Conjugative plasmids: vessels of the communal gene pool

Abstract

Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic 'individual' can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as 'backbone modules' to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of 'accessory elements' that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized 'private genes'.

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

“…The behavior of this environmental resistome may, thus, govern the spread of antibiotic resistance genes to pathogens (Finley et al, 2013). Plasmids serve as main vessels of gene flow in microbial communities, linking distinct genetic pools (Norman et al, 2009;Halary et al, 2010). The in situ host range of plasmids may, then, well govern the taxonomic breadth across which gene flow occurs.…”

What traits are carried on mobile genetic elements, and why?

“…There are increasing hints of important separations of functions between the vertically transmitted core genome, which encodes fundamental cellular processes, and the horizontally transmissible accessory genome, which encodes for a variety of secondary metabolites conferring resistance to specific toxins or antibiotics or the ability to exploit a specific niche (Hacker and Carniel, 2001;Norman et al, 2009). The accessory genome contains recently acquired functions, mobile genetic elements (MGEs), non-expressed genes and genes under particular modes of selection such as diversifying selection, frequency-dependent selection and periodic selection.…”

Network analyses structure genetic diversity in independent genetic worlds

“…Biologists became able to simultaneously sequence many of the key players involved in the DNA flow of a given environment, offering a much more integrated view (5,7). Consequently, the evolutionary analyses of many metagenomes focused more on the global genetic diversity (or global functional diversity) of an environment rather than on traditional issues of systematics (8,9).…”