Classic Spotlight: Hfq, from a Specific Host Factor for Phage Replication to a Global Player in Riboregulation

Today, Hfq is recognized as a bacterial RNA chaperone dynamically interacting with different RNA species and playing a crucial role in RNA-based regulation. Hfq forms homohexameric ring-like complexes exposing different faces for interaction with RNAs. It is a member of the Sm and Sm-like (Lsm) protein family that is widespread in all domains of life. In recent years, Hfq has attracted much attention for its activity in promoting imperfect base pairing of regulatory small RNAs (sRNAs) with their mRNA targets, affecting either RNA stability or mRNA translation. With increasing recognition of the relevance of sRNA-based regulation in prokaryotes, Hfq has become the focus of extensive research. The current knowledge on its functional role and mechanistic insights into its mode of action have been comprehensively reviewed (1–3). Genome-wide RNA coimmunoprecipitation studies showed that Hfq targets a plethora of RNAs in vivo (4–6). Although diverse RNA species are bound by Hfq, it seems to interact preferentially with sRNAs and mRNAs. Hfq entered the scene in the 1960s, originally identified as a mysterious Escherichia coli host factor promoting replication of the Q RNA phage (7, 8), which inspired the name of this protein (host factor Q phage). It took more than 20 years before the hfq gene was identified and sequenced (9). Strong pleiotropic effects of an hfq mutation, the high abundance of the protein, and its preference for binding to AU-rich RNA fueled early speculations about a phage infection-independent role in E. coli. The first studies reporting Hfq-dependent regulation of a host mRNA were published by Muffler et al. (10) and in the Journal of Bacteriology (JB) by Brown and Elliott (11) at about the same time in 1996. Both studies identified Hfq as an important factor for translation of the rpoS mRNA encoding the stationary-phase sigma factor RpoS ( ) in E. coli. This alternative sigma factor serves as the master regulator of the general stress response and is one of the key factors in the regulatory network controlling biofilm formation (12). Only a year later, papers in JB provided hints about a role of Hfq as a global regulator involved in the expression of -dependent and -independent genes (13) and proposed the 5= untranslated region as the regulatory target in the rpoS mRNA (14). Based on suppressor mutations upstream of rpoS alleviating the negative effect of an hfq mutation on rpoS expression, Brown and Elliott (14) suggested that the secondary structure of the rpoS mRNA plays an important role in Hfq-dependent regulation of rpoS. These findings set the stage for subsequent discoveries of numerous Hfq-regulated mRNAs and associated regulatory mechanisms. sRNA-mediated and Hfq-dependent activation of rpoS mRNA translation has since been discovered (reviewed in reference 15), and the induced change in the rpoS mRNA secondary structure has become a paradigm of translational activation by sRNAs (16). Three sRNAs—ArcZ, reflecting the redox state of the respiratory chain, DrsA, induced by low temperature, and RprA, activated by cell envelope stress—provide distinct inputs for integration of multiple environmental signals leading to enhanced levels of RpoS (15). The discoveries of regulatory RNAs and Hfq revealed a new layer of regulation that had been missed for decades of genetic and molecular research. Although not ubiquitous, Hfq is widespread in the bacterial world. Its function as a flexible RNA matchmaker explains its important and pleiotropic role in bacterial physiology. Yet there is still much to discover about the physiological role of Hfq and the molecular mechanisms making this protein a globally important RNA chaperone in bacteria.