Spatial and Temporal Proteomics Reveals the Distinct Distributions and Dynamics of O-GlcNAcylated Proteins

Overview

Journal Cell Rep

Publisher Cell Press

Specialties Biology
Cell Biology
Molecular Biology

Date 2022 Jun 15

PMID 35705054

Authors

Senhan Xu

Ming Tong

Suttipong Suttapitugsakul

Ronghu Wu

Affiliations

Soon will be listed here.

Abstract

Protein O-GlcNAcylation plays critical roles in many cellular events, and its dysregulation is related to multiple diseases. Integrating bioorthogonal chemistry and multiplexed proteomics, we systematically and site specifically study the distributions and dynamics of protein O-GlcNAcylation in the nucleus and the cytoplasm of human cells. The results demonstrate that O-GlcNAcylated proteins with different functions have distinct distribution patterns. The distributions vary site specifically, indicating that different glycoforms of the same protein may have different distributions. Moreover, we comprehensively analyze the dynamics of O-GlcNAcylated and non-modified proteins in these two compartments, respectively, and the half-lives of glycoproteins in different compartments are markedly different, with the median half-life in the cytoplasm being much longer. In addition, glycoproteins in the nucleus are more dramatically stabilized than those in the cytoplasm under the O-GlcNAcase inhibition. The comprehensive spatial and temporal analyses of protein O-GlcNAcylation provide valuable information and advance our understanding of this important modification.

Citing Articles

Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.

Xiong Y, Lu Z, Shao Y, Meng P, Wang G, Zhou X Natl Sci Rev. 2024; 11(11):nwae341.

PMID: 39534244 PMC: 11556338. DOI: 10.1093/nsr/nwae341.

O-GlcNAcylation in ischemic diseases.

Shi R, He T, Lin M, Xu J, Gu J, Xu H Front Pharmacol. 2024; 15:1377235.

PMID: 38783961 PMC: 11113977. DOI: 10.3389/fphar.2024.1377235.

A Systematic Investigation of Proteoforms with N-Terminal Glycine and Their Dynamics Reveals Its Impacts on Protein Stability.

Xu S, Xu X, Wang Z, Wu R Angew Chem Int Ed Engl. 2023; 63(6):e202315286.

PMID: 38117010 PMC: 10981938. DOI: 10.1002/anie.202315286.

Glycobiology and proteomics: has mass spectrometry moved the field forward?.

Xu S, Wu R Expert Rev Proteomics. 2023; 20(12):303-307.

PMID: 37667879 PMC: 10841282. DOI: 10.1080/14789450.2023.2255748.

Systematic analysis of the impact of phosphorylation and O-GlcNAcylation on protein subcellular localization.

Xu S, Suttapitugsakul S, Tong M, Wu R Cell Rep. 2023; 42(7):112796.

PMID: 37453062 PMC: 10530397. DOI: 10.1016/j.celrep.2023.112796.

References

Boyce M, Carrico I, Ganguli A, Yu S, Hangauer M, Hubbard S . Metabolic cross-talk allows labeling of O-linked beta-N-acetylglucosamine-modified proteins via the N-acetylgalactosamine salvage pathway. Proc Natl Acad Sci U S A. 2011; 108(8):3141-6. PMC: 3044403. DOI: 10.1073/pnas.1010045108. View

Cvitkovic I, Jurica M . Spliceosome database: a tool for tracking components of the spliceosome. Nucleic Acids Res. 2012; 41(Database issue):D132-41. PMC: 3531166. DOI: 10.1093/nar/gks999. View

la Cour T, Kiemer L, Molgaard A, Gupta R, Skriver K, Brunak S . Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel. 2004; 17(6):527-36. DOI: 10.1093/protein/gzh062. View

Joiner C, Li H, Jiang J, Walker S . Structural characterization of the O-GlcNAc cycling enzymes: insights into substrate recognition and catalytic mechanisms. Curr Opin Struct Biol. 2019; 56:97-106. PMC: 6656603. DOI: 10.1016/j.sbi.2018.12.003. View

Tan W, Jiang P, Zhang W, Hu Z, Lin S, Chen L . Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation. Mol Cell. 2021; 81(9):1890-1904.e7. DOI: 10.1016/j.molcel.2021.02.009. View

Zhao L, Feng Z, Yang X, Liu J . The regulatory roles of O-GlcNAcylation in mitochondrial homeostasis and metabolic syndrome. Free Radic Res. 2016; 50(10):1080-1088. PMC: 5466075. DOI: 10.1080/10715762.2016.1239017. View

Carmo-Fonseca M . The rules and roles of nucleocytoplasmic shuttling proteins. FEBS Lett. 2001; 498(2-3):157-63. DOI: 10.1016/s0014-5793(01)02487-5. View

Elias J, Gygi S . Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007; 4(3):207-14. DOI: 10.1038/nmeth1019. View

Han J, Valdez J, Ho D, Lee C, Kim H, Wang X . Nuclear factor-erythroid-2 related transcription factor-1 (Nrf1) is regulated by O-GlcNAc transferase. Free Radic Biol Med. 2017; 110:196-205. DOI: 10.1016/j.freeradbiomed.2017.06.008. View

10.

Yuzwa S, Macauley M, Heinonen J, Shan X, Dennis R, He Y . A potent mechanism-inspired O-GlcNAcase inhibitor that blocks phosphorylation of tau in vivo. Nat Chem Biol. 2008; 4(8):483-90. DOI: 10.1038/nchembio.96. View

11.

Sletten E, Bertozzi C . Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl. 2009; 48(38):6974-98. PMC: 2864149. DOI: 10.1002/anie.200900942. View

12.

Larance M, Ahmad Y, Kirkwood K, Ly T, Lamond A . Global subcellular characterization of protein degradation using quantitative proteomics. Mol Cell Proteomics. 2012; 12(3):638-50. PMC: 3591657. DOI: 10.1074/mcp.M112.024547. View

13.

Lundberg E, Borner G . Spatial proteomics: a powerful discovery tool for cell biology. Nat Rev Mol Cell Biol. 2019; 20(5):285-302. DOI: 10.1038/s41580-018-0094-y. View

14.

Suttapitugsakul S, Tong M, Sun F, Wu R . Enhancing Comprehensive Analysis of Secreted Glycoproteins from Cultured Cells without Serum Starvation. Anal Chem. 2021; 93(4):2694-2705. PMC: 8034805. DOI: 10.1021/acs.analchem.0c05126. View

15.

Yang W, Kim J, Nam H, Ju J, Kim H, Kim Y . Modification of p53 with O-linked N-acetylglucosamine regulates p53 activity and stability. Nat Cell Biol. 2006; 8(10):1074-83. DOI: 10.1038/ncb1470. View

16.

Pandurangan A, Stahlhacke J, Oates M, Ben Smithers , Gough J . The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. Nucleic Acids Res. 2018; 47(D1):D490-D494. PMC: 6324026. DOI: 10.1093/nar/gky1130. View

17.

Elbatrawy A, Kim E, Nam G . O-GlcNAcase: Emerging Mechanism, Substrate Recognition and Small-Molecule Inhibitors. ChemMedChem. 2020; 15(14):1244-1257. DOI: 10.1002/cmdc.202000077. View

18.

Nabbi A, Riabowol K . Rapid Isolation of Nuclei from Cells In Vitro. Cold Spring Harb Protoc. 2015; 2015(8):769-72. DOI: 10.1101/pdb.prot083733. View

19.

Lange A, Mills R, Lange C, Stewart M, Devine S, Corbett A . Classical nuclear localization signals: definition, function, and interaction with importin alpha. J Biol Chem. 2006; 282(8):5101-5. PMC: 4502416. DOI: 10.1074/jbc.R600026200. View

20.

Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View