| Content Provider |
World Health Organization (WHO)-Global Index Medicus |
| Author |
Mathews, David H. Wedekind, Joseph E. Aytenfisu, Asaminew Walter, Nils G. Spitale, Robert C. Liberman, Joseph A. Suddala, Krishna C. Belashov, Ivan A. Salim, Mohammad Chan, Dalen |
| Description |
Author Affiliation: Liberman JA ( Department of Biochemistry and Biophysics, and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642); Suddala KC ( Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109); Aytenfisu A ( Department of Biochemistry and Biophysics, and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642); Chan D ( Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697.); Belashov IA ( Department of Biochemistry and Biophysics, and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642); Salim M ( Department of Biochemistry and Biophysics, and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642); Mathews DH ( Department of Biochemistry and Biophysics, and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642); Spitale RC ( Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697.); Walter NG ( Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109); Wedekind JE ( Department of Biochemistry and Biophysics, and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642); |
| Abstract |
$PreQ_{1}-III$ riboswitches are newly identified RNA elements that control bacterial genes in response to $preQ_{1}$ (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or $HL_{out}-type$ pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the $preQ_{1}-III$ riboswitch aptamer forms a $HL_{out}-type$ pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, we determined the crystal structure of the class III $preQ_{1}$ riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. $PreQ_{1}$ binds tightly $(K_{D,app}$ 6.5 ± 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3′ RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that $preQ_{1}$ enhances P4 reorientation toward P1–P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking $(k_{dock}$ ∼0.6 $s^{−1})$ and undocking $(k_{undock}$ ∼1.1 $s^{−1}).$ Discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs. |
| ISSN |
00278424 |
| e-ISSN |
10916490 |
| Journal |
Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number |
27 |
| Volume Number |
112 |
| Language |
English |
| Publisher |
National Academy of Sciences |
| Publisher Date |
2015-07-01 |
| Publisher Place |
United States |
| Access Restriction |
Open |
| Subject Keyword |
Aptamers, Nucleotide Genetics RNA, Bacterial Ribosomes Riboswitch Chemistry Metabolism Binding Sites Clostridium Crystallography, X-Ray Kinetics Molecular Dynamics Simulation Molecular Sequence Data Nucleoside Q Pyrimidinones Pyrroles RNA Folding Thermodynamics Research Support, Non-U.S. Gov't Multidisciplinary |
| Content Type |
Text |
| Resource Type |
Article |
| Subject |
Multidisciplinary |
