title: The RNA binding protein Hfq interacts specifically with tRNAs.
abstract: Hfq is an RNA binding protein that has been studied extensively for its role in the biology of small noncoding RNAs (ncRNAs) in bacteria, where it facilitates post-transcriptional gene regulation during stress responses. We show that Hfq also binds with high specificity and nanomolar affinity to tRNAs despite their lack of a canonical A/U rich single-stranded sequence. This affinity is comparable to that of Hfq for its validated ncRNA targets. Two sites on tRNAs are protected by Hfq binding, one on the D-stem and the other on the T-stem. Mutational analysis and competitive binding experiments indicate that Hfq uses its proximal surface (also called the L4 face) to bind tRNAs, the same surface that interacts with ncRNAs but a site distinct from where poly(A) oligonucleotides bind. hfq knockout strains are known to have broad pleiotropic phenotypes, but none of them are easily explained by or imply a role for tRNA binding. We show that hfq deletion strains have a previously unrecognized phenotype associated with mistranslation and significantly reduced translational fidelity. We infer that tRNA binding and reduced fidelity are linked by a role for Hfq in tRNA modification.
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
authors.forename: Taewoo
authors.initials: T
authors.lastname: Lee
authors.forename: Andrew L
authors.initials: AL
authors.lastname: Feig
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D048168:Escherichia coli K12 / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D005798:Genes, Bacterial; D035001:Host Factor 1 Protein / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D012343:RNA, Transfer