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Cells use every possible mechanism to regulate components of regulatory circuits. We have recently been investigating a novel and unexpectedly complex level of regulation of translation and mRNA stability. Small non-coding RNAs of 80-100 nucleotides positively and negatively regulate translation and messenger RNA stability for key prokaryotic regulatory proteins, frequently by complementary pairing. A given small RNA can simultaneously regulate multiple target messages. Therefore, signals for synthesis of the small RNA are rapidly transduced into regulation of these targets. The small RNAs require an RNA binding protein, Hfq, that acts to stimulate RNA-RNA pairing. There are intriguing similarities between these small prokaryotic regulatory RNAs and RNAi and microRNAs in eukaryotes. Finding both small RNAs and their targets in sequenced genomes remains a challenge.
