Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution

Abstract

Plasmids cannot be understood as mere tools for genetic exchange: they are themselves subject to the forces of evolution. Their genomic and phylogenetic features have been less studied in this respect. Focusing on the IncW incompatibility group, which includes the smallest known conjugative plasmids, we attempt to unveil some common trends in plasmid evolution. The functional modules of IncW genetic backbone are described, with emphasis on their architecture and relationships to other plasmid groups. Some plasmid regions exhibit strong phylogenetic mosaicism, in striking contrast to others of unusual synteny conservation. The presence of genes of unknown function that are widely distributed in plasmid genomes is also emphasized, exposing the existence of ill-defined yet conserved plasmid functions. Conjugation is an essential hallmark of IncW plasmid biology and special attention is given to the organization and evolution of its transfer modules. Genetic exchange between plasmids and their hosts is analysed by following the evolution of the type IV secretion system. Adaptation of the trw conjugative machinery to pathogenicity functions in Bartonella is discussed as an example of how plasmids can change their host modus vivendi. Starting from the phage paradigm, our analysis articulates novel concepts that apply to plasmid evolution.

Structure of a VirD4 coupling protein bound to a VirB type IV secretion machinery

“…Relaxosome formation requires two auxiliary proteins, plasmid‐encoded TrwA, and host‐encoded IHF. trwN‐D and trwABC are located in two operons, the expression of which is coordinated by three distinct promoters (de Paz et al , 2005; Fernandez‐Lopez et al , 2006). For clarity, we will use both the “Trw” and “VirB” nomenclatures.…”

Conjugative plasmids: vessels of the communal gene pool

“…Some studies of isolates from different genera or different parts of the world (Norman et al 2008;Sevastsyanovich et al 2008) indicate that backbone genes have different phylogenetic origins for different modules, and sometimes even for individual module genes (Fernandez-Lopez et al 2006). This suggests that plasmid innovation can occur, from time to time, by interacting with other plasmid backbones, which leads to insertion or replacement of backbone modules or to allelic replacements of individual genes.…”

Rebooting the genome: The role of negative feedback in horizontal gene transfer

“…25 An analysis of their regulatory networks showed that these genetic elements have evolved sophisticated control mechanisms to alleviate the opposite demands of vertical and horizontal reproduction. The massive introduction of antibiotics has changed the conditions under which these genetic elements survive.…”