SummaryThe conserved RNA-binding protein Hfq, originally discovered in Escherichia coli as a host factor for Q b b b b replicase, has emerged as a pleiotropic regulator that modulates the stability or the translation of an increasing number of mRNAs. During the past 5 years, Hfq-mediated control has been an area of increasing focus because the protein has been linked to the action of many versatile RNA-based regulators that use basepairing interactions to regulate the expression of target mRNAs. The recent findings that Hfq assists in bimolecular RNA-RNA interactions and is similar structurally and functionally to eukaryotic Sm proteins have further fuelled interest in this important post-transcriptional regulator. Here, we summarize the history of Hfq and highlight results that have led to an important gain in insight into the physiology, biochemistry and evolution of Hfq and its homologues.

The physiological role of Escherichia coli Spot 42 RNA has remained obscure, even though the 109-nucleotide RNA was discovered almost three decades ago. Structural features of Spot 42 RNA and previous work suggested to us that the RNA might be a regulator of discoordinate gene expression of the galactose operon, a control that is only understood at the phenomenological level. The effects of controlled expression of Spot 42 RNA or deleting the gene (spf) encoding the RNA supported this hypothesis. Down-regulation of galK expression, the third gene in the gal operon, was only observed in the presence of Spot 42 RNA and required growth conditions that caused derepression of the spf gene. Subsequent biochemical studies showed that Spot 42 RNA specifically bound at the galK Shine-Dalgarno region of the galETKM mRNA, thereby blocking ribosome binding. We conclude that Spot 42 RNA is an antisense RNA that acts to differentially regulate genes that are expressed from the same transcription unit. Our results reveal an interesting mechanism by which the expression of a promoter distal gene in an operon can be modulated and underline the importance of antisense control in bacterial gene regulation.

SummaryThe Escherichia coli ompA mRNA, encoding a highly abundant outer membrane protein, has served as a model for regulated mRNA decay in bacteria. The halflife of this transcript correlates inversely with the bacterial growth rate and is growth stage-dependent. The stability of the messenger is determined by the 5 ′ ′ ′ ′ -untranslated region which possesses cleavage sites for RNase E. Hfq binds to this region, is essential for controlling the stability and has been suggested to directly regulate ompA mRNA decay. Here we report that the 78 nucleotide SraD RNA, which is highly conserved among Enterobacteriaceae, acts in destabilizing the ompA transcript when rapidly grown cells enter the stationary phase of growth. During this growth-stage the expression of SraD RNA becomes strongly increased. The SraD-mediated decay of ompA mRNA depends on Hfq and in vitro studies revealed that Hfq facilitates binding of the regulatory RNA to the translational initiation region of the messenger. Deletion of sraD , however, does not significantly affect the stability of the ompA mRNA in slowly growing cells. Our results indicate that distinct regulatory circuits are responsible for growth phase-and growth rate-dependent control of the ompA mRNA stability.