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

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) bin...

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Bibliographic Details
Published in:Nucleic acids research 2012-11, Vol.40 (21), p.11023-11035
Main Authors: Horstmann, Nicola, Orans, Jillian, Valentin-Hansen, Poul, Shelburne, 3rd, Samuel A, Brennan, Richard G
Format: Article
Language:English
Subjects:
Adenine
Adenosine
Amino Acid Motifs
Aromatics
Bacillus subtilis
BASIC BIOLOGICAL SCIENCES
Conformation
Crystal structure
Escherichia coli
Gene expression
Gram-Positive Bacteria
Host Factor 1 Protein - chemistry
Host Factor 1 Protein - metabolism
Lysine - chemistry
Models, Molecular
Poly A - chemistry
Post-transcription
Protein Binding
purines
Purines - chemistry
Purines - metabolism
RNA
RNA - chemistry
Staphylococcus aureus
Structural Biology
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Summary: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)(3)A, 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)(3)A ≈ (AG)(3)A ≥ (AC)(3)A > (AA)(3)A 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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gks809