Identification of putative binding interface of PI(3,5)P2 lipid on rice black-streaked dwarf virus (RBSDV) P10 protein

Haoqiu Liu; Xin Yi Peck; Yeu Khai Choong; Woei Shyuan Ng; Wilfried Engl; Palur Venkata Raghuvamsi; Ziqing Winston Zhao; Ganesh S Anand; Yijun Zhou; J Sivaraman; Qiufang Xu; Sek-Man Wong

doi:10.1016/j.virol.2022.03.010

Identification of putative binding interface of PI(3,5)P₂ lipid on rice black-streaked dwarf virus (RBSDV) P10 protein

Virology. 2022 May:570:81-95. doi: 10.1016/j.virol.2022.03.010. Epub 2022 Apr 1.

Authors

Affiliations

¹ Key Laboratory of Food Quality and Safety of Jiangsu Province, State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, PR China; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore; National University of Singapore Research Institute, Suzhou, Jiangsu, 215123, PR China. Electronic address: liuhaoqiu@u.nus.edu.
² Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore. Electronic address: e0036186@u.nus.edu.
³ Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore. Electronic address: yeukhai.choong@u.nus.edu.
⁴ Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore; Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore, 117557, Singapore. Electronic address: w.shyuan@u.nus.edu.
⁵ Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore; Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore, 117557, Singapore. Electronic address: chmwe@nus.edu.sg.
⁶ Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore. Electronic address: raghuvamsi@u.nus.edu.
⁷ Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore; Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore, 117557, Singapore; Mechanobiology Institute (MBI), National University of Singapore, Singapore, 117411, Singapore. Electronic address: zhaozw@nus.edu.sg.
⁸ Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore; Department of Chemistry, Eberly College of Science, Pennsylvania State University, Pennsylvania, 16802, United States. Electronic address: gsa5089@psu.edu.
⁹ Key Laboratory of Food Quality and Safety of Jiangsu Province, State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, PR China. Electronic address: yjzhou@jaas.ac.cn.
¹⁰ Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore. Electronic address: dbsjayar@nus.edu.sg.
¹¹ Key Laboratory of Food Quality and Safety of Jiangsu Province, State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, PR China. Electronic address: xuqiufang@jaas.ac.cn.
¹² Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore; National University of Singapore Research Institute, Suzhou, Jiangsu, 215123, PR China; Temasek Life Sciences Laboratory, Singapore, 117604, Singapore. Electronic address: dbswsm@nus.edu.sg.

PMID: 35390696
DOI: 10.1016/j.virol.2022.03.010

Abstract

Rice black-streaked dwarf virus (RBSDV) is an important reovirus that infects both plants and its transmission vector small brown planthopper, causing severe crop loss. High affinity binding between RBSDV P10 and PI(3,5)P₂ lipid layer was measured using biolayer interferometry (BLI). Subcellular co-localization of PI(3,5)P₂ and RBSDV P10 was observed on membranous structures in insect cells with stochastic optical reconstruction microscopy (STORM) imaging. Putative interacting sites of PI(3,5)P₂ lipid on a computational predicted RBSDV P10 structure were mapped to its "C-domain" (250-470 aa), using HDXMS data. The BLI and STORM results showed binding and co-localization of RBSDV P10, and PI(3,5)P₂ on vesicle-like membranous structures were corroborated with the prediction of the binding interface. Understanding the lipid binding sites on viral proteins will lead to developing strategies to block viral-lipid interaction and disrupt viral pathogenesis in insect vectors and to block virus transmission and achieve disease control of crops in the field.

Keywords: AlphaFold; HDXMS; Lipid binding; Phosphatidylinositol phosphates; STORM; Viral protein.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Hemiptera*
Lipids
Oryza*
Plant Diseases
Plant Viruses* / genetics
Reoviridae*

Substances

Lipids

Supplementary concepts

Rice black streaked dwarf virus