Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response

The main adaptive immune response to bacteria is mediated by B cells and CD4+ T-cells. However, some bacterial proteins reach the cytosol of host cells and are exposed to the host CD8+ T-cells response. Both gram-negative and gram-positive bacteria can translocate proteins to the cytosol through type III and IV secretion and ESX-1 systems, respectively. The translocated proteins are often essential for the bacterium survival. Once injected, these proteins can be degraded and presented on MHC-I molecules to CD8+ T-cells. The CD8+ T-cells, in turn, can induce cell death and destroy the bacteria's habitat. In viruses, escape mutations arise to avoid this detection. The accumulation of escape mutations in bacteria has never been systematically studied. We show for the first time that such mutations are systematically present in most bacteria tested. We combine multiple bioinformatic algorithms to compute CD8+ T-cell epitope libraries of bacteria with secretion systems that translocate proteins to the host cytosol. In all bacteria tested, proteins not translocated to the cytosol show no escape mutations in their CD8+ T-cell epitopes. However, proteins translocated to the cytosol show clear escape mutations and have low epitope densities for most tested HLA alleles. The low epitope densities suggest that bacteria, like viruses, are evolutionarily selected to ensure their survival in the presence of CD8+ T-cells. In contrast with most other translocated proteins examined, Pseudomonas aeruginosa's ExoU, which ultimately induces host cell death, was found to have high epitope density. This finding suggests a novel mechanism for the manipulation of CD8+ T-cells by pathogens. The ExoU effector may have evolved to maintain high epitope density enabling it to efficiently induce CD8+ T-cell mediated cell death. These results were tested using multiple epitope prediction algorithms, and were found to be consistent for most proteins tested. Author Summary: Bacterial proteins are mainly exposed to B-cells and CD4+ T-cells, while CD8+ T-cells (CTL) typically respond to viruses. The limitation of the CTL response to viruses results from processing pathways of epitopes presented to CTLs. These epitopes usually stem from proteins expressed in the cytosol. Such proteins are eventually degraded and presented on MHC-I molecules to CTLs. However bacterial Type III secretion system (T3SS) effectors also have an access to the host cytosol and may also be exposed to CTL response. Thus, we can assume that this group of proteins undergoes selection against the presentation of CTL epitopes, as seen in viral proteins. Using multiple epitope prediction algorithms, we show that most T3SS effectors, as well as LLO, and ActA in Listeria monocytogenes and ESAT-6 proteins in Mycobacterium tuberculosis, are systematically selected to reduce the number and quality of their epitopes. The exception in this respect is the Pseudomonas aeruginosa effector ExoU that has high density of high quality epitopes. Since ExoU is known to induce rapid cell death in hosts cells, we assume that P.aeruginosa utilize the immune response to induce such death. The E.coli epitope density is highly variable among strains.