Identification of novel origins of transfer across bacterial plasmids

Abstract

Conjugative plasmids are important drivers of bacterial evolution, but most plasmids lack genes for conjugation. It is currently not known if the latter can transfer because origins of transfer by conjugation (oriT), which would allow their mobilization by conjugative plasmids, are poorly known. Here, we identify and characterize occurrences of known oriT families across thousands of plasmids confirming that most conjugative and mobilizable plasmids still lack identifiable families of oriTs. They reveal clear patterns in terms of intergenic position, distance to the relaxases, and MOB-type association. This allowed to develop a computational method to discover novel oriTs. As a proof of concept, we identify 21 novel oriTs from the nosocomial pathogens Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii, some of them responsible for the mobility of critical antimicrobial resistance genes. These 21 oriT families share key characteristics of the others and fill most of the missing diversity of oriTs in relaxase-encoding plasmids both in terms of frequency and phylogeny. We confirmed experimentally the function of six of them. The ability to identify novel oriTs paves the way to explore conjugation across bacterial plasmids, notably among the majority lacking conjugation-related genes.

Hijackers, hitchhikers, or co-drivers? The mysteries of microbial mobilizable genetic elements

“…the presence of genes encoding relaxases and oriTs suggest that the hitcher is mobilized by conjugaeon and the presence of genes encoding terminases or cos/pac sites suggest the element is mobilized by phages. Yet, some conjugaeve elements and phages are poorly known, some HGEs lack protein coding genes homologous to the helper, and DNA moefs such as oriTs or cos/pac are open unknown or hard to idenefy (60). It is also likely that the mobilizaeon of completely novel HGEs differs from the known mechanisms.…”