Mycoplasma gallisepticum S6 strain:S6 Transcriptome or Gene expression

Avian bacterial pathogen M. gallisepticum is a good model for transcriptional regulation studies due its small genome and relative simplicity. Here we used RNA-seq combined with MS-spec proteomics to accurately map CDSs, TSSs and transcription terminators (TT) and decipher it's role in stress-induced transcriptional response. We identified 1061 TSS at FDR 10%, and shown that almost all transcription in M. gallisepticum is initiated from classic TATAAT promoters, surrounded by A/T-rich sequences rarely accompanied by -35 element. Our analysis revealed prominent complexity of operon structure: in average, each coding operon has one internal TSS and TT, besides primary ones. Our new transcriptomic approach based on intervals between two closest transcription initiators and/or terminators allowed us identify two classes of TTs: strong, unregulated, hairpin-contained and weak, heat-shock regulated, hairpinless. Comparison of gene expression levels under different conditions (such as heat, osmotic and peroxide stresses) shows widespread and divergent transcription regulation in M. gallisepticum. Modeling reveals that structure of core promoter could play a major role in gene expression regulation. We have shown that under heat shock activation of cryptic promoters together with suppression of hairpinless TTs lead to widespread seemingly not-functional transcription.