Toxin-antitoxin (TA) modules are found in both bacterial plasmids and genomes.. They ensure plasmid maintenance via a mechanism known as post-segregational killing. However the biological importance of the large number of chromosomal TA loci identified thus far is still the subject of great debate. Some have been linked to stress response, biofilm formation, persistence, and development, but many systems still need to be characterized. Here we have examined the biogenesis and decay of the Type I toxin-antitoxin system SibC/ibsC. SibC is a cis-encoded sRNA that prevents the toxic effect of the IbsC protein by binding to its mRNA and inhibiting its translation. We have shown that ribonucleases RNase E, RNase III, and RNase P all play a role in SibC biogenesis and decay. Interestingly, we have also demonstrated a role for Hfq in the stability of SibC and its regulatory effect on ibsC. These findings suggest that gene expression regulation mediated by cis-encoded sRNAs is more complicated and shares more features with trans-encoded sRNA regulation than previously thought. We have also analyzed the role of MazF, an mRNA interferase encoded by the Type II toxin-antitoxin system mazEF, in general mRNA decay. Surprisingly, we have shown that although MazF does not play a role in general mRNA in E.coli, a deletion of the downstream gene MazG does. MazG has been shown to regulate the stringent response by lowering the levels of ppGpp, the alarmone that redirects transcription to allow the cells to survive nutrient starvation. The link between the stringent response, MazG, and mRNA needs to further analyzed.