Regulation of gene expression plays a key role in the ability of bacteria to rapidly adapt to changing environments and to colonize extremely diverse habitats. It has been known for decades that multiple regulators, among which two-component systems (TCSs), control the transcription of many bacterial genes. More recently, the discovery of a plethora of small regulatory RNAs (sRNAs) and their characterization highlighted the importance of post-transcriptional regulation in bacterial gene expression. It is now clear that the timely expression of many bacterial genes responds to a complex network of both transcriptional and post-transcriptional regulators. However, the properties of the resulting mixed regulatory circuits on the dynamics of gene expression and in the bacterial adaptive response have been poorly addressed so far.
A first major objective of the BactRNA project was to tackle this question by characterizing the circuits that are formed between two widespread classes of bacterial regulators, the sRNAs and the two-component systems, and deciphering their importance in bacterial physiology and virulence. In this regard, results obtained in the course of the BactRNA project not only identified multiple examples of sRNAs controlling TCS synthesis, resulting in a possible connection between different TCSs. They also unraveled the ability of specific antisense RNAs, whose regulatory action is typically restricted to their cognate sense gene, to control expression of multiple genes in trans. Furthermore, the detailed study of one mixed circuit involved in bacterial virulence revealed an unexpected example of a dual feedback control of a TCS mediated either by a small protein (negative feedback) or by the upstream gene in the same operon (positive feedback).
In addition, the study of sRNAs also led to major breakthroughs regarding the basic mechanisms of gene expression, and especially the crucial step of translation initiation. For instance, we previously showed that repressor sRNAs can target activating stem-loop structures located within the coding region of mRNAs that promote translation initiation, in striking contrast with the previously recognized inhibitory role of mRNA structures in translation.
A second major objective of BactRNA was thus to address how these secondary structures or more generally other mRNA elements impact translation, and their possible relation with sRNA control. For this, we studied the action of sRNAs on mRNAs known or suspected to carry translation activating stem-loops, which highlighted exquisite details of sRNA function, among which the role of sRNA transcriptional terminators in gene regulation, or the control of a single gene subject to both sRNA- and riboswitch-control. Most importantly, we also performed a transcriptome-wide analysis of the contacts between the 30S ribosomal small subunit and the mRNAs, which showed multiple binding-sites outside of the translation initiation region, thereby revisiting the canonical model of 30S recruitment and translation initiation in bacteria.
Overall, by identifying new actors and new modes of regulation of bacterial gene expression, this fundamental research project greatly improved our understanding of how these microorganisms can so rapidly and successfully adapt to many different environments. On the longer term, results of this project may provide clues towards the development of anti-bacterial strategies, which is essential given the current antibioresistance threat.
