Physiologic RNA targets and refined sequence specificity of coronavirus EndoU

  1. David J. Barton6
  1. 1Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, School of Medicine, University of Colorado, Aurora 80045, Colorado, USA
  2. 2Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
  3. 3Institute of Virology and Immunology IVI, 3001 Bern and 3147 Mittelhausern, Switzerland
  4. 4Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
  5. 5Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, Colorado 80045, USA
  6. 6Department of Immunology and Microbiology, Program in Molecular Biology, School of Medicine, University of Colorado, Aurora, Colorado 80045, USA
  1. Corresponding author: David.Barton{at}CUAnschutz.edu

Abstract

Coronavirus EndoU inhibits dsRNA-activated antiviral responses; however, the physiologic RNA substrates of EndoU are unknown. In this study, we used mouse hepatitis virus (MHV)-infected bone marrow–derived macrophage (BMM) and cyclic phosphate cDNA sequencing to identify the RNA targets of EndoU. EndoU targeted viral RNA, cleaving the 3′ side of pyrimidines with a strong preference for UA and CA sequences (endoYA). EndoU-dependent cleavage was detected in every region of MHV RNA, from the 5′ NTR to the 3′ NTR, including transcriptional regulatory sequences (TRS). Cleavage at two CA dinucleotides immediately adjacent to the MHV poly(A) tail suggests a mechanism to suppress negative-strand RNA synthesis and the accumulation of viral dsRNA. MHV with EndoU (EndoUmut) or 2′–5′ phosphodiesterase (PDEmut) mutations provoked the activation of RNase L in BMM, with corresponding cleavage of RNAs by RNase L. The physiologic targets of EndoU are viral RNA templates required for negative-strand RNA synthesis and dsRNA accumulation. Coronavirus EndoU cleaves UA and CA sequences (endoYA) within viral (+) strand RNA to evade dsRNA-activated host responses.

Keywords

  • Received May 29, 2020.
  • Accepted September 12, 2020.

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