Hfq orchestrates a robust RNA-RNA interaction network in Acinetobacter baumannii

Across bacteria, RNA binding proteins, such as Hfq, often play a key role in facilitating post-transcriptional regulation by chaperoning interactions between small regulatory RNAs (sRNAs) and their mRNA targets. Acinetobacter baumannii, a problematic gram-negative bacterial pathogen, produces over a hundred sRNAs, of which only a few have experimentally validated mRNA targets. While previous studies have identified hfq as a candidate essential gene in the model multidrug-resistant A. baumannii strain AB5075, the role of Hfq in mediating the regulatory effects of sRNAs remains largely unexplored. Here, we use RIL-seq to identify Hfq-associated sRNA-mRNA interaction partners in strain AB5075. Our results indicate that A. baumannii Hfq coordinates a robust network of RNA-RNA interactions. We detected RNA interactions with 98 distinct sRNA species, including nearly 40 previously undescribed sRNAs. The results further indicate that A. baumannii utilizes sRNAs to regulate the expression of numerous transcripts that encode virulence factors and antibiotic resistance determinants. Collectively, our study provides new insights into the regulatory potential for dozens of sRNAs in A. baumannii and highlights the importance of post-transcriptional regulation in this emerging pathogen.IMPORTANCEAcinetobacter baumannii represents a burgeoning threat to human health and consistently ranks as a critical pathogen by the World Health Organization due to extensive antimicrobial resistance among clinical isolates. While much effort has focused on understanding how A. baumannii acquires antimicrobial resistance traits, our knowledge of key processes governing gene expression in this organism is lacking. In particular, very little is known regarding post-transcriptional regulation in A. baumannii. Here, we demonstrate that Hfq, a highly conserved RNA chaperone, coordinates the regulatory activities for nearly 100 small regulatory RNAs (sRNAs), including many that have not been described before. We also find that several Hfq-associated sRNAs directly regulate mRNA transcripts, which encode antibiotic resistance determinants and virulence factors. Collectively, our study provides evidence for the existence of a complex post-transcriptional regulatory network in A. baumannii and offers new insights into how the organism uses Hfq and sRNAs to coordinate gene expression.