Comparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics

Abstract

bComamonas 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-1␤ 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. Comamonas species are ubiquitous in the environment and have been isolated from soil, mud, water, activated sludge, clinical samples, and organic pollutant-and heavy metal-contaminated environments (1). Comamonas species play an important role in matter cycling in nature and have been noted for their capabilities to degrade various aromatics (1-5). Interestingly, many Comamonas strains have been found to harbor plasmids, most of which have been confirmed to be related to the catabolism of xenobiotic aromatics (4, 6-8). For example, the plasmid pI2, responsible for the degradation of aniline/3-chloroaniline, was isolated from Comamonas testosteroni I2 (4, 9, 10). Another transferable plasmid, pTB30, which is involved in the mineralization of 3-chloroaniline, was isolated from C. testosteroni TB30 (9, 11). In addition, the plasmid pCNB1, encoding the catabolic pathway to convert 4-chloronitrobenzene to 5-chloro-4-hydroxy-2-oxovalerate, was sequenced in Comamonas sp. strain CNB-1 (12, 13). Recently, the plasmid pBHB was characterized in Comamonas sp. strain 7D-2. This plasmid is involved in the mineralization of the herbicide bromoxynil (3,5-dibromo-4-hydroxybenzonitrile), which includes the reductive dehalogenation of the bromoxynil nitrile hydrolyte 3,5-dibromo-4-hydroxybenzoate (DBHB) (14).Plasmids are among the most important elements in the evolutio...

Comparative symbiotic plasmid analysis indicates that symbiosis gene ancestor type affects plasmid genetic evolution

“…The expression of rhizobial chromosome genes was downregulated under symbiotic conditions, but the expression of plasmid genes, including the eight genes -fixA, fixB, fixC, nifA, nifB, nifD, nifK and nifH, was up-regulated under symbiotic conditions (Peng et al 2014). These results were in general agreement with Chen's study, where he found that the core genes were analogous to the backbone genes of plasmid pBHB to some extent and were responsible for the core functions (Chen et al 2016). However, nodB, as a deacetylase encoding gene, was absent from the common genes (Perret et al 2000).…”

“…These results were in general agreement with Chen's study, where he found that the core genes were analogous to the backbone genes of plasmid pBHB to some extent and were responsible for the core functions (Chen et al . ). However, nodB , as a deacetylase encoding gene, was absent from the common genes (Perret et al .…”

PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera

“…The catabolic PromA plasmids have a nearly identical backbone to the previously described PromA γ plasmids isolated in Japan (Yanagiya et al, 2018). It has been reported before that BHR plasmids isolated from different geographic locations can be highly conserved (Heuer et al, 2004;Chen et al, 2015;Li et al, 2016), however, some degree of divergence in the backbone structures of PromA plasmid groups were reported before (Li et al, 2014). In this case, the nearly identical backbone genes indicate that these plasmids had a recent common ancestor, probably without any accessory genes.…”

Proma Plasmids are Instrumental in the Dissemination of Linuron Catabolic Genes between Different Genera

“…Remarkably, the catabolic PromA plasmids have a near-identical backbone to the previously-described PromA γ plasmids isolated in Japan (Yanagiya et al, 2018). It has been reported before that BHR plasmids isolated from different geographic locations can be highly-conserved (Li et al, 2016; Heuer et al, 2004; Chen et al, 2015b), however, some degree of divergence in the backbone structures of PromA plasmid groups were reported before (Li et al, 2014). In this case, the near-identical backbone genes indicate that these plasmids had a recent common ancestor, probably without any accessory genes.…”