Toxin-antitoxin (TA) genes are ubiquitous among bacteria and are associated with persistence and dormancy. Following exposure to unfavorable environmental stimuli, several species (Escherichia coli, Staphylococcus aureus, Myxococcus xanthus) employ toxin proteins such as RelE and MazF to downregulate growth or initiate cell death. Mycobacterium tuberculosis possesses three Rel TA modules (RelMtb): RelBEMtb, RelFGMtb and RelJKMtb (Rv1246c-Rv1247c, Rv2865-Rv2866, and Rv3357-Rv3358, respectively), which inhibit mycobacterial growth when the toxin gene (relE, relG, relK) is expressed independently of the antitoxin gene (relB, relF, relJ). In the present study, we examined the in vivo mechanism of the RelEMtb toxin protein, the impact of RelEMtb on M. tuberculosis physiology and the environmental conditions that regulate all three relMtb modules. RelEMtb negatively impacts growth and the structural integrity of the mycobacterial envelope, generating cells with aberrant forms that are prone to extensive aggregation. At a time coincident with growth defects, RelEMtb mediates mRNA degradation in vivo resulting in significant changes to the proteome. We establish that relMtb modules are stress responsive, as all three operons are transcriptionally activated following mycobacterial exposure to oxidative stress or nitrogen-limiting growth environments. Here we present evidence that the relMtb toxin:antitoxin family is stress-responsive and, through the degradation of mRNA, the RelEMtb toxin influences the growth, proteome and morphology of mycobacterial cells.