"Defining the transcriptional and post-transcriptional landscape under normal growth and stress conditions in Mycobacterium smegmatis
The success of Mycobacterium tuberculosis to infect, survive and proliferate during long periods in the human lungs largely depends on the rigorous control of gene expression. Transcriptome wide analysis are key to understanding gene regulation in a global scale. Here, we combine 5’end-directed libraries with RNAseq expression libraries to get insight into the transcriptome organization and post-transcriptional mRNA cleavage landscape in mycobacteria during normal growth and under two physiologically relevant conditions: hypoxia and oxidative stress. By using the model organism M. smegmatis we identified 6,126 transcriptional start sites (TSSs) with high confidence during normal growth, 67% of which were categorized as primary TSSs for annotated genes, while the remaining were classified in internal, antisense or orphan, according to their genomic context. Interestingly, over 25% of the RNA transcripts lack a leader sequence, and the 71% of CDSs having a 5’UTR lack of a ribosome-binding site, indicating that M. smegmatis can initiate translation in a robust way, like M. tuberculosis. Our approach allowed us to identify over 3,000 cleavage sites with a bias toward mRNA regulatory regions, highlighting the importance of post-transcriptional regulation in gene expression. We show that, in conditions associated with the host environments during infection, mycobacteria change their transcriptomic profiles and endonucleolitic RNA cleavage is markedly reduced, presumably leading to an increase in transcripts half-life. Finally, we demonstrate that M. smegmatis and M. tuberculosis share a large number of similarities at the transcriptomic level, suggesting that similar regulatory mechanisms govern both species.