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In Silico Identiﬁcation of Epitopes in Mycobacterium avium subsp. paratuberculosis Proteins That Were Upregulated under Stress Conditions

Johne’s disease in ruminants is caused by Mycobacterium avium subsp. paratuberculosis . Diagnosis of M. avium subsp. paratuberculosis infection is difﬁcult, especially in the early stages. To date, ideal antigen candidates are not available for efﬁcient im-munization or immunodiagnosis. This study reports the in silico selection and subsequent analysis of epitopes of M. avium subsp. paratuberculosis proteins that were found to be upregulated under stress conditions as a means to identify immunogenic candidate proteins. Previous studies have reported differential regulation of proteins when M. avium subsp. paratuberculosis is exposed to stressors which induce a response similar to dormancy. Dormancy may be involved in evading host defense mechanisms, and the host may also mount an immune response against these proteins. Twenty-ﬁve M. avium subsp. paratuberculosis proteins that were previously identiﬁed as being upregulated under in vitro stress conditions were analyzed for B and T cell epitopes by use of the prediction tools at the Immune Epitope Database and Analysis Resource. Major histocompatibility complex class I T cell epitopes were predicted using an artiﬁcial neural network method, and class II T cell epitopes were predicted using the consensus method. Conformational B cell epitopes were predicted from the relevant three-dimensional structure template for each protein. Based on the greatest number of predicted epitopes, eight proteins (MAP2698c [encoded by desA2 ], MAP2312c [encoded by fadE19 ], MAP3651c [encoded by fadE3_2 ],