title: A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins.
abstract: Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species ofStreptococcusreveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.
authors.affiliation: UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Coluzzi
authors.affiliation: UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France.
authors.forename: Gérard
authors.initials: G
authors.lastname: Guédon
authors.affiliation: UMR7503 Laboratoire Lorrain de Recherche en Informatique et ses Applications, Centre National de la Recherche Scientifique, Université de Lorraine, Vandœuvre-lès-Nancy, France.
authors.forename: Marie-Dominique
authors.initials: MD
authors.lastname: Devignes
authors.affiliation: UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France.
authors.forename: Chloé
authors.initials: C
authors.lastname: Ambroset
authors.affiliation: UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Valentin
authors.initials: V
authors.lastname: Loux
authors.affiliation: UR1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lacroix
authors.affiliation: UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Payot
authors.affiliation: UMR1128 DynAMic, Institut National de la Recherche Agronomique, Université de Lorraine, Vandœuvre-lès-Nancy, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Leblond-Bourget
keywords: Streptococcus; TcpA coupling protein; conjugation; mobilizable elements; relaxase