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.