Beyond Mutation: Epigenetic Drivers of Phenotypic Diversity and Survival in Mycobacteria

Abstract

M. tuberculosis is the causative agent of a global health epidemic that kills ~1.5 million people each year. The outcomes of infection with Mtb are highly variable. Although many patients are able to control the infection in a quiescent state, others develop active disease. Furthermore, the progression of TB lesions has been shown to vary within a single individual. This phenotypic variability in the infecting population of Mtb may be responsible for the high rate of treatment failures, which can exceed 20% in some endemic areas (World Health Organization, 2015). Although genetic mutation can drive a portion of the observed phenotypic variability, mutation rates in mycobacteria are exceedingly low. Epigenetic factors are therefore likely to be responsible for the majority of observed diversity in infection and treatment outcomes.

Here, we investigated epigenetic drivers of phenotypic variability and survival in mycobacteria. We found evidence of high rates of phenotypic variability in response to drug treatment of M. smegmatis, a non-pathogenic, model for TB. Specifically, we found that two distinct subpopulations are able to grow in the presence of drug. These subpopulations exhibited heritability of their transcriptional profiles, growth properties, and ability to grow on drug across generations. We next found that hupB, a histone-like protein, is critical for the formation of these epigenetically regulated subpopulations. We also show that hupB regulates gene expression and is post-translationally modified, and that modification of hupB may drive the formation of one of these phenotypically drug-resistant subpopulations. These findings suggest that modification of a histone-like protein may drive epigenetic inheritance and phenotypic variability in mycobacteria, which allows it to withstand antibiotic treatment. Finally, we also investigated alternative post-transcriptional mechanisms of hupB regulation.