Remodeling of RNA-Binding Proteome and RNA-mediated regulation as a new layer of control of sporulation

Abstract

Sporulation allows certain bacteria to survive extreme conditions for extended periods posing challenges to public health and food safety. Transcriptional level of regulation relying on {sigma} factors has been well studied in the non-pathogenic model bacterium Bacillus subtilis, while post-transcriptional control remains poorly understood. RNA-binding proteins (RBPs) and small non-coding RNAs (sRNAs) modulate gene expression by affecting mRNA stability or translation. Recent studies suggest that RNA-mediated regulation plays a role in sporulation, but its networks and interactions remain largely uncharacterized, highlighting the need for further investigation. To address this knowledge gap, we adapted OOPS (Orthogonal Organic Phase Separation), a high-throughput method to specifically purify RNA binding proteome (RBPome). By monitoring its dynamics, we observed RBPome is highly remodeled during B. subtilis process. Our approach led to the identification of novel RBPs and potential RNA-mediated post-transcriptional regulators of sporulation. This work provides important insights into the interplay between RNAs and RBPs, advancing the understanding of post-transcriptional regulation in Gram-positive spore-forming bacteria. It also offers new resources for exploring the molecular mechanisms that govern sporulation. IMPORTANCEUnderstanding how bacteria survive extreme conditions is key to tackling challenges in health, food safety, and industry. This study reveals a previously unexplored layer of control in Bacillus subtilis, a model organism for spore-forming bacteria--those that can produce spores, which are highly resistant, dormant cells able to endure harsh environments. By mapping, for the first time, the full set of proteins that interact with RNA during sporulation, this work uncovers how bacteria fine-tune their internal programs. The identification of novel RNA-binding proteins sheds light on how bacteria adapt at the molecular level and lays a valuable foundation for future mechanistic studies that will deepen our understanding of bacterial adaptation and resilience.