Featured interactome of homocysteine-inducible endoplasmic reticulum protein uncovers novel binding partners in response to ER stress

Rui Su; Jialing Yin; Xiaolan Ruan; Yanxi Chen; Pin Wan; Zhen Luo

doi:10.1016/j.csbj.2023.09.006

Featured interactome of homocysteine-inducible endoplasmic reticulum protein uncovers novel binding partners in response to ER stress

Comput Struct Biotechnol J. 2023 Sep 9:21:4478-4487. doi: 10.1016/j.csbj.2023.09.006. eCollection 2023.

Authors

Rui Su^{1

2}, Jialing Yin³, Xiaolan Ruan³, Yanxi Chen³, Pin Wan^{4

5}, Zhen Luo^{3

5

6}

Affiliations

¹ Henan Key Laboratory of Immunology and Targeted Drug, Xinxiang Medical University, Xinxiang 453003, China.
² Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China.
³ Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China.
⁴ Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan 430072, China.
⁵ Foshan Institute of Medical Microbiology, Foshan 528315, China.
⁶ Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China.

Abstract

Homocysteine-inducible endoplasmic reticulum protein (HERP) is an endoplasmic reticulum (ER)-resident protein and important for the adaptation of cellular protein homeostasis by ER-associated degradation (ERAD) system. HERP interactors are critical for cellular viability and the reaction to ER stress. To explore the exact mechanisms by which HERP performed the biological functions, we conducted an interaction analysis of HERP protein in HeLa cells by co-immunoprecipitation (Co-IP) and liquid chromatography-mass spectrometer (LC-MS)/MS coupled with label-free quantification (LFQ). Among the interactome results, 123 proteins significantly interacted with HERP, which leads to numerous biological processes including protein import into nucleus, ubiquitin-dependent ERAD pathway, negative regulation of apoptotic process, and protein transport from ER, along with multiple pathways including several diseases, protein processing in ER, fatty acid metabolism, and steroid biosynthesis. Furthermore, we selected several prey proteins from the interactome data and confirmed that HERP interacted with ancient ubiquitous protein 1 (AUP1), Fas-associated factor family member 2 (FAF2), tripartite motif containing 47 (TRIM47), acyl-CoA synthetase long-chain family member 3 (ACSL3), sequestosome 1 (SQSTM1), and poly(rC) binding protein 2 (PCBP2) by Co-IP and confocal microscopy experiments, respectively. Moreover, the expression and location of several interacted proteins were obviously altered in response to ER stress induced by Thapsigargin stimulation and Enterovirus 71 infection. In conclusion, our findings revealed that the vital proteins interacted with HERP to mediate signaling transduction, thus providing novel clues for the mechanisms of HERP associated with ERAD and metabolism in response to ER stress under physiological and pathological conditions.

Keywords: Bioinformatic analysis; ER stress; HERP; Protein interactome.