New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration.

Chloé Ambroset,Nathalie Leblond-Bourget,Gérard Guédon,Marie-Dominique Devignes,Valentin Loux,Sophie Payot,Thomas Lacroix,Charles Coluzzi

doi:10.3389/fmicb.2015.01483

Abstract

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.

Highlights

Streptococci are Gram positive bacteria belonging to the phylum of Firmicutes
A total of 105 integrative and conjugative elements (ICEs) and 26 decayed ICEs (dICEs) were identified among the 124 streptococcal genomes analyzed in this work (Supplementary Table S1)
ICE denomination indicates whether the element is an ICE or a dICE, followed by letters and numbers allowing species and strain identification

Summary

Introduction

Streptococci are Gram positive bacteria belonging to the phylum of Firmicutes. This genus comprises 110 recognized species (1July 24, 2015). Almost all streptococci are commensal or pathogen of humans and/or animals. Numerous streptococci, such as Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus mutans or Streptococcus agalactiae, are responsible for a wide. ICEs in Streptococci variety of diseases worldwide, ranging from mild to invasive infections that have a severe impact on human and animal health and lead to significant morbidity and mortality (Mitchell, 2003; Kohler, 2007). Streptococci are ubiquitously present as commensal inhabitants of the gastro-intestinal tracts of healthy adults and/or newborns. Two species deriving from commensal streptococci, S. thermophilus and S. macedonicus are used as starters in dairy industry to transform milk in yogurt and/or cheese (Franciosi et al, 2009)

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Discussion

Conclusion