title: Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  Overall, 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.
authors.affiliation: Université de Toulouse, ENVT, UMR 1225 Interactions Hôtes - Agents Pathogènes, 31076 Toulouse, France.
authors.forename: Laurent X
authors.initials: LX
authors.lastname: Nouvel
authors.forename: Pascal
authors.initials: P
authors.lastname: Sirand-Pugnet
authors.forename: Marc S
authors.initials: MS
authors.lastname: Marenda
authors.forename: Eveline
authors.initials: E
authors.lastname: Sagné
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.forename: Sophie
authors.initials: S
authors.lastname: Mangenot
authors.forename: Chantal
authors.initials: C
authors.lastname: Schenowitz
authors.forename: Daniel
authors.initials: D
authors.lastname: Jacob
authors.forename: Aurélien
authors.initials: A
authors.lastname: Barré
authors.forename: Stéphane
authors.initials: S
authors.lastname: Claverol
authors.forename: Alain
authors.initials: A
authors.lastname: Blanchard
authors.forename: Christine
authors.initials: C
authors.lastname: Citti
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow; D005788:Gene Pool; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D005810:Multigene Family; D016254:Mutagenesis, Insertional; D045644:Mycoplasma agalactiae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040901:Proteomics / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial