Small RNAs in Bacteria

Small RNA (sRNA) molecules in bacteria play key roles in the regulation of gene expression, in controlling protein functionality, and in guiding defense against invading DNA. sRNAs involved in transcription regulation are divided in a cis- and a trans-encoded class. cis-Encoded sRNAs are encoded by the same genomic locus as their target mRNA, residing either on the transcript they regulate (riboswitches), or derived from the opposite strand (antisense sRNAs). trans-Encoded sRNAs are encoded elsewhere on the genome and require the RNA chaperone Hfq for exerting their function. Other sRNAs regulate nucleic acid-binding proteins by mimicking the nucleic acid sequence and structure, leading to sequestration of the protein. Clustered regularly interspaced short palindromic repeat (CRISPR) RNAs (crRNAs) represent yet another class of sRNA that serves as a guide in defense against invading nucleic acids, such as viruses and conjugative plasmids. In addition, prokaryotic Argonaute has recently been proposed to function in antiviral or anti-plasmid defense that is guided by small nucleic acids. In this article, the function and molecular mechanism of the different classes of sRNAs are reviewed.