Graduate student Colleen Bianco (left) and Professor Carin Vanderpool (right) spearheaded a study that centered on how E. coli and Salmonella bacteria use RNA-based regulatory mechanisms to modify their membrane lipids in response to different stimuli. Their findings, with collaborator Kathrin Frölich (Ludwig Maximilian University of Munich, Germany) as a co-author, were published in a paper titled “Bacterial Cyclopropane Fatty Acid Synthase mRNA is targeted by activating and repressing small RNAs” in the Journal of Bacteriology.
Bacteria have many strategies to coordinate expression of genes, with the ultimate goal of optimizing cell structure and metabolic activities for whatever environment they find themselves in. Regulatory RNAs are versatile regulators of gene expression because they can be produced and destroyed quickly, depending on the need, and they act rapidly to control cellular protein production. Within the broad class of regulatory RNAs, small RNAs (sRNAs) in bacteria are single short strands of nucleic acid that are involved in controlling myriad metabolic processes and stress responses. Work in the Vanderpool Lab focuses on characterizing sRNAs, defining sRNA regulatory networks – the sets of genes regulated by each sRNA, and understanding their impacts on bacterial cell physiology and metabolism. Their latest paper tackled a regulatory circuit involving multiple sRNAs that contribute to regulation of a single mRNA that encodes an enzyme responsible for membrane lipid modification.
For her doctoral thesis work, Bianco has been studying the cfa mRNA, which encodes a cyclopropane fatty acyl phospholipid synthase involved in membrane lipid modification. Bacteria can modulate the abundance of Cfa enzyme to make the cell membrane either more or less permeable to the extracellular environment. When faced with acid stress, E. coli increases the amount of Cfa enzyme to prevent proton buildup within the cell, playing a pivotal role in the acid stress response.
Dr. John Cronan, Professor in the Department of Microbiology and world renowned expert on bacterial lipids, published some of the first work revealing the function of the Cfa enzyme in the 1970s, and work from his lab was instrumental in showing that cfa expression was induced in response to acid stress. Decades later, Bianco’s work revisited this topic from a new angle, demonstrating that multiple sRNAs responding to different external stimuli collaborate to tune the ability of cfa mRNA to produce Cfa enzyme.
Bianco et al. showed how each sRNA interacts with cfa mRNA to either reduce or enhance the levels of Cfa enzyme produced by the mRNA. Specifically, they showed that two sRNAs that turn up Cfa enzyme production do so by interfering with RNA degradation machinery that would otherwise rapidly destroy the cfa mRNA. These activating sRNAs are particularly important for increasing Cfa levels during acid stress. Another sRNA produced in response to other signals has the opposite effect – causing cfa mRNA to be degraded even more rapidly than usual and thereby reducing the amount of Cfa.
Vanderpool stressed that this system is a circuit. “Small RNAs allow different environmental factors to be integrated for one output,” she said. The environmental conditions determine the levels of activating and repressing sRNAs, which in turn control how much Cfa is made at any given time. When conditions change, as they do often for bacteria living in natural environments, the system recalibrates.
Future work will attempt to better understand exactly what environmental signals are controlling levels of each sRNA and how sRNA-mediated control of lipid modifications is advantageous to bacterial cells trying to cope with different stress conditions. The bacterial cell membrane is the first line of defense against conditions or molecules (like antibiotics) that inhibit bacterial cell growth, metabolism and proliferation. Bianco and Vanderpool think that their basic research to understand the regulatory processes that govern bacterial membrane structure and function could lead to future work that exploits these regulatory mechanisms for therapeutic or biotechnological applications.
