Integrative and conjugative elements and their hosts: composition, distribution and organization

Abstract

Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species’ pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses revealed that ICEs are structured in functional modules. Integrases and conjugation systems have different evolutionary histories, even if the gene repertoires of ICEs can be grouped in function of conjugation types. Our characterization of the composition and organization of ICEs paves the way for future functional and evolutionary analyses of their cargo genes, composed of a majority of unknown function genes.

Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis

“…The evidence we provide here tends to support a horizontal gene transfer or homologous recombination events from ancestors of Magnetovibrio to Terasakiella. Recombination between related and unrelated organisms can be mediated by several mechanisms, including conjugation systems such as integrative and conjugative elements (ICEs) composed with a Type IV secretion system, a relaxase and a recombinase (Cury et al, 2017). Searching such a system using CONJScan (Guglielmini et al, 2014), we detected a fully delimited type T ICE in the draft genome of Ca.…”

Diverse conjugative elements silence natural transformation inLegionellaspecies

“…In L. geestiana HL-0438-2026, the RocRp homolog is found again on a 53.3 kb episomal element but this time encoding a type F conjugative system (Fig. 5B) (46). In L. israelensis 09060433301 isolated in Norway, the RocRp homolog belong to an ICE with an unclassified conjugative system previously reported in the L. pneumophila genomic islands (LGI) LpcGI-2 and LppGI-2 of L. pneumophila (47).…”

“…In L. geestiana HL-0438-2026, the RocRp homolog is found again on a 53.3 kb episomal element but this time encoding an F-type conjugative system ( Fig. 5B) (46). In L. israelensis HL-0427-4011, the RocR homolog is found in a large genomic element of 114.7 kb inserted in a tRNA-Thr gene and carrying an integrase gene (intS).…”

“…Presence of rocR and rocRp sequences in Legionella genus genomes were investigated using local blastn on all the 835 Legionella/Fluoribacter/Tatlockia genome assemblies (697 Lp, 138 non-Lp) available from the NCBI assembly database on March 6 th , 2019. Detection of conjugative elements was performed using MacSyFinder (67) and the ConjScan module (46).…”

“…The plasmid of L. sp. km542 encodes a F-type conjugative element whereas the integrated conjugative element (ICE) and plasmid from L. geestiana DSM21217 and in L. israelensis DSM19235 encode P-type systems (46), and the three elements share no other homology ( Fig. 5B).…”