Sigma factor M induces an ESX-4-focused regulon in Mycobacterium abscessus

Mycobacteria encode as many as five distinct Type VII (ESX) secretion systems that function in nutrient acquisition, cell-cell interaction, membrane integrity and pathogenesis. The biological activities of ESX systems are determined by the effector proteins they secrete. ESX-4 is the ancestral secretion system and is conserved throughout mycobacteria, including Mycobacterium abscessus where it has been shown to support survival in phagosomes. ESX-4 and putative effector genes in Mycobacterium tuberculosis and Mycobacterium smegmatis are co-induced by a conserved sigma factor, SigM. Identifying the activities conferred by ESX-4 in promoting M. abscessus survival begins with identifying potential secreted substrates. We hypothesized that, in M. abscessus , SigM co-regulates the expression of genes encoding ESX-4 components and secreted effector proteins. We generated a precise deletion of the sigM - rsmA locus, encoding SigM and its dedicated anti-sigma factor. Performing RNA-seq using this deletion strain and a SigM-expressing complementation derivative, we identified SigM-responsive mRNAs in M. abscessus . Analysis of responsive promoters defined a consensus SigM-binding site, indicating direct induction by SigM. Together these data defined 15 SigM-targeted loci transcribing 50 genes with annotations and structures consistent with ESX secretion. While SigM induces multiple esx4 locus promoters in M. smegmatis , only the promoter encoding the primary EsxU/EsxT secreted substrates are direct targets in M. abscessus , suggesting that production of the secretion apparatus is controlled by other transcription factors. The putative effector complexes identified here present strong candidates for the pathogenic roles previously reported for ESX-4 in M. abscessus infection models.