Small Regulatory RNAs (sRNAs): Key Players in Prokaryotic Metabolism, Stress Response, and Virulence

Abstract

Small RNAs (sRNAs) gained worldwide attention in the late 2002, when the journal Science published a special issue entitled “Small RNAs – Breakthrough of the Year.” However, small antisense RNAs in bacteria involved in the regulation of plasmid replication and maintenance, phage life cycles, and transposition had been investigated in great depth for more than 20 years. Whereas these sRNAs were discovered only fortuitously, systematic computer-based searches have only been used since 2001. Currently, it is estimated that a bacterial genome encodes ∼200–300 sRNAs with diverse functions. To date (2011), about 140 sRNAs are known in Escherichia coli and Salmonella. However, only about 25 of these have been assigned a biological function, indicating that defining their functions continues to be a challenging issue. Systematic searches have also been performed for a few Gram-positive bacterial species. sRNAs in bacteria can be divided into two major groups: The first group regulates gene expression by a base-pairing mechanism with target mRNA, whereas the second group acts by binding of small proteins. This chapter covers mechanisms of action, biological functions, integration in regulatory circuits, and evolutionary aspects of base-pairing and protein-binding sRNAs.