Small RNAs and Small Proteins Involved in Resistance to Cell Envelope Stress and Acid Shock in Escherichia coli : Analysis of a Bar-Coded Mutant Collection

Abstract

ABSTRACT More than 80 small regulatory RNAs (sRNAs) and 60 proteins of 16 to 50 amino acids (small proteins) are encoded in the E scherichia coli genome. The vast majority of the corresponding genes have no known function. We screened 125 DNA bar-coded mutants to identify novel cell envelope stress and acute acid shock phenotypes associated with deletions of genes coding for sRNAs and small proteins. Nine deletion mutants ( ssrA , micA , ybaM , ryeF , yqcG , sroH , ybhT , yobF , and glmY ) were sensitive to cell envelope stress and two were resistant ( rybB and blr ). Deletion mutants of genes coding for four small proteins ( yqgB , mgrB , yobF , and yceO ) were sensitive to acute acid stress. We confirmed each of these phenotypes in one-on-one competition assays against otherwise-wild-type lacZ mutant cells. A more detailed investigation of the SsrA phenotype suggests that ribosome release is critical for resistance to cell envelope stress. The bar-coded deletion collection we generated can be screened for sensitivity or resistance to virtually any stress condition.