Interplay of Exoribonucleases, Hfq and Small RNAs Structural Determinants in the Control of Gene Expression

Dissertation presented to obtain the Ph.D degree in Biology

Small non-coding RNAs (sRNAs) are regulatory molecules that typically are not translated into proteins. These molecules are often highly structured and very stable and can affect many genetic pathways in all domains of life. Bacterial small regulatory RNAs (sRNAs) parallel microRNAs in their ability to control multiple targets. Small RNAs can bind to proteins or to mRNA targets. The sRNAs that act by an antisense mechanism can have full (cis-encoded) or partial complementarity (trans-encoded) with their targets. Most of the trans-encoded sRNAs studied so far in Escherichia coli bind the RNA chaperone Hfq. The 5’ end of antisense RNAs is usually found to be critical for the interaction with targets, generally inhibiting translation and promoting mRNA decay. RNases are key elements in the control of RNA levels in the cell and not surprisingly are also critical in the regulation of sRNAs. In E. coli there are three 3’-5’exoribonucleases that accomplish most of the mRNA exodegradative activity: ribonuclease II (RNase II), ribonuclease R (RNase R) and polynucleotide phosphorylase (PNPase).(...)