TY - JOUR
T1 - Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract
AU - Horstmann, Nicola
AU - Orans, Jillian
AU - Valentin-Hansen, Poul
AU - Shelburne, Samuel A.
AU - Brennan, Richard G.
N1 - Funding Information:
The American Heart Association [09 GRNT2280109 to S.A.S.]; National Institutes of Health [K08 Career Development Award AI-064564 to S.A.S.]; the Danish Natural Science Research Council (to P.V.-H.); the Robert A. Welch Foundation [G-0040 to R.G.B.]; the authors also acknowledge the Advanced Light Source supported by the Director, Office of science, Office of Basic Energy Sciences, Material Sciences Division, of the US Department of Energy [contract No. DE-AC03-76SF00098], Lawrence Berkeley National Laboratory. Funding for open access charge: American Heart Association [09 GRNT2280109 to S.A.S.]; National Institutes of Health [K08 Career Development Award AI-064564 to S.A.S.]; the Danish Natural Science Research Council (to P.V.-H.) and Robert A. Welch Foundation [G-0040 to R.G.B.].
PY - 2012/11
Y1 - 2012/11
N2 - 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 RNA-binding 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 Gram-positive 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.
AB - 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 RNA-binding 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 Gram-positive 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.
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U2 - 10.1093/nar/gks809
DO - 10.1093/nar/gks809
M3 - Article
C2 - 22965117
AN - SCOPUS:84870625738
VL - 40
SP - 11023
EP - 11035
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 21
ER -