All organisms including bacteria use diverse modes of cellular control as they cope with changing environments. RNA-protein complexes are central to these processes. While deep sequencing approaches have revealed a wealth of RNAs, the world of bacterial RNA-binding proteins (RBPs) is still largely uncharted. Typically, RBPs interact with their RNA targets via distinct RNA-binding domains (RBDa). However, a growing number of proteins that lack these domains seem to interact with RNA as well. In prokaryotes, such unconventional RBPs (ucRBPs) remain largely unexplored, in part because methods for global RNA interactome capture (RIC) in bacteria are missing. We developed a novel RIC approach for bacteria that relies on primary transcript capture (CoCAP). Our pilot study captured known RBPs but also uncovered numerous new RBP candidates pointing towards a wealth of unexplored RBPs involved in cellular control in bacteria.
My bacRBP project explores the identity and functional diversity of such novel RBPs in bacteria with a focus on ucRBPs that play crucial roles in cellular physiology. I will tackle this through three objectives (Fig. 1) leveraging two model bacteria (Salmonella and Campylobacter):
1) Elucidate bacterial primary RBPomes during stress- and infection-relevant conditions.
2) Identify mechanisms and cellular functions of two widely conserved KH-domain RBPs.
3) Determine how unconventional RBPs influence and are influenced by bound RNAs.
Our work will provide a broadly applicable method for primary RBPome capture, vastly expand the set of bacterial RBPs, and reveal new layers of cellular control by ucRBPs.
Figure 1: Objectives of bacRBP. Our overarching hypothesis is that a vast, unexplored universe of unconventional RBPs exists in bacteria that mediate key biological processes. In Objective 1, we aim to expand the set of known bacterial RBPs by applying CoCAP to Salmonella and C. jejuni as well as examine potential functions of selected transcriptional regulator RBP candidates. In Objective 2 we explore the cellular roles and underlying molecular mechanisms of the KH-domain proteins KhpA/B in C. jejuni. In Objective 3, we aim to find out whether unconventional RBPs affect bound RNAs or vice versa.
