Independent Loss of Immunogenic Proteins in Mycobacterium ulcerans Suggests Immune Evasion

The highly immunogenic mycobacterial proteins ESAT-6, CFP-10, and HspX represent potential target antigens for the development of subunit vaccines and immunodiagnostic tests. Recently, the complete genome sequence revealed the absence of these coding sequences inMycobacterium ulcerans , the causative agent of the emerging human disease Buruli ulcer. Genome reduction and the acquisition of a cytopathic and immunosuppressive macrolide toxin plasmid are regarded as crucial for the emergence of this pathogen from its environmental progenitor,Mycobacterium marinum . Earlier, we have shown the evolution ofM. ulcerans into two distinct lineages. Here, we show that while the genome ofM. marinum M contains two copies of theesxB-esxA gene cluster at different loci (designated MURD4 and MURD152), both copies are deleted from the genome ofM. ulcerans strains belonging to the classical lineage. Members of the ancestral lineage instead retained some but disrupted most functional MURD4 or MURD152 copies, either by newly identified genomic insertion-deletion events or by conversions of functional genes to pseudogenes via point mutations. Thus, theesxA (ESAT-6),esxB (CFP-10), andhspX genes are located in hot-spot regions for genomic variation where functional disruption seems to be favored by selection pressure. Our detailed genomic analyses have identified a variety of independent genomic changes that have led to the loss of expression of functional ESAT-6, CFP-10, and HspX proteins. Loss of these immunodominant proteins helps the bacteria bypass the host's immunological response and may represent part of an ongoing adaptation ofM. ulcerans to survival in host environments that are screened by immunological defense mechanisms.