Skip to main content
NCBI home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2023 Jan 11;66(3):837–844. doi: 10.1007/s11426-022-1455-x

Simultaneous capture of ISG15 conjugating and deconjugating enzymes using a semi-synthetic ISG15-Dha probe

Chuntong Li 1,3, Tian Wang 1, Lujun Liang 1, Guochao Chu 1, Jiachen Zhang 1,2, Wei He 2,✉, Lei Liu 1,3,✉, Jinghong Li 1,3,✉
PMCID: PMC9840423  PMID: 36684644

Abstract

ISG15 is a ubiquitin-like (Ubl) protein attached to substrate proteins by ISG15 conjugating enzymes whose dysregulation is implicated in a multitude of disease processes, but the probing of these enzymes remains to be accomplished. Here, we describe the development of a new activity-based probe ISG15-Dha (dehydroalanine) through protein semi-synthesis. In vitro cross-linking and cell lysate proteomic profiling experiments showed that this probe can sequentially capture ISG15 conjugating enzymes including E1 enzyme UBA7, E2 enzyme UBE2L6, E3 enzyme HERC5, the previously known ISG15 deconjugating enzyme (USP18), as well as some other enzymes (USP5 and USP14) which we additionally confirmed to impart deISGylation activity. Collectively, ISG15-Dha provides a new tool that can simultaneously capture ISG15 conjugating and deconjugating enzymes for biochemical or pharmacological studies.

graphic file with name 11426_2022_1455_Fig1_HTML.jpg

Electronic Supplementary Material

Supplementary material is available for this article at 10.1007/s11426-022-1455-x and is accessible for authorized users.

Keywords: ISG15-Dha probe, semi-synthesis, activity based probe, proteomics, ISGylation

Supplementary Information

11426_2022_1455_MOESM1_ESM.docx (1.7MB, docx)

Supplementary material, approximately 1.71 MB.

Acknowledgements

This work was supported by the National Key Research & Development Program of China (2021YFA1200104, 2022YFC3401500), the National Natural Science Foundation of China (21621003, 22137005, 21971133, 22027807, 22034004, 92253302, 22227810), and the Tsinghua University Spring Breeze Fund (2020Z99CFY043, 2021Z99CFZ002). We thank Xiaolin Tian, Dingfei Yan, and Prof. Haiteng Deng in the MOE Key Laboratory of Bioinformatics of Tsinghua University for sample analysis. We thank Maoshen Sun for his help with the measurement of Michaelis constant.

Conflict of interest The authors declare no conflict of interest.

Footnotes

Supporting information The supporting information is available online at http://chem.scichina.com and http://link.springer.com/journal/11426. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.

Contributor Information

Wei He, Email: whe@mail.tsinghua.edu.cn.

Lei Liu, Email: lliu@mail.tsinghua.edu.cn.

Jinghong Li, Email: jhli@mail.tsinghua.edu.cn.

References

  • 1.McNab F, Mayer-Barber K, Sher A, Wack A, O’Garra A. Nat Rev Immunol. 2015;15:87–103. doi: 10.1038/nri3787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Perng YC, Lenschow DJ. Nat Rev Microbiol. 2018;16:423–439. doi: 10.1038/s41579-018-0020-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.van der Veen AG, Ploegh HL. Annu Rev Biochem. 2012;81:323–357. doi: 10.1146/annurev-biochem-093010-153308. [DOI] [PubMed] [Google Scholar]
  • 4.Cappadocia L, Lima CD. Chem Rev. 2018;118:889–918. doi: 10.1021/acs.chemrev.6b00737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Honke N, Shaabani N, Zhang DE, Hardt C, Lang KS. Cell Death Dis. 2016;7:e2444. doi: 10.1038/cddis.2016.326. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Jiménez Fernández D, Hess S, Knobeloch KP. Front Chem. 2019;7:923. doi: 10.3389/fchem.2019.00923. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, Schulz L, Widera M, Mehdipour AR, Tascher G, Geurink PP, Wilhelm A, van der Heden van Noort GJ, Ovaa H, Müller S, Knobeloch KP, Rajalingam K, Schulman BA, Cinatl J, Hummer G, Ciesek S, Dikic I. Nature. 2020;587:657–662. doi: 10.1038/s41586-020-2601-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Liu GQ, Lee JH, Parker ZM, Acharya D, Chiang JJ, van Gent M, Riedl W, Davis-Gardner ME, Wies E, Chiang C, Gack MU. Nat Microbiol. 2021;6:467–478. doi: 10.1038/s41564-021-00884-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Munnur D, Teo Q, Eggermont D, Lee HHY, Thery F, Ho J, van Leur SW, Ng WWS, Siu LYL, Beling A, Ploegh H, Pinto-Fernandez A, Damianou A, Kessler B, Impens F, Mok CKP, Sanyal S. Nat Immunol. 2021;22:1416–1427. doi: 10.1038/s41590-021-01035-8. [DOI] [PubMed] [Google Scholar]
  • 10.Zhang M, Li J, Yan H, Huang J, Wang F, Liu T, Zeng L, Zhou F. Front Cell Dev Biol. 2021;9:788410. doi: 10.3389/fcell.2021.788410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Lee BH, Lee MJ, Park S, Oh DC, Elsasser S, Chen PC, Gartner C, Dimova N, Hanna J, Gygi SP, Wilson SM, King RW, Finley D. Nature. 2010;467:179–184. doi: 10.1038/nature09299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Ekkebus R, van Kasteren SI, Kulathu Y, Scholten A, Berlin I, Geurink PP, de Jong A, Goerdayal S, Neefjes J, Heck AJR, Komander D, Ovaa H. J Am Chem Soc. 2013;135:2867–2870. doi: 10.1021/ja309802n. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Mulder MPC, Witting K, Berlin I, Pruneda JN, Wu KP, Chang JG, Merkx R, Bialas J, Groettrup M, Vertegaal ACO, Schulman BA, Komander D, Neefjes J, El Oualid F, Ovaa H. Nat Chem Biol. 2016;12:523–530. doi: 10.1038/nchembio.2084. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Mulder MPC, Merkx R, Witting KF, Hameed DS, El Atmioui D, Lelieveld L, Liebelt F, Neefjes J, Berlin I, Vertegaal ACO, Ovaa H. Angew Chem Int Ed. 2018;57:8958–8962. doi: 10.1002/anie.201803483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Pao KC, Wood NT, Knebel A, Rafie K, Stanley M, Mabbitt PD, Sundaramoorthy R, Hofmann K, van Aalten DMF, Virdee S. Nature. 2018;556:381–385. doi: 10.1038/s41586-018-0026-1. [DOI] [PubMed] [Google Scholar]
  • 16.Bi X, Pasunooti KK, Liu CF. Sci China Chem. 2018;61:251–265. doi: 10.1007/s11426-017-9122-3. [DOI] [Google Scholar]
  • 17.Si Y, Liang L, Tang S, Qi Y, Huang Y, Liu L. Sci China Chem. 2018;61:412–417. doi: 10.1007/s11426-017-9189-6. [DOI] [Google Scholar]
  • 18.Hameed DS, Sapmaz A, Burggraaff L, Amore A, Slingerland CJ, Westen GJP, Ovaa H. Angew Chem Int Ed. 2019;58:14477–14482. doi: 10.1002/anie.201906790. [DOI] [PubMed] [Google Scholar]
  • 19.Li YM, Li YT, Pan M, Kong XQ, Huang YC, Hong ZY, Liu L. Angew Chem Int Ed. 2014;53:2198–2202. doi: 10.1002/anie.201310010. [DOI] [PubMed] [Google Scholar]
