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Xie L, Bowman ME, Louie GV, Zhang C, Ardejani MS, Huang X, Chu Q, Donaldson CJ, Vaughan JM, Shan H, Powers ET, Kelly JW, Lyumkis D, Noel JP, Saghatelian A. Biochemistry and Protein Interactions of the CYREN Microprotein. Biochemistry 2023; 62:3050-3060. [PMID: 37813856 DOI: 10.1021/acs.biochem.3c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Over the past decade, advances in genomics have identified thousands of additional protein-coding small open reading frames (smORFs) missed by traditional gene finding approaches. These smORFs encode peptides and small proteins, commonly termed micropeptides or microproteins. Several of these newly discovered microproteins have biological functions and operate through interactions with proteins and protein complexes within the cell. CYREN1 is a characterized microprotein that regulates double-strand break repair in mammalian cells through interaction with Ku70/80 heterodimer. Ku70/80 binds to and stabilizes double-strand breaks and recruits the machinery needed for nonhomologous end join repair. In this study, we examined the biochemical properties of CYREN1 to better understand and explain its cellular protein interactions. Our findings support that CYREN1 is an intrinsically disordered microprotein and this disordered structure allows it to enriches several proteins, including a newly discovered interaction with SF3B1 via a distinct short linear motif (SLiMs) on CYREN1. Since many microproteins are predicted to be disordered, CYREN1 is an exemplar of how microproteins interact with other proteins and reveals an unknown scaffolding function of this microprotein that may link NHEJ and splicing.
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Affiliation(s)
- Lina Xie
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gordon V Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Cheng Zhang
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maziar S Ardejani
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xuemei Huang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States
| | - Qian Chu
- Department of Pharmacy, China Pharmaceutical University, Nanjing 210009, Jiangsu, China
| | - Cynthia J Donaldson
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joan M Vaughan
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Huanqi Shan
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Evan T Powers
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dimitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Saghatelian
- Clayton Foundation Peptide Biology Laboratories, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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Xiao H, Zhang M, Wu H, Wu J, Hu X, Pei X, Li D, Zhao L, Hua Q, Meng B, Zhang X, Peng L, Cheng X, Li Z, Yang W, Zhang Q, Zhang Y, Lu Y, Pan Z. CIRKIL Exacerbates Cardiac Ischemia/Reperfusion Injury by Interacting With Ku70. Circ Res 2022; 130:e3-e17. [PMID: 35105170 DOI: 10.1161/circresaha.121.318992] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Ku70 participates in several pathological processes through mediating repair of DNA double-strand breaks. Our previous study has identified a highly conserved long noncoding RNA cardiac ischemia reperfusion associated Ku70 interacting lncRNA (CIRKIL) that was upregulated in myocardial infarction. The study aims to investigate whether CIRKIL regulates myocardial ischemia/reperfusion (I/R) through binding to Ku70. METHODS CIRKIL transgenic and knockout mice were subjected to 45-minute ischemia and 24-hour reperfusion to establish myocardial I/R model. RNA pull-down and RNA immunoprecipitation assay were used to detect the interaction between CIRKIL and Ku70. RESULTS The expression of CIRKIL was increased in I/R myocardium and H2O2-treated cardiomyocytes. Overexpression of CIRKIL increased the expression of γH2A.X, a specific marker of DNA double-strand breaks and aggravated cardiomyocyte apoptosis, whereas knockdown of CIRKIL produced the opposite changes. Transgenic overexpression of CIRKIL aggravated cardiac dysfunction, enlarged infarct area, and worsened cardiomyocyte damage in I/R mice. Knockout of CIRKIL alleviated myocardial I/R injury. Mechanistically, CIRKIL directly bound to Ku70 to subsequently decrease nuclear translocation of Ku70 and impair DNA double-strand breaks repair. Concurrent overexpression of Ku70 mitigated CIRKIL overexpression-induced myocardial I/R injury. Furthermore, knockdown of human CIRKIL significantly suppressed cell damage induced by H2O2 in adult human ventricular cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes. CONCLUSIONS CIRKIL is a detrimental factor in I/R injury acting via regulating nuclear translocation of Ku70 and DNA double-strand breaks repair. Thus, CIRKIL might be considered as a novel molecular target for the treatment of cardiac conditions associated with I/R injury.
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Affiliation(s)
- Hongwen Xiao
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Mingyu Zhang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Hao Wu
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.).,College of Pharmacy and Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, P.R. China. (H.W., D.L., Q.H., Y.L.)
| | - Jiaxu Wu
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Xiaoxi Hu
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Xinyu Pei
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Danyang Li
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.).,College of Pharmacy and Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, P.R. China. (H.W., D.L., Q.H., Y.L.)
| | - Lu Zhao
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Qi Hua
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.).,College of Pharmacy and Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, P.R. China. (H.W., D.L., Q.H., Y.L.)
| | - Bo Meng
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Xiaowen Zhang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Lili Peng
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Xiaoling Cheng
- Department of Medicinal Chemistry, Harbin Medical University, P.R. China. (X.C.)
| | - Zhuoyun Li
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Wanqi Yang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Qi Zhang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Yang Zhang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
| | - Yanjie Lu
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.).,College of Pharmacy and Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, P.R. China. (H.W., D.L., Q.H., Y.L.)
| | - Zhenwei Pan
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, P.R. China. (H.X., M.Z., H.W., J.W., X.H., X.P., D.L., L.Z., Q.H., B.M., X.Z., L.P., Z.L., W.Y., Q.Z., Y.Z., Y.L., Z.P.)
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