Synthetic Genetic Interactions Reveal a Dense and Cryptic Regulatory Network of Small Noncoding RNAs in Escherichia coli

Abstract

ABSTRACT Over the past 20 years, we have learned that bacterial small noncoding RNAs (sRNAs) can rapidly effect changes in gene expression in response to stress. However, the broader role and impact of sRNA-mediated regulation in promoting bacterial survival has remained elusive. Indeed, there are few examples where disruption of sRNA-mediated gene regulation results in a discernible change in bacterial growth or survival. The lack of phenotypes attributable to loss of sRNA function suggests that either sRNAs are wholly dispensable or functional redundancies mask the impact of deleting a single sRNA. We investigated synthetic genetic interactions among sRNA genes in Escherichia coli by constructing pairwise deletions in 54 genes, including 52 sRNAs. Some 1,373 double deletion strains were studied for growth defects under 32 different nutrient stress conditions and revealed 1,131 genetic interactions. In one example, we identified a profound synthetic lethal interaction between ArcZ and CsrC when E. coli was grown on pyruvate, lactate, oxaloacetate, or d-/l-alanine, and we provide evidence that the expression of ppsA is dysregulated in the double deletion background, causing the conditionally lethal phenotype. This work employs a unique platform for studying sRNA-mediated gene regulation and sheds new light on the genetic network of sRNAs that underpins bacterial growth. IMPORTANCE sRNAs have long been purported to be a critical mechanism by which bacteria respond to stress; however, uncovering growth phenotypes for sRNA deletion strains in E. coli and related bacteria has proven particularly challenging. In contrast, the deletion of hfq, a chaperone required for the activity of many sRNAs in E. coli, results in striking growth defects in E. coli under a variety of medium conditions and chemical stressors. Here, we examined the importance of hfq and sRNA deletion strains for E. coli growth in nutrient-limited medium supplemented with 30 different carbon sources. We then systematically combined sRNA deletion mutations, creating a library of 1,373 sRNA double deletion strains, which we screened for growth under the same conditions, yielding 43,936 individual growth measurements. Our data uncovered more than 1,000 growth phenotypes for sRNA double deletion strains, shedding light on complicated networks of sRNA regulation that underpin bacterial survival under nutrient stress.

Keywords

• systems biology
• bacterial carbon metabolism
• small noncoding RNA