Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment.

Julie Lao,Valentin Loux,Gérard Guédon,Nathalie Leblond-Bourget,Sophie Payot,Florence Charron-Bourgoin,Hélène Chiapello,Thomas Lacroix,Virginie Libante

doi:10.3390/genes11090999

Abstract

Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.

Highlights

Conjugation is a horizontal gene transfer (HGT) mechanism that massively contributes to the evolution of prokaryotic genomes [1,2,3]
integrative and conjugative elements (ICEs) belonging to the ICESt3 and Tn916 families were previously reported in some strains of S. salivarius [12,32,33], the real prevalence and diversity of ICEs in this species was still unknown
The present analysis identified 69 ICEs and eight slightly decayed ICEs in the 75 analyzed genomes, revealing a high prevalence of ICEs in this species

Summary

Introduction

Conjugation is a horizontal gene transfer (HGT) mechanism that massively contributes to the evolution of prokaryotic genomes [1,2,3]. It is mediated by extrachromosomal elements (i.e., plasmids), and by other mobile genetic elements (MGEs) that are integrated into the chromosome or plasmids of their host (for a review [2]). The ICE recombination module includes the genes and sequences dedicated to the excision from and integration into the bacterial chromosome or plasmid. It encodes one (or several) protein(s) belonging to one of the three phylogenetically and structurally unrelated families of enzymes: tyrosine

Objectives

Methods

Findings

Conclusion