Evolutionary study and structural basis of proton sensing by Mus GPR4 and Xenopus GPR4

Xin Wen; Pan Shang; Haidi Chen; Lulu Guo; Naikang Rong; Xiaoyu Jiang; Xuan Li; Junyan Liu; Gongming Yang; Jiacheng Zhang; Kongkai Zhu; Qingbiao Meng; Xuefei He; Zhihai Wang; Zili Liu; Haoran Cheng; Yilin Zheng; Bifei Zhang; Jiaojiao Pang; Zhaoqian Liu; Peng Xiao; Yuguo Chen; Lunxu Liu; Fengming Luo; Xiao Yu; Fan Yi; Pengju Zhang; Fan Yang; Cheng Deng; Jin-Peng Sun

doi:10.1016/j.cell.2024.12.001

Evolutionary study and structural basis of proton sensing by Mus GPR4 and Xenopus GPR4

Cell. 2024 Dec 31:S0092-8674(24)01380-1. doi: 10.1016/j.cell.2024.12.001. Online ahead of print.

Authors

Xin Wen¹, Pan Shang², Haidi Chen³, Lulu Guo⁴, Naikang Rong², Xiaoyu Jiang², Xuan Li⁵, Junyan Liu⁶, Gongming Yang², Jiacheng Zhang⁷, Kongkai Zhu⁴, Qingbiao Meng², Xuefei He⁸, Zhihai Wang², Zili Liu², Haoran Cheng², Yilin Zheng², Bifei Zhang², Jiaojiao Pang⁹, Zhaoqian Liu¹⁰, Peng Xiao², Yuguo Chen⁹, Lunxu Liu¹¹, Fengming Luo⁸, Xiao Yu⁵, Fan Yi¹², Pengju Zhang¹³, Fan Yang¹⁴, Cheng Deng¹⁵, Jin-Peng Sun¹⁶

Affiliations

¹ Key Laboratory Experimental Teratology of the Ministry of Education, New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China; NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, Advanced Medical Research Institute, Shandong University, Jinan, China.
² Key Laboratory Experimental Teratology of the Ministry of Education, New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
³ Department of Respiratory and Critical Care Medicine, Center for High Altitude Medicine, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China.
⁴ NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, Advanced Medical Research Institute, Shandong University, Jinan, China.
⁵ Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
⁶ Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.
⁷ State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
⁸ Department of Respiratory and Critical Care Medicine, Center for High Altitude Medicine, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
⁹ Emergency Department, Qilu Hospital, Shandong University, Jinan 250012, China.
¹⁰ Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha 410008, China.
¹¹ Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China.
¹² Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China. Electronic address: fanyi@sdu.edu.cn.
¹³ Key Laboratory Experimental Teratology of the Ministry of Education, New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China. Electronic address: zhpj@sdu.edu.cn.
¹⁴ Key Laboratory Experimental Teratology of the Ministry of Education, New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China; NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, Advanced Medical Research Institute, Shandong University, Jinan, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China; Department of Physiology and Pathophysiology, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China. Electronic address: yangfan1357@163.com.
¹⁵ Department of Respiratory and Critical Care Medicine, Center for High Altitude Medicine, Institutes for Systems Genetics, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China. Electronic address: dengcheng@wchscu.cn.
¹⁶ Key Laboratory Experimental Teratology of the Ministry of Education, New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China; NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, Advanced Medical Research Institute, Shandong University, Jinan, China; Department of Physiology and Pathophysiology, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China. Electronic address: sunjinpeng@sdu.edu.cn.

PMID: 39753131
DOI: 10.1016/j.cell.2024.12.001

Abstract

Animals have evolved pH-sensing membrane receptors, such as G-protein-coupled receptor 4 (GPR4), to monitor pH changes related to their physiology and generate adaptive reactions. However, the evolutionary trajectory and structural mechanism of proton sensing by GPR4 remain unresolved. Here, we observed a positive correlation between the optimal pH of GPR4 activity and the blood pH range across different species. By solving 7-cryoelectron microscopy (cryo-EM) structures of Xenopus tropicalis GPR4 (xtGPR4) and Mus musculus GPR4 (mmGPR4) under varying pH conditions, we identified that protonation of H^ECL2-45.47 and H^7.36 enabled polar network establishment and tighter association between the extracellular loop 2 (ECL2) and 7 transmembrane (7TM) domain, as well as a conserved propagating path, which are common mechanisms underlying protonation-induced GPR4 activation across different species. Moreover, protonation of distinct extracellular H^ECL2-45.41 contributed to the more acidic optimal pH range of xtGPR4. Overall, our study revealed common and distinct mechanisms of proton sensing by GPR4, from a structural, functional, and evolutionary perspective.

Keywords: GPCR; GPR4; cryo-EM; evolution; proton sensing.