Mobility of Plasmids

Abstract

International audiencePlasmids are key vectors of horizontal gene transfer and essential genetic engineering tools. They code for genes involved in many aspects of microbial biology, including detoxication, virulence, ecological interactions, and antibiotic resistance. While many studies have decorticated the mechanisms of mobility in model plasmids, the identification and characterization of plasmid mobility from genome data are unexplored. By reviewing the available data and literature, we established a computational protocol to identify and classify conjugation and mobilization genetic modules in 1,730 plasmids. This allowed the accurate classification of proteobacterial conjugative or mobilizable systems in a combination of four mating pair formation and six relaxase families. The available evidence suggests that half of the plasmids are nonmobilizable and that half of the remaining plasmids are conjugative. Some conjugative systems are much more abundant than others and preferably associated with some clades or plasmid sizes. Most very large plasmids are nonmobilizable, with evidence of ongoing domestication into secondary chromosomes. The evolution of conjugation elements shows ancient divergence between mobility systems, with relaxases and type IV coupling proteins (T4CPs) often following separate paths from type IV secretion systems. Phylogenetic patterns of mobility proteins are consistent with the phylogeny of the host prokaryotes, suggesting that plasmid mobility is in general circumscribed within large clades. Our survey suggests the existence of unsuspected new relaxases in archaea and new conjugation systems in cyanobacteria and actinobacteria. Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts

Selfish genetic elements, genetic conflict, and evolutionary innovation

“…This suggests that opportunities for lateral acquisition, rather than benefits to the host, explain relative abundances of these elements. It is also clear, however, that mobile elements in bacteria (e.g., plasmids) can encode proteins that increase survival of their bacterial hosts, such as antibiotic resistance (24). Evidence suggests that mobile elements in bacteria can be maintained by a combination of selfish features that promote their acquisition and retention in bacterial genomes and (in some cases) beneficial effects on their bacterial hosts.…”

Additional conjugation systems for inter-domain plasmid transfer to the diatom Phaeodactylum tricornutum

“…Interdomain conjugation has 55 also been reported for mammalian and fungal cells using RP4-based systems (Sikorski et al, 1990; ; Waters, 2001;; Schröder et al, 2011) (15)(16)(17). Plasmids such as F, RP4/RK2, and Ti contain both the MPF and the DTR functions and are self-transmissible or conjugative (Smillie et al, 2010) (10). Other plasmids such as RSF1010 contain only the MOB or DTR and are known as mobilizable.…”

“…according to their phylogenetic relationships (11) and similar approaches for the MPF genes have also allowed phylogenetic clustering (10).…”

Bacterial computing with engineered populations

“…Besides the main chromosome, most bacteria contain additional autonomous, small, dispensable DNA molecules called plasmids [40]. Plasmid sizes range from about 1500 to 250 000 bp (1.5-250 kb).…”