itself rather than that of its extracytoplasmic binding receptor gene. The plasmid pBHB is riddled with transposons and insertion sequence (IS) elements, and ISs play important roles in the evolution of pBHB. The analysis of the origin of the bhb genes on pBHB suggested that these accessory genes evolved independently. Our work provides insights into the evolutionary strategies of Comamonas plasmids, especially into the adaptation mechanism employed by pBHB for haloaromatics.
authors.affiliation: Department of Microbiology, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
authors.forename: Kai
authors.initials: K
authors.lastname: Chen
authors.affiliation: Department of Microbiology, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
authors.forename: Xihui
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Microbiology, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
authors.forename: Long
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Microbiology, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
authors.forename: Zhenjiu
authors.initials: Z
authors.lastname: Gou
authors.affiliation: Department of Microbiology, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
authors.forename: Shunpeng
authors.initials: S
authors.lastname: Li
authors.affiliation: Institute of Plant Sciences, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel jiang_jjd@njau.edu.cn shiri.freilich@gmail.com.
authors.forename: Shiri
authors.initials: S
authors.lastname: Freilich
authors.affiliation: Department of Microbiology, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China jiang_jjd@njau.edu.cn shiri.freilich@gmail.com.
authors.forename: Jiandong
authors.initials: J
authors.lastname: Jiang
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001711:Biotransformation; D020585:Comamonas / Q000235:genetics* / Q000378:metabolism*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D023061:Gene Order; D005798:Genes, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D005810:Multigene Family; D009570:Nitriles / Q000378:metabolism*; D010802:Phylogeny; D010957:Plasmids; D026801:Synteny
chemical_list: D001426:Bacterial Proteins; D009570:Nitriles; C006826:bromoxynil