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Lai LB, Tanimoto A, Lai SM, Chen WY, Marathe IA, Westhof E, Wysocki VH, Gopalan V. A novel double kink-turn module in euryarchaeal RNase P RNAs. Nucleic Acids Res 2017; 45:7432-7440. [PMID: 28525600 PMCID: PMC5499556 DOI: 10.1093/nar/gkx388] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/25/2017] [Indexed: 01/18/2023] Open
Abstract
RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns. Mutagenesis of each of the putative K-turns singly or in combination decreased the number of bound L7Ae copies, and either eliminated or changed the L7Ae footprint on the mutant RPRs. In addition, our results support an unprecedented ‘double K-turn’ module in type A and type M archaeal RPR variants.
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Affiliation(s)
- Lien B Lai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Akiko Tanimoto
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Stella M Lai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Wen-Yi Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ila A Marathe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Westhof
- Université de Strasbourg, Centre National de la Recherche Scientifique, Architecture et Réactivité de l'ARN, UPR9002, F-67084, Strasbourg, France
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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Abstract
Electrophoretic mobility shift assay, or EMSA, is a well-established technique for separating macromolecules under native conditions based on a combination of shape, size, and charge. The use of EMSA can provide both general and specific information concerning the interaction between two macromolecules such as RNA and protein. Here we present a protocol for the practical use of EMSA to assess protein-RNA interactions and ribonucleoprotein (RNP) assembly. The conceptual framework of the assay is discussed along with a step-by-step procedure for the binding of archaeal ribosomal protein L7Ae to a box C/D sRNA. Potential pitfalls and common mistakes to avoid are emphasized with technical tips and a notes section. This protocol provides a starting point for the design and implementation of EMSA in studying a wide variety of RNP complexes.
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