20 Versatile Roles of Small RNA Regulators in Bacteria

Abstract

In this chapter, we focus on RNAs that function as regulators in bacteria. Traditionally these RNAs have been denoted “small RNAs” (sRNAs) based on their size, which ranges from about 50 to about 500 nucleotides but averages around 100 nucleotides. These RNAs also are sometimes referred to as noncoding RNAs, the predominant term used for regulatory RNAs in eukaryotic cells. Most has been learned about the sRNAs found in Escherichia coli, and this chapter focuses on these. However, with increasing interest in sRNA regulators, more and more are being identified in other bacteria, many pathogenic, and we discuss general similarities and differences between the E. coli sRNAs and those found in other bacteria. The majority of the E. coli sRNAs act by base-pairing, although a few also modulate protein function; we describe what is known about both the mechanisms of action and the physiological roles of these RNAs.

IDENTIFICATION OF sRNAs
The most abundant sRNAs in E. coli were detected first upon size fractionation of in-vivo-labeled total RNA. Subsequently, a few other sRNAs were discovered serendipitously as signals on northern blots, as an RNA that copurified with a specific protein or as a result of phenotypes associated with overexpression. More systematic searches for E. coli sRNA molecules were carried out beginning in 2001. The computation-based searches focused on intergenic regions. In two searches, straight sequence conservation between closely related organisms was detected (Argaman et al. 2001; Wassarman et al. 2001); in another case, the algorithms detected conservation of RNA structural...