Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease

Frazier, Meredith N.; Wilson, Isha M.; Krahn, J.M.; Butay, Kevin John; Dillard, Lucas; Borgnia, Mario J.; Stanley, Robin E.

doi:10.1093/nar/gkac589

Cited by 19 publications

(36 citation statements)

References 53 publications

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“…X-ray crystallography and cryogenic electron microscopy (cryoEM) studies conducted throughout the SARS-CoV-2 pandemic have advanced our understanding of the substrate binding mechanisms employed by Nsp15 for both ssRNA and dsRNA (24)(25)(26). However, the precise molecular mechanisms underlying the recognition of poly(U) by Nsp15 remain unknown.…”

Section: Mainmentioning

confidence: 99%

Structural basis for polyuridine tract recognition by SARS-CoV-2 Nsp15

Ito,

Yang,

Zhou

et al. 2023

Preprint

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SARS-CoV-2 non-structural protein 15 (Nsp15) is critical for productive viral replication and evasion of host immunity. The uridine-specific endoribonuclease activity of Nsp15 mediates the cleavage of the polyuridine [poly(U)] tract of the negative-strand coronavirus genome to minimize the formation of dsRNA that activates the host antiviral interferon signaling. However, the molecular basis for the recognition and cleavage of the poly(U) tract by Nsp15 is incompletely understood. Here, we present cryogenic electron microscopy (cryoEM) structures of SARS-CoV-2 Nsp15 bound to viral replication intermediate dsRNA containing poly(U) tract at 2.7-3.3 Å resolution. The structures reveal one copy of dsRNA binds to the sidewall of an Nsp15 homohexamer, spanning three subunits in two distinct binding states. The target uracil is dislodged from the base-pairing of the dsRNA by amino acid residues W332 and M330 of Nsp15, and the dislodged base is entrapped at the endonuclease active site center. Up to 20 A/U base pairs are anchored on the Nsp15 hexamer, which explains the basis for a substantially shortened poly(U) sequence in the negative strand coronavirus genome compared to the long poly(A) tail in its positive strand. Our results provide mechanistic insights into the unique immune evasion strategy employed by coronavirus Nsp15.

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Section: Mainmentioning

confidence: 99%

Structural basis for polyuridine tract recognition by SARS-CoV-2 Nsp15

Ito,

Yang,

Zhou

et al. 2023

Preprint

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“…37 More recently, structures of Nsp15 bound to double-strand (ds)RNA show that Nsp15 binds and cleaves dsRNA through the contribution of three protomers, supporting the importance of a hexameric arrangement for binding to dsRNA substrates. 38…”

Section: Structural Insights Into Alphavirus Cell Entrymentioning

confidence: 99%

Positive‐strand RNA viruses—a Keystone Symposia report

Cable¹,

Denison

Kielian

et al. 2023

Annals of the New York Academy of Sciences

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Positive-strand RNA viruses have been the cause of several recent outbreaks and epidemics, including the Zika virus epidemic in 2015, the SARS outbreak in 2003, and the ongoing SARS-CoV-2 pandemic. On June 18-22, 2022, researchers focusing on positive-strand RNA viruses met for the Keystone Symposium "Positive-Strand RNA Viruses" to share the latest research in molecular and cell biology, virology, immunology, vaccinology, and antiviral drug development. This report presents concise summaries of the scientific discussions at the symposium.

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“…One of these, NSP15, a universally conserved endoU-ribonuclease, counteracts activation of all three pathways. It cleaves both ssRNA and dsRNA species 3’ of uridine bases to antagonize antiviral signaling 51•• , 52 , 53 , 54 , 55 , 56 . Localizing to ROs, apparently in transient association with RTCs, NSP15 may act as a gatekeeper to prevent escape of dsRNA from the protective surroundings of the ROs 51•• , 52 , 57 , 58 .…”

Section: Coronavirus Isr Antagonistsmentioning

confidence: 99%