Frequent Homologous Recombination Events in Mycobacterium tuberculosis PE/PPE Multigene Families: Potential Role in Antigenic Variability

Abstract

The PE and PPE (PE/PPE) multigene families of Mycobacterium tuberculosis are particularly GC-rich and share extensive homologous repetitive sequences. We hypothesized that they may undergo homologous recombination events, a mechanism rarely described in the natural evolution of mycobacteria. To test our hypothesis, we developed a specific oligonucleotide-based microarray targeting nearly all of the PE/PPE genes, aimed at detecting signals for homologous recombination. Such a microarray has never before been reported due to the multiplicity and highly repetitive and homologous nature of these sequences. Application of the microarray to a collection of M. tuberculosis clinical isolates (n ‫؍‬ 33) representing prevalent spoligotype strain families in Tunisia allowed successful detection of six deleted genomic regions involving a total of two PE and seven PPE genes. Some of these deleted genes are known to be immunodominant or involved in virulence. The four precisely determined deletions were flanked by 400-to 500-bp stretches of nearly identical sequences lying mainly at the conserved N-terminal region of the PE/PPE genes. These highly homologous sequences thus serve as substrates to mediate both intergenic and intragenic homologous recombination events, indicating an important function in generating strain variation. Importantly, all recombination events yielded a new inframe fusion chimeric gene. Hence, homologous recombination within and between PE/PPE genes likely increased their antigenic variability, which may have profound implications in pathogenicity and/or host adaptation. The finding of high prevalence (ϳ45% and ϳ58%) for at least two of the genomic deletions suggests that they likely confer advantageous biological attributes.

PPE38 Modulates the Innate Immune Response and Is Required for Mycobacterium marinum Virulence

“…It is not surprising that several PE/PPE genes, including PPE38, PE_PGRS33, PE_PGRS16, and PE_PGRS26, were found to exhibit extensive polymorphisms in clinical isolates of M. tuberculosis (41,47,66,67). Consequently, it was speculated that these proteins represent a source of antigenic variation which allows the pathogen to evade antigen-specific host responses (22,41,66).…”

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

“…This includes the highly GC-rich and polymorphic PE/PPE gene family, esx genes, and Insertion Sequences. Gene conversion resulting from frequent intrachromosomal homologous recombination has been reported between members of each of these families (Ho et al 2000;McEvoy et al 2007;Karboul et al 2008;Uplekar et al 2011). Hence, exclusion of these regions prevents spurious inclusion of intrachromosomal recombination events in the analyses of recombination presented below.…”

Mycobacterium tuberculosis Resists Stress by Regulating PE19 Expression

“…This theory has been fueled by observations that there is variation in certain pe_pgrs gene sequences among clinical isolates (10,11) and that recombination leading to gene deletions can occur between different copies of the pe and ppe genes (12). There is, however, little evidence to support rapid alterations of pe and ppe gene sequences in vivo (13).…”