| In the last decade, our understanding of bacterial gene regulation has undergone a dramatic shift, as small RNA (sRNA) regulators are increasingly understood to be key components of complex regulatory networks controlling bacterial gene expression. Two classes of sRNAs found in bacteria regulate genes in response to environmental signals; one class utilizes base pairing to regulate target mRNA stability or translation, and the other relies on sequestration of proteins. Base pairing sRNAs can be further categorized as trans-encoded or cis-encoded. Trans-encoded sRNAs are located at a distance and share limited complementarity with their targets, whereas cis-encoded sRNAs are located on the strand opposite their target mRNA, generating the potential for extensive base pairing. While the vast majority of sRNAs act by base pairing, some sRNAs function by binding and modifying the activity of proteins.;In Escherichia coli, an sRNA of unknown function, IS061, was previously found to be expressed from the intergenic region between abgR, encoding a transcription regulator involved in modulating the cellular response to p-aminobenzoyl-glutamate, and ydaL, encoding a protein with DNA endonuclease activity. Here we show that while IS061, renamed McaS for multi-cellular adhesive small RNA, is antisense to abgR, it does not regulate abgR expression or levels. McaS is the first base pairing sRNA that is cis-encoded but not cis-acting; furthermore, McaS is the only known sRNA regulator that functions both by base pairing and protein binding. We found that this unique multi-function sRNA regulates multiple aspects of E. coli biofilm formation by regulating two master transcription regulators, FlhD and CsgD, and also through sequestration of CsrA, an RNA binding protein that represses biofilm formation.;The finding that McaS is encoded opposite abgR yet does not act as an antisense RNA has important implications for the hundreds of reported antisense RNAs and raises the question of how many are functional. By examining the E. coli genome for candidate antisense RNAs similar to McaS using next generation sequencing technologies and rigorously testing their expression and effects, we can begin to better understand the prevalence and roles of antisense RNA-based gene regulation in E. coli.. |
