ORF3a-Mediated Incomplete Autophagy Facilitates Severe Acute Respiratory Syndrome Coronavirus-2 Replication

Yafei Qu; Xin Wang; Yunkai Zhu; Weili Wang; Yuyan Wang; Gaowei Hu; Chengrong Liu; Jingjiao Li; Shanhui Ren; Maggie Z X Xiao; Zhenshan Liu; Chunxia Wang; Joyce Fu; Yucai Zhang; Ping Li; Rong Zhang; Qiming Liang

doi:10.3389/fcell.2021.716208

ORF3a-Mediated Incomplete Autophagy Facilitates Severe Acute Respiratory Syndrome Coronavirus-2 Replication

Front Cell Dev Biol. 2021 Jul 27:9:716208. doi: 10.3389/fcell.2021.716208. eCollection 2021.

Authors

Yafei Qu¹, Xin Wang¹, Yunkai Zhu², Weili Wang¹, Yuyan Wang², Gaowei Hu², Chengrong Liu¹, Jingjiao Li¹, Shanhui Ren², Maggie Z X Xiao³, Zhenshan Liu¹, Chunxia Wang⁴, Joyce Fu⁵, Yucai Zhang⁴, Ping Li⁶, Rong Zhang², Qiming Liang^{1

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Affiliations

¹ Research Center of Translational Medicine, Shanghai Institute of Immunology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
² Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Biosafety Level 3 Laboratory, Fudan University, Shanghai, China.
³ Faculty of Medicine, University of Alberta, Edmonton, AB, Canada.
⁴ Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.
⁵ Department of Statistics, University of California, Riverside, Riverside, CA, United States.
⁶ Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Gongshang University, Hangzhou, China.
⁷ Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
⁸ State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China.

Abstract

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent for the coronavirus disease 2019 (COVID-19) pandemic and there is an urgent need to understand the cellular response to SARS-CoV-2 infection. Beclin 1 is an essential scaffold autophagy protein that forms two distinct subcomplexes with modulators Atg14 and UVRAG, responsible for autophagosome formation and maturation, respectively. In the present study, we found that SARS-CoV-2 infection triggers an incomplete autophagy response, elevated autophagosome formation but impaired autophagosome maturation, and declined autophagy by genetic knockout of essential autophagic genes reduces SARS-CoV-2 replication efficiency. By screening 26 viral proteins of SARS-CoV-2, we demonstrated that expression of ORF3a alone is sufficient to induce incomplete autophagy. Mechanistically, SARS-CoV-2 ORF3a interacts with autophagy regulator UVRAG to facilitate PI3KC3-C1 (Beclin-1-Vps34-Atg14) but selectively inhibit PI3KC3-C2 (Beclin-1-Vps34-UVRAG). Interestingly, although SARS-CoV ORF3a shares 72.7% amino acid identity with the SARS-CoV-2 ORF3a, the former had no effect on cellular autophagy response. Thus, our findings provide the mechanistic evidence of possible takeover of host autophagy machinery by ORF3a to facilitate SARS-CoV-2 replication and raise the possibility of targeting the autophagic pathway for the treatment of COVID-19.

Keywords: COVID-19; ORF3a; SARS-CoV-2; UVRAG; autophagy.