The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography

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dc.contributor.authorRoman, Christina
dc.contributor.authorLewicka, Anna
dc.contributor.authorKoirala, Deepak
dc.contributor.authorLi, Nan-Sheng
dc.contributor.authorPiccirilli, Joseph A.
dc.date.accessioned2022-08-23T14:48:34Z
dc.date.available2022-08-23T14:48:34Z
dc.date.issued2021-07-30
dc.description.abstractThe programmed −1 ribosomal frameshifting element (PFSE) of SARS-CoV-2 is a well conserved structured RNA found in all coronaviruses’ genomes. By adopting a pseudoknot structure in the presence of the ribosome, the PFSE promotes a ribosomal frameshifting event near the stop codon of the first open reading frame Orf1a during translation of the polyprotein pp1a. Frameshifting results in continuation of pp1a via a new open reading frame, Orf1b, that produces the longer pp1ab polyprotein. Polyproteins pp1a and pp1ab produce nonstructural proteins NSPs 1–10 and NSPs 1–16, respectively, which contribute vital functions during the viral life cycle and must be present in the proper stoichiometry. Both drugs and sequence alterations that affect the stability of the −1 programmed ribosomal frameshifting element disrupt the stoichiometry of the NSPs produced, which compromise viral replication. For this reason, the −1 programmed frameshifting element is considered a promising drug target. Using chaperone assisted RNA crystallography, we successfully crystallized and solved the three-dimensional structure of the PFSE. We observe a three-stem H-type pseudoknot structure with the three stems stacked in a vertical orientation stabilized by two triple base pairs at the stem 1/stem 2 and stem 1/stem 3 junctions. This structure provides a new conformation of PFSE distinct from the bent conformations inferred from midresolution cryo-EM models and provides a high-resolution framework for mechanistic investigations and structure-based drug design.en_US
dc.description.sponsorshipWe thank S. Yang (Case Western Reserve University) for assistance with analysis of preliminary small angle X-ray scattering data for several PFSE constructs. We are grateful to lab members M. Moore, H. Reese. and M. Disare for insightful comments and critical review of the manuscript. We thank P. Rice, E. Ozkan, B. Dickinson, and J. Staley for valuable insights and discussion throughout the course of this project. This work was supported by NIH/NIGMS Grant GM102489. C.R. was supported by the HHMI Gilliam Fellowship and NIH Chemical Biology Training Grant T32GM008720. This work also used the Advanced Photon Source on the Northeastern Collaborative Access Team beamline, 24-ID-C and 24-ID-E (GM124165), a Pilatus detector (RR029205), and an Eiger detector (OD021527) at the APS (DE-AC02-06CH11357). We are very grateful for the support from the APS NE-CAT Beamline hosts.en_US
dc.description.urihttps://pubs.acs.org/doi/10.1021/acschembio.1c00324en_US
dc.format.extent13 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m2vyok-o7i3
dc.identifier.citationChristina Roman, Anna Lewicka, Deepak Koirala, Nan-Sheng Li, and Joseph A. Piccirilli. The SARS-CoV-2 Programmed −1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography. ACS Chemical Biology 2021 16 (8), 1469-1481. DOI: 10.1021/acschembio.1c00324en_US
dc.identifier.urihttps://doi.org/10.1021/acschembio.1c00324
dc.identifier.urihttp://hdl.handle.net/11603/25553
dc.language.isoen_USen_US
dc.publisherACSen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Chemistry & Biochemistry Department Collection
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.en_US
dc.rightsAttribution 4.0 International (CC BY 4.0)*
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/*
dc.titleThe SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallographyen_US
dc.typeTexten_US
dcterms.creatorhttps://orcid.org/0000-0001-6424-3173en_US

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