PT  - JOURNAL ARTICLE
AU  - Syed Nabeel-Shah
AU  - Hyunmin Lee
AU  - Nujhat Ahmed
AU  - Edyta Marcon
AU  - Shaghayegh Farhangmehr
AU  - Shuye Pu
AU  - Giovanni L. Burke
AU  - Kanwal Ashraf
AU  - Hong Wei
AU  - Guoqing Zhong
AU  - Hua Tang
AU  - Jianyi Yang
AU  - Benjamin J. Blencowe
AU  - Zhaolei Zhang
AU  - Jack F. Greenblatt
TI  - SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and alters gene expression via direct interaction with host mRNAs
AID  - 10.1101/2020.10.23.342113
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.10.23.342113
4099  - http://biorxiv.org/content/early/2020/10/23/2020.10.23.342113.short
4100  - http://biorxiv.org/content/early/2020/10/23/2020.10.23.342113.full
AB  - The COVID-19 pandemic has caused over one million deaths thus far. There is an urgent need for the development of specific viral therapeutics and a vaccine. SARS-CoV-2 nucleocapsid (N) protein is highly expressed upon infection and is essential for viral replication, making it a promising target for both antiviral drug and vaccine development. Here, starting from a functional proteomics workflow, we initially catalogued the protein-protein interactions of 21 SARS-CoV-2 proteins in HEK293 cells, finding that the stress granule resident proteins G3BP1 and G3BP2 copurify with N with high specificity. We demonstrate that N protein expression in human cells sequesters G3BP1 and G3BP2 through its physical interaction with these proteins, attenuating stress granule (SG) formation. The ectopic expression of G3BP1 in N-expressing cells was sufficient to reverse this phenotype. Since N is an RNA-binding protein, we performed iCLIP-sequencing experiments in cells, with or without exposure to oxidative stress, to identify the host RNAs targeted by N. Our results indicate that SARS-CoV-2 N protein binds directly to thousands of mRNAs under both conditions. Like the G3BPs stress granule proteins, N was found to predominantly bind its target mRNAs in their 3’UTRs. RNA sequencing experiments indicated that expression of N results in wide-spread gene expression changes in both unstressed and oxidatively stressed cells. We suggest that N regulates host gene expression by both attenuating stress granules and binding directly to target mRNAs.Competing Interest StatementThe authors have declared no competing interest.