Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity

Laurent X Nouvel,Christine Citti,Stéphane Claverol,Alain Blanchard,Eveline Sagné,Sophie Mangenot,Valérie Barbe,Marc S Marenda,Chantal Schenowitz,Daniel Jacob,Aurélien Barré,Pascal Sirand-Pugnet

doi:10.1186/1471-2164-11-86

Abstract

BackgroundWhile the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study.ResultsThe two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms.ConclusionOverall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.

Highlights

While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed
Whole genome and proteome comparison Whole genome sequencing of the M. agalactiae strain 5632 revealed that it is composed of 1,006.7 kbp and is ca.130 kpb larger than the genome of the PG2 type strain [12]
Multiple genome sequencing of closely related bacterial species can address various significant issues which range from a better understanding of forces driving microbial evolution to the design of novel vaccines

Summary

Introduction

While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. While our genomic era is accumulating a tremendous amount of data with more than 900 microbial genomes currently available in public databases (Microbial Genome Resource, NCIB), only 15 other mycoplasma genomes have been completed [6,7,8], including 3 strains of the M. hyopneumoniae species [9,10]. This number is surprising low owing the small size of mycoplasma genomes and the several species that are relevant for public and animal health because they are known as pathogenic for man or for a wide range of animals [11]

Methods

Results

Discussion

Conclusion