UnifyRNA

Bacteria are extremely versatile organisms that respond and adapt to a wide variety of environmental changes through their amazing ability to extensively regulate gene expression. The first level of control that has been described is transcription and to date, even though some gaps persist because of its huge complexity, the transcriptional regulatory network of model bacteria such as E. coli has been thoroughly characterized. Two-component systems (TCS), that allow sensing and adaptation to the environment through activation by phosphorylation of a regulator, are among the most widespread transcriptional regulators in bacteria. However, post-transcriptional control is known to affect gene expression as well. Its importance has been early recognized in bacteria because genes subject to translational control encode proteins whose amount may represent a large portion of the total cellular mass (e.g. genes for ribosomal proteins). Furthermore, the identification and characterization of small RNAs (sRNAs) as widespread post-transcriptional regulators in bacteria has brought a renewal of interest to the field. sRNAs have been found in many bacteria and are involved in fundamental biological processes, such as quorum-sensing or cell enveloppe homeostasis. A large family of those regulatory molecules act by pairing to target-mRNAs via imperfect and short duplexes, which allows a single sRNA to directly regulate multiple genes. This pairing ultimately leads to changes in translation and/or stability of the target-mRNA according to extremely diverse molecular mechanisms. Importantly, it has recently become obvious that post-transcriptional control exerted by sRNAs and transcriptional control are intimately connected. Indeed, not only is the synthesis of sRNAs extensively regulated at the transcriptional level, but several of them were also shown to directly regulate the expression of transcriptional regulators (TR), forming a feedback loop in many cases. As a result, biological functions as important as motility or group behaviour are controlled by mixed regulatory circuits, whose properties remain mostly uncharacterized. The UnifyRNA project will therefore aim at unraveling the role of sRNAs in these mixed circuits by focusing on two examples of choice that we have identified in E. coli. The first one is the feedback loop linking the two OmrA/OmrB apparently redundant sRNAs and the EnvZ-OmpR TCS, different regulators that control cell-surface related processes such as outer membrane composition, adhesion or motility. The other example is the control of the PhoQ-PhoP TCS, involved in magnesium homeostasis and bacterial virulence, by multiple sRNAs such as MicA and GcvB, a system for which we have evidence of surprising complexity. The expected results will not only be of fundamental interest given the central role of PhoQ-PhoP and EnvZ-OmpR in bacterial physiology, but they will also allow to apprehend the functions, the specific properties and the biological roles of mixed regulatory circuits of E. coli and how they integrate into larger global networks. This is especially important given the fact that both TCS and sRNAs are widespread regulators in bacteria and that other examples of sRNAs regulating TCS have been reported. At last, results obtained during these studies should provide important clues in order to apprehend the complete set of targets of OmrA/B sRNAs and, as a result, their biological role. Using a multidisciplinary approach combining transcriptomics, proteomics, molecular genetics, single cell microscopy and systems biology, the UnifyRNA project will provide an important advance in our understanding of the biology of small regulatory RNAs in bacteria.