The ruminant pathogen Mycoplasma agalactiae possesses a family of abundantly expressed variable surface lipoproteins called Vpmas. Phenotypic switches between Vpma members have previously been correlated with DNA rearrangements within a locus of vpma genes and are proposed to play an important role in disease pathogenesis. In this study, six vpma genes were characterized in the M. agalactiae type strain PG2. All vpma genes clustered within an 8-kb region and shared highly conserved 5 untranslated regions, lipoprotein signal sequences, and short N-terminal sequences. Analyses of the vpma loci from consecutive clonal isolates showed that vpma DNA rearrangements were site specific and that cleavage and strand exchange occurred within a minimal region of 21 bp located within the 5 untranslated region of all vpma genes. This process controlled expression of vpma genes by effectively linking the open reading frame (ORF) of a silent gene to a unique active promoter sequence within the locus. An ORF (xer1) immediately adjacent to one end of the vpma locus did not undergo rearrangement and had significant homology to a distinct subset of genes belonging to the integrase family of site-specific xer recombinases. It is proposed that xer1 codes for a site-specific recombinase that is not involved in chromosome dimer resolution but rather is responsible for the observed vpma-specific recombination in M. agalactiae.Mycoplasmas belong to a group of cell wall-less pathogens that are widespread in nature and cause diseases that are generally chronic and difficult to eradicate in humans, animals, plants, and insects. Among free-living organisms, they possess one of the smallest genomes, which is mainly responsible for their parasitic lifestyle. Yet, despite having a limited coding capacity relative to other bacteria, mycoplasmas have developed quite an extensive repertoire of molecular mechanisms to generate surface protein variability at a high frequency either by phase or size variation (10,28,42). Many of these surface proteins belong to multigene families of lipoproteins that have the ability to switch the expression of individual components on and off and are suspected of playing a role in host cell adhesion. The ability of these proteins to switch expression between different forms is believed to be important in immune evasion and rapid adaptation in the host.Mycoplasma agalactiae is the major etiological agent of the syndrome contagious agalactia, which primarily causes mastitis, arthritis, and keratoconjunctivitis in sheep and goats (4). Recently, a family of related but distinct surface lipoproteins, designated Vpmas, has been identified in this pathogen, and Vpma expression has been shown to undergo high-frequency variation (16). Vpmas are abundantly expressed in M. agalactiae and display an unusual processing of lipoproteins in which a peptidase II-like enzyme cleaves 2 amino acids (aa) (position Ϫ2) N terminal to the cysteine residue rather than at the cysteine to which the lipid anchor is attached. This atypical proc...