Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract

Horstmann, Nicola; Orans, Jillian; Valentin-Hansen, Poul; Shelburne III, Samuel A.; Brennan, Richard G.

doi:10.1093/nar/gks809

Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract

Journal Article · Sat Sep 08 00:00:00 EDT 2012 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gks809· OSTI ID:1903837

Horstmann, Nicola ^[1]; Orans, Jillian ^[2]; Valentin-Hansen, Poul ^[3]; Shelburne III, Samuel A. ^[4]; Brennan, Richard G. ^[2]

UT MD Anderson Cancer Center, Houston, TX (United States); OSTI
Duke University, Durham, NC (United States)
University of Southern Denmark, Odense (Denmark)
UT MD Anderson Cancer Center, Houston, TX (United States)

Hfq is a post-transcriptional regulator that plays a key role in bacterial gene expression by binding AU-rich sequences and A-tracts to facilitate the annealing of sRNAs to target mRNAs and to affect RNA stability. To understand how Hfq from the Gram-positive bacterium Staphylococcus aureus (Sa) binds A-tract RNA, we determined the crystal structure of an Sa Hfq–adenine oligoribonucleotide complex. The structure reveals a bipartite RNAbinding motif on the distal face that is composed of a purine nucleotide-specificity site (R-site) and a non-discriminating linker site (L-site). The (R–L)- binding motif, which is also utilized by Bacillus subtilis Hfq to bind (AG)₃A, differs from the (A–R–N) tripartite poly(A) RNA-binding motif of Escherichia coli Hfq whereby the Sa Hfq R-site strongly prefers adenosine, is more aromatic and permits deeper insertion of the adenine ring. R-site adenine-stacking residue Phe30, which is conserved among Grampositive bacterial Hfqs, and an altered conformation about β3 and β4 eliminate the adenosine-specificity site (A-site) and create the L-site. Binding studies show that Sa Hfq binds (AU)₃A≈(AG)₃A ≥ (AC)₃A > (AA)₃A and L-site residue Lys33 plays a significant role. The (R–L) motif is likely utilized by Hfqs from most Gram-positive bacteria to bind alternating (A–N)_n RNA.

View Accepted Manuscript (DOE)

Research Organization:: Duke University, Durham, NC (United States)

Sponsoring Organization:: American Heart Association; Danish Natural Science Research Council; National Institutes of Health (NIH); Robert A. Welch Foundation; USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division (MSE)

Grant/Contract Number:: AC02-05CH11231; AC03-76SF00098

OSTI ID:: 1903837

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 21 Vol. 40; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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