title: Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: Nicola
authors.initials: N
authors.lastname: Horstmann
authors.forename: Jillian
authors.initials: J
authors.lastname: Orans
authors.forename: Poul
authors.initials: P
authors.lastname: Valentin-Hansen
authors.forename: Samuel A
authors.initials: SA
authors.lastname: Shelburne
authors.forename: Richard G
authors.initials: RG
authors.lastname: Brennan
mesh_terms: D020816:Amino Acid Motifs; D006094:Gram-Positive Bacteria; D035001:Host Factor 1 Protein / Q000737:chemistry* / Q000378:metabolism; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D011061:Poly A / Q000737:chemistry*; D011485:Protein Binding; D011687:Purines / Q000737:chemistry / Q000378:metabolism; D012313:RNA / Q000737:chemistry*; D013211:Staphylococcus aureus
chemical_list: D035001:Host Factor 1 Protein; D011687:Purines; D011061:Poly A; D012313:RNA; D008239:Lysine