Abstract
The avian bacterial pathogen Mycoplasma gallisepticum is a good model for transcriptional regulation studies due to its small genome and relative simplicity. In this study, we used RNA-Seq experiments combined with MS-based proteomics to accurately map coding sequences (CDSs), transcription start sites (TSSs) and transcription terminators (TTs) and to decipher their roles in stress-induced transcriptional responses. We identified 1061 TSSs at an FDR (false discovery rate) of 10% and showed that almost all transcription in M. gallisepticum is initiated from classic TATAAT promoters, which are surrounded by A/T-rich sequences and rarely accompanied by a −35 element. Our analysis revealed the pronounced complexity of the operon structure: on average, each coding operon has one internal TSS and TT in addition to the primary ones. Our new transcriptomic approach based on the intervals between the two closest transcription initiators and/or terminators allowed us to identify two classes of TTs: strong, unregulated and hairpin-containing TTs and weak, heat shock-regulated and hairpinless TTs. Comparing the gene expression levels under different conditions (such as heat, osmotic and peroxide stresses) revealed widespread and divergent transcription regulation in M. gallisepticum. Modeling suggested that the structure of the core promoter plays a major role in gene expression regulation. We have shown that the heat stress activation of cryptic promoters combined with the suppression of hairpinless TTs leads to widespread, seemingly non-functional transcription.
