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

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.

Identification and Subtyping of Clinically Relevant Human and Ruminant Mycoplasmas by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

“…Furthermore, within individual species, the dendrograms generated from the MALDI-TOF MS spectra achieved epidemiologically relevant strain clustering. For instance, the M. agalactiae strains were separated into two branches that correspond to the two reference strains, namely, PG2 and 5632, which are described as representing each end of the genetic spectrum encountered in M. agalactiae (30). The strains from wild ungulates, namely, Capra ibex or chamois, interestingly were grouped together, as was previously reported with the use of partial sequencing of a housekeeping gene (31).…”

“…For instance, three strains of M. hominis were included, as this species is known to be highly heterogeneous (29). Both M. agalactiae PG2 type strain and 5632 were acquired as well, as they are considered to be situated at each end of the genetic spectrum encountered in M. agalactiae (30). This proved successful because, for instance, several strains from wild ungulates (e.g., Capra ibex) that are known to be genetically different from domestic ruminant strains (31) were correctly identified as M. agalactiae.…”

Critical Role of Dispensable Genes inMycoplasma agalactiaeInteraction with Mammalian Cells

“…In a recent study comparing M. agalactiae strains using whole-genomic and proteomic approaches, the differential expression of some drp genes was found in association with the membrane fraction. These data suggested that this family may participate in generating surface diversity, with some drp genes presenting features of lipoproteins and being expressed and others serving as sequence reservoirs (34). Interestingly, the drp genes are part of the gene pool which has undergone HGT with members of the phylogenetically distant mycoides cluster.…”

“…Remarkably, whole-genome sequence analysis has revealed that extensive horizontal gene transfer (HGT) events, affecting up to 18% of the M. agalactiae genome, occurred between M. agalactiae and members of the mycoides cluster, illustrating the unexpected plasticity and adaptability of the mycoplasma genome (44,45). Recent advances in whole-genome sequencing have greatly facilitated the study of mycoplasmas (2,33,34,44,45). Unfortunately, these data alone have been of little help in identifying the mechanism underlying diseases caused by mycoplasmas.…”

Proteomics and Pathway Analyses of the Milk Fat Globule in Sheep Naturally Infected by Mycoplasma agalactiae Provide Indications of the In Vivo Response of the Mammary Epithelium to Bacterial Infection

“…The microorganism is believed to be unable to penetrate cells, although it is known to adhere tightly to the colonized epithelium (34,37). Despite recent in-depth genomic and proteomic analyses (7,27,40), which have led to fundamental insights into its genomic and proteomic composition, very few proteins of M. agalactiae have been proved to be virulence determinants. These include a family of variable surface proteins, named Vpma proteins (16), the immunodominant adhesin P40 (14), and P48, a homologue of the macrophage-activating lipopeptide (MALP) of M. fermentans (36).…”