Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331

Abstract

Plasmid pTer331 from the bacterium Collimonas fungivorans Ter331 is a new member of the pIPO2/pSB102 family of environmental plasmids. The 40 457-bp sequence of pTer331 codes for 44 putative ORFs, most of which represent genes involved in replication, partitioning and transfer of the plasmid. We confirmed that pTer331 is stably maintained in its native host. Deletion analysis identified a mini-replicon capable of replicating autonomously in Escherichia coli and Pseudomonas putida. Furthermore, plasmid pTer331 was able to mobilize and retromobilize IncQ plasmid pSM1890 at typical rates of 10(-4) and 10(-8), respectively. Analysis of the 91% DNA sequence identity between pTer331 and pIPO2 revealed functional conservation of coding sequences, the deletion of DNA fragments flanked by short direct repeats (DR), and sequence preservation of long DRs. In addition, we experimentally established that pTer331 has no obvious contribution in several of the phenotypes that are characteristic of its host C. fungivorans Ter331, including the ability to efficiently colonize plant roots. Based on our findings, we hypothesize that cryptic plasmids such as pTer331 and pIPO2 might not confer an individual advantage to bacteria, but, due to their broad-host-range and ability to retromobilize, benefit bacterial populations by accelerating the intracommunal dissemination of the mobile gene pool.

Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger

“…Many of the genes located on plasmid pTer331 (Mela et al, 2008) showed increased expression in response to the fungus. The same was true for genes in clusters N (Cf_1047-1074) and O (Cf_2102-2115), both of which carry genes belonging to putative prophages.…”

VirB3 to VirB6 and VirB8 to VirB11, but Not VirB7, Are Essential for Mediating Persistence ofBrucellain the Reticuloendothelial System

“…Both T4A and T4B secretion systems have been shown to translocate or secrete a range of different substrates from DNA bound to protein to single proteins to multisubunit toxins (4, 8, 11, 12, 16, 36, 37, 39-41, 43, 53, 55, 61, 64). The closest homologues of the virB locus are T4A systems encoded by the conjugative plasmids pSB102, pIPO2T, and pTer331 (38,51,60).The best-studied T4SS is the VirB system of Agrobacterium tumefaciens, which is therefore used as a model for the T4A systems. The current model for assembly of the VirB T4SS postulates a core structure in the periplasmic space composed of the proteins VirB6, VirB7, VirB8, VirB9, and VirB10 (13).…”

“…Both T4A and T4B secretion systems have been shown to translocate or secrete a range of different substrates from DNA bound to protein to single proteins to multisubunit toxins (4, 8, 11, 12, 16, 36, 37, 39-41, 43, 53, 55, 61, 64). The closest homologues of the virB locus are T4A systems encoded by the conjugative plasmids pSB102, pIPO2T, and pTer331 (38,51,60).…”

Root Exudation: The Ecological Driver of Hydrocarbon Rhizoremediation

“…Of the three mechanisms of lateral gene transfer, conjugation is one of the most important for exchanging genes [275,276]. Plasmids are autoreplicatives extrachromosomal molecules of DNA, mostly circular but otherwise linear [277], and are transmitted both vertically (from mother cell to daughter during bacterial division) and horizontally (from a donor cell to a recipient cell). Plasmids are mosaic genomes that include two distinct regions [278]: (1) skeleton genes, often conserved among members of the same family of plasmids, ensure replication and maintenance of the plasmid in the cell and transfer [279]; and (2) accessory genes encoding functions that are frequently beneficial to the host cell.…”