Cari Vanderpool

Bacteria must sense and respond to rapidly changing and often stressful environments, and their ability to enact rapid changes in gene expression is key to survival. My research program explores RNA-based and phage-related mechanisms of gene regulation, focusing on how small RNAs (sRNAs), RNA chaperones, and phages shape bacterial physiology, metabolism, and host interactions. These regulatory processes act post-transcriptionally to modulate transcription elongation, translation, and mRNA stability, allowing cells to swiftly rewire gene expression. While hundreds of sRNAs and numerous phage-encoded regulators are predicted across bacterial genomes, their molecular roles and ecological functions remain poorly understood.

For nearly two decades, my lab has combined genomics, genetics, and biochemistry to uncover how sRNAs and their protein partners operate at the molecular level and how their activity links to broader physiology. Our work has defined the regulons of multiple sRNAs, revealed novel mechanisms of hierarchical and multi-target regulation, and connected these interactions to stress adaptation and metabolic balance in Escherichia coli, Salmonella, and gut-associated Bacteroides. These studies have shown how RNA regulation integrates environmental signals with physiological responses.

A growing direction of my lab is the study of bacteriophage interactions, particularly in plant-associated microbes. In collaboration with colleagues, we are investigating phages infecting Rhizobium leguminosarum, an important symbiont of legumes. We have isolated and characterized diverse rhizobiophages, mapped their host ranges across natural isolates, and identified bacterial surface structures and genetic loci that determine susceptibility and resistance. This work reveals how accessory genomes and defense systems influence phage–host dynamics and uncovers novel genes involved in phage resistance. Because rhizobia play central roles in plant nitrogen fixation, these studies extend RNA and phage biology into the plant–microbe interface, with implications for agriculture and ecosystem health.

Moving forward, we will continue to dissect novel mechanisms of sRNA regulation in enteric bacteria, characterize RNA-binding proteins and RNA–protein networks in gut Bacteroides, and expand our investigation of phage–bacteria interactions in symbiotic systems. We will also explore prophage-derived sRNAs and small proteins as mediators of bacterial defense and ecological adaptation. These projects, supported by a strong team of collaborators, integrate systems-level discovery with detailed mechanistic dissection to connect RNA biology and phage defense to cellular physiology and microbial ecology.

Together, this work provides fundamental insights into microbial regulation while highlighting its relevance to microbiomes, symbioses, and plant-associated ecosystems. By linking molecular biology to ecological context, my group aims to uncover principles of microbial survival that impact health, agriculture, and the environment.