Functional characterization of a pair of KH-domain containing RNA-binding proteins in Campylobacter jejuni

RNA-binding proteins (RBPs) are emerging as integral regulators of RNA networks controlling the physiology and virulence-associated processes in bacterial pathogens. Homologs of well-studied RBPs like Hfq and ProQ are missing in several bacteria, including Campylobacter jejuni, the leading cause of bacterial gastroenteritis in humans. The RBP players involved in post-transcriptional regulation of such pathogens remain to be discovered. Using a novel unbiased RBP capture method, our lab identified several new RBP candidates in C. jejuni, including a largely unexplored KH-domain protein, KhpB. Reciprocal co-immunoprecipitation (coIP) revealed that KhpB interacts with another KH-domain protein, KhpA. Both KH-domain proteins are widely conserved among many bacteria. Hence to gain insights into the cellular functions of these KH-domain proteins, we examined the phenotype of khpA/B deletions and their molecular interactome in C. jejuni. Notably, deletion of khpA or khpB decreased the pathogen"s abilities to adhere and invade Caco-2 cells. Using RNA co-immunoprecipitation and sequencing (RIP-seq) of epitope-tagged KhpA and KhpB, we identified many distinct and overlapping sets of mRNAs and a few sRNAs as potential RNA binding partners of KhpA/B, suggesting their roles as RBPs. RNA binding of KhpA/B to specific RNAs was further demonstrated using in-vitro binding assays like electrophoretic mobility shift assays (EMSA). RIP-seq upon deletion of partner Khp protein reveals loss of ~97% of the co-purified RNA targets, thus highlighting their inter-dependent RNA-binding property. Moreover, mass spectrometry-based protein interactome analysis of KhpA/B uncovered several potential protein interaction partners of KhpA/B. Overall, our findings suggest that KhpA/B fulfill diverse cellular functions in bacteria harboring this class of RNA-binding proteins.