Hfq: the flexible RNA matchmaker

Abstract

The RNA chaperone protein Hfq is critical to the function of small, base pairing RNAs in many bacteria. In the past few years, structures and modeling of wild type Hfq and assays of various mutants have documented that the homohexameric Hfq ring can contact RNA at four sites (proximal face, distal face, rim and C-terminal tail) and that different RNAs bind to these sites in various configurations. These studies together with novel in vitro and in vivo experimental approaches are beginning to give mechanistic insights into how Hfq acts to promote small RNA-mRNA pairing and indicate that flexibility is integral to the Hfq role in RNA matchmaking.

Figure 1

Recent reports have added new details to the model of how Hfq binds to sRNAs and mRNAs and stimulates their interactions. (a) E. coli Hfq (teal for the proximal face and rim views and green for the distal face view) employs four solvent exposed surfaces to interact with RNA; sRNAs (red) have been found to contact the proximal and distal faces, rim and C-terminus, and mRNAs (blue) have been shown to contact the distal face, rim and C-terminus (not shown). Red and blue arrows denote sRNA and mRNA binding to Hfq, respectively. Some of the interactions occur concurrent with transcription of the RNAs, although Hfq binding to Rho-independent terminator of sRNAs most likely occurs after transcription termination, when the U-rich end of the terminator is accessible. Hfq binding to mRNAs and sRNAs is proposed to be in random order. Initial binding is likely to involve only a subset of subunits allowing for rapid displacement by other RNAs. (b) Many RNAs bind multiple surfaces, resulting in changes in RNA secondary structure and protection against RNase degradation, particularly for sRNAs. (c) The free surface(s) of Hfq not already bound to RNA interacts with the cognate RNA partner, positioning the unbound seed region of the sRNA in close proximity to the unbound complementary region of the mRNA. (d) Basic residues on the Hfq rim surface neutralize the negative charge of the RNAs and help to catalyze initial nucleation. (e) Hfq also promotes base pairing of the remaining complementary region. (f) Lower affinity of duplex RNA for Hfq causes free RNAs to compete off sRNA-mRNA pairs, allowing Hfq to serve as a matchmaker for another pair of RNAs. Lists of Class I and Class II sRNAs can be found in [25].

Figure 1

Recent reports have added new details to the model of how Hfq binds to sRNAs and mRNAs and stimulates their interactions. (a) E. coli Hfq (teal for the proximal face and rim views and green for the distal face view) employs four solvent exposed surfaces to interact with RNA; sRNAs (red) have been found to contact the proximal and distal faces, rim and C-terminus, and mRNAs (blue) have been shown to contact the distal face, rim and C-terminus (not shown). Red and blue arrows denote sRNA and mRNA binding to Hfq, respectively. Some of the interactions occur concurrent with transcription of the RNAs, although Hfq binding to Rho-independent terminator of sRNAs most likely occurs after transcription termination, when the U-rich end of the terminator is accessible. Hfq binding to mRNAs and sRNAs is proposed to be in random order. Initial binding is likely to involve only a subset of subunits allowing for rapid displacement by other RNAs. (b) Many RNAs bind multiple surfaces, resulting in changes in RNA secondary structure and protection against RNase degradation, particularly for sRNAs. (c) The free surface(s) of Hfq not already bound to RNA interacts with the cognate RNA partner, positioning the unbound seed region of the sRNA in close proximity to the unbound complementary region of the mRNA. (d) Basic residues on the Hfq rim surface neutralize the negative charge of the RNAs and help to catalyze initial nucleation. (e) Hfq also promotes base pairing of the remaining complementary region. (f) Lower affinity of duplex RNA for Hfq causes free RNAs to compete off sRNA-mRNA pairs, allowing Hfq to serve as a matchmaker for another pair of RNAs. Lists of Class I and Class II sRNAs can be found in [25].