Abstract
We have solved the X-ray crystal structure of the RNA chaperone protein Hfq from the alpha-proteobacterium Caulobacter crescentus to 2.15-Å resolution, resolving the conserved core of the protein and the entire C-terminal domain (CTD). The structure reveals that the CTD of neighboring hexamers pack in crystal contacts, and that the acidic residues at the C-terminal tip of the protein interact with positive residues on the rim of Hfq, as has been recently proposed for a mechanism of modulating RNA binding. De novo computational models predict a similar docking of the acidic tip residues against the core of Hfq. We also show that C. crescentus Hfq has sRNA binding and RNA annealing activities and is capable of facilitating the annealing of certain Escherichia coli sRNA:mRNA pairs in vivo. Finally, we describe how the Hfq CTD and its acidic tip residues provide a mechanism to modulate annealing activity and substrate specificity in various bacteria.
Highlights
We have solved the X-ray crystal structure of the RNA chaperone protein Hfq from the alpha-proteobacterium Caulobacter crescentus to 2.15-Å resolution, resolving the conserved core of the protein and the entire C-terminal domain (CTD)
The CTD of Ec Hfq limits its annealing of minimal RNAs, which we propose is due to competition between the CTD and RNA binding to the basic patches on the rim of the protein [26]
As there are currently no small noncoding RNAs (sRNAs)-mRNA regulatory pathways in C. crescentus known to rely on Hfq, we examined whether Cc Hfq could be transferred into E. coli to facilitate interactions between sRNAmRNA pairs in vivo
Summary
We have solved the X-ray crystal structure of the RNA chaperone protein Hfq from the alpha-proteobacterium Caulobacter crescentus to 2.15-Å resolution, resolving the conserved core of the protein and the entire C-terminal domain (CTD). | | | | Hfq Caulobacter sRNA RNA–protein interaction natively unstructured protein that polyuridine recognition by the proximal pore is strongly conserved [7,8,9,10] and likely to be maintained in most Hfq homologs, whereas the more variable distal face may have different RNA-binding preferences in different species [8, 11,12,13]. Most RNA binding and annealing data are derived from observations with Escherichia coli Hfq (Ec Hfq hereinafter) and closely related homologs [5] These studies have identified the distal and proximal faces and a basic patch on the circumferential rim as surfaces that engage RNA. Sequence and structural analyses of bacterial and archaeal Hfq proteins suggest
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