Comparative Genomics of the Conjugation Region of F-like Plasmids: Five Shades of F

Abstract

The F plasmid is the foremost representative of a large group of conjugative plasmids, prevalent in Escherichia coli, and widely distributed among the Enterobacteriaceae. These plasmids are of clinical relevance, given their frequent association with virulence determinants, colicins, and antibiotic resistance genes. Originally defined by their sensitivity to certain male-specific phages, IncF plasmids share a conserved conjugative system and regulatory circuits. In order to determine whether the genetic architecture and regulation circuits are preserved among these plasmids, we analyzed the natural diversity of F-like plasmids. Using the relaxase as a phylogenetic marker, we identified 256 plasmids belonging to the IncF/ MOBF12group, present as complete DNA sequences in the NCBI database. By comparative genomics, we identified five major groups of F-like plasmids. Each shows a particular operon structure and alternate regulatory systems. Results show that the IncF/MOBF12 conjugation gene cluster conforms a diverse and ancient group, which evolved alternative regulatory schemes in its adaptation to different environments and bacterial hosts.

Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes

“…To the contrary, LSU-61 lacks a nested mobile element of 2,080 bp comprised of IS30/IS911 (Supplementary Figure S7B). Plasticity in the transfer machinery accounts for the observed variation in plasmid size of pSFO157, pO157, and pO157_2 (Fernandez-Lopez et al, 2016). The pSFO157 plasmid found in SF O157:NM strains resembles most closely the conjugal transfer region of the F-plasmid (Frost et al, 1994), with deletions in the conjugal transfer machinery (traP, trbD trbG, and traV) mediated by IS insertions.…”

“…We note here that although these plasmids carry different portions of the conjugal transfer machinery, neither type is considered to be transferable on its own due to the absence of a functional traB gene. This locus is critical for F pilus assembly and is either truncated (41%) in pSFO157 and pO157_2 or absent in pO157 (Kim et al, 1993;Fernandez-Lopez et al, 2016). Comprehensive analysis of these on average 94-kb plasmids (Figure 5) showed that InDels are mostly associated with mobile insertion elements, but also other loci dispersed throughout the plasmid (e.g., pseudogene insF-hp), some of which are clade-defining signatures in plasmids (e.g., clade 3).…”

Mobile Genetic Elements Associated with Antimicrobial Resistance

“…The F ("fertility factor") plasmid was the first example of a conjugative plasmid found in bacteria and is the basis of the designation IncF for plasmids with common sensitivity to specific phages and serological cross-reactivity, reflecting a common conjugation system (MPF F ). This F-type mating apparatus may be associated with different replicons, with incompatibility testing originally defining subgroups FI to FVII (195). Combinations of three replicons (FIIA/FIC, FIA, and FIB) are commonly found together in multireplicon plasmids, including the F plasmid.…”

In Silico Typing and Comparative Genomic Analysis of IncFII K Plasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles

“…With the increase in the amount of whole-genome/plasmid sequencing data, there is a need for large-scale plasmid analysis, which currently is rare (23,24). Comparative genomic studies of mobile genetic elements (MGEs) have provided insights into common structural features, diverse gene pools, biological traits, and their evolution (25,26).…”