Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop

Biochemistry. 2024 May 21;63(10):1287-1296. doi: 10.1021/acs.biochem.3c00716. Epub 2024 May 10.

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshift stimulatory element (FSE) is necessary for programmed -1 ribosomal frameshifting (-1 PRF) and optimized viral efficacy. The FSE has an abundance of context-dependent alternate conformations, but two of the structures most crucial to -1 PRF are an attenuator hairpin and a three-stem H-type pseudoknot structure. A crystal structure of the pseudoknot alone features three RNA stems in a helically stacked linear structure, whereas a 6.9 Å cryo-EM structure including the upstream heptameric slippery site resulted in a bend between two stems. Our previous research alluded to an extended upstream multibranch loop that includes both the attenuator hairpin and the slippery site-a conformation not previously modeled. We aim to provide further context to the SARS-CoV-2 FSE via computational and medium resolution cryo-EM approaches, by presenting a 6.1 Å cryo-EM structure featuring a linear pseudoknot structure and a dynamic upstream multibranch loop.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • COVID-19 / virology
  • Cryoelectron Microscopy*
  • Frameshifting, Ribosomal*
  • Humans
  • Models, Molecular
  • Nucleic Acid Conformation*
  • RNA, Viral* / chemistry
  • RNA, Viral* / genetics
  • RNA, Viral* / metabolism
  • SARS-CoV-2* / chemistry
  • SARS-CoV-2* / genetics