Super-resolution proximity labeling reveals anti-viral protein network and its structural changes against SARS-CoV-2 viral proteins
Yun-Bin Lee,
Minkyo Jung,
Jeesoo Kim,
Afandi Charles,
Wanda Christ,
Jiwoong Kang,
Myeong-Gyun Kang,
Chulhwan Kwak,
Jonas Klingström,
Anna Smed-Sörensen,
Jong-Seo Kim,
Ji Young Mun,
Hyun-Woo Rhee
Affiliations
Yun-Bin Lee
Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
Minkyo Jung
Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
Jeesoo Kim
School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea
Afandi Charles
Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
Wanda Christ
Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden
Jiwoong Kang
Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
Myeong-Gyun Kang
Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
Chulhwan Kwak
Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
Jonas Klingström
Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden; Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
Anna Smed-Sörensen
Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
Jong-Seo Kim
School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; Corresponding author
Ji Young Mun
Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Corresponding author
Hyun-Woo Rhee
Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Corresponding author
Summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in human cells by interacting with host factors following infection. To understand the virus and host interactome proximity, we introduce a super-resolution proximity labeling (SR-PL) method with a “plug-and-playable” PL enzyme, TurboID-GBP (GFP-binding nanobody protein), and we apply it for interactome mapping of SARS-CoV-2 ORF3a and membrane protein (M), which generates highly perturbed endoplasmic reticulum (ER) structures. Through SR-PL analysis of the biotinylated interactome, 224 and 272 peptides are robustly identified as ORF3a and M interactomes, respectively. Within the ORF3a interactome, RNF5 co-localizes with ORF3a and generates ubiquitin modifications of ORF3a that can be involved in protein degradation. We also observe that the SARS-CoV-2 infection rate is efficiently reduced by the overexpression of RNF5 in host cells. The interactome data obtained using the SR-PL method are presented at https://sarscov2.spatiomics.org. We hope that our method will contribute to revealing virus-host interactions of other viruses in an efficient manner.