  • 20.Qi YK, Si YY, Du SS, Liang J, Wang KW, Zheng JS. Sci China Chem. 2019;62:299–312. doi: 10.1007/s11426-018-9401-8. [DOI] [Google Scholar]
  • 21.Zuo C, Shi WW, Chen XX, Glatz M, Riedl B, Flamme I, Pook E, Wang J, Fang GM, Bierer D, Liu L. Sci China Chem. 2019;62:1371–1378. doi: 10.1007/s11426-019-9513-2. [DOI] [Google Scholar]
  • 22.Lu L, Guo Y, Wang T, Liang L, Zhao S, Wang F, Liu L. Sci China Chem. 2020;63:237–243. doi: 10.1007/s11426-019-9623-0. [DOI] [Google Scholar]
  • 23.Gui W, Shen S, Zhuang Z. J Am Chem Soc. 2020;142:19493–19501. doi: 10.1021/jacs.9b12426. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Sui X, Wang Y, Du YX, Liang LJ, Zheng Q, Li YM, Liu L. Chem Sci. 2020;11:12633–12646. doi: 10.1039/D0SC03295F. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Liang LJ, Chu GC, Qu Q, Zuo C, Mao J, Zheng Q, Chen J, Meng X, Jing Y, Deng H, Li YM, Liu L. Angew Chem Int Ed. 2021;60:17171–17177. doi: 10.1002/anie.202105870. [DOI] [PubMed] [Google Scholar]
  • 26.Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Angew Chem Int Ed, 2022, 61 [DOI] [PubMed]
  • 27.Li Y, Varejão N, Reverter D. Nat Commun. 2022;13:1819. doi: 10.1038/s41467-022-29485-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.James TW, Frias-Staheli N, Bacik JP, Levingston Macleod JM, Khajehpour M, García-Sastre A, Mark BL. Proc Natl Acad Sci USA. 2011;108:2222–2227. doi: 10.1073/pnas.1013388108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Loch CM, Cuccherini CL, Leach CA, Strickler JE. Mol Cell Proteomics. 2011;10:M110.002402. doi: 10.1074/mcp.M110.002402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Basters A, Geurink PP, Röcker A, Witting KF, Tadayon R, Hess S, Semrau MS, Storici P, Ovaa H, Knobeloch KP, Fritz G. Nat Struct Mol Biol. 2017;24:270–278. doi: 10.1038/nsmb.3371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Xin BT, Gan J, Fernandez DJ, Knobeloch KP, Geurink PP, Ovaa H. Org Biomol Chem. 2019;17:10148–10152. doi: 10.1039/C9OB02127B. [DOI] [PubMed] [Google Scholar]
  • 32.Clasman JR, Everett RK, Srinivasan K, Mesecar AD. Antiviral Res. 2020;174:104661. doi: 10.1016/j.antiviral.2019.104661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Ma C, Sacco MD, Xia Z, Lambrinidis G, Townsend JA, Hu Y, Meng X, Szeto T, Ba M, Zhang X, Gongora M, Zhang F, Marty MT, Xiang Y, Kolocouris A, Chen Y, Wang J. ACS Cent Sci. 2021;7:1245–1260. doi: 10.1021/acscentsci.1c00519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Wang T, Li C, Wang M, Zhang J, Zheng Q, Liang L, Chu G, Tian X, Deng H, He W, Liu L, Li J. Angew Chem Int Ed. 2022;61:e202206205. doi: 10.1002/anie.202206205. [DOI] [PubMed] [Google Scholar]
  • 35.Bernardes GJL, Chalker JM, Errey JC, Davis BG. J Am Chem Soc. 2008;130:5052–5053. doi: 10.1021/ja800800p. [DOI] [PubMed] [Google Scholar]
  • 36.Eid E, Boross GN, Sun H, Msallam M, Singh SK, Brik A. Bioconjugate Chem. 2020;31:889–894. doi: 10.1021/acs.bioconjchem.0c00026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Witting KF, van der Heden van Noort GJ, Kofoed C, Talavera Ormeño C, el Atmioui D, Mulder MPC, Ovaa H. Angew Chem Int Ed. 2018;57:14164–14168. doi: 10.1002/anie.201809232. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 38.Fairhead M, Howarth M. Methods Mol Biol. 2015;1266:171–184. doi: 10.1007/978-1-4939-2272-7_12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Dastur A, Beaudenon S, Kelley M, Krug RM, Huibregtse JM. J Biol Chem. 2006;281:4334–4338. doi: 10.1074/jbc.M512830200. [DOI] [PubMed] [Google Scholar]
  • 40.Dastur AR. Dissertation for the Doctoral Degree. Austin: The University of Texas at Austin; 2007. Characterization of herc5: The major ligase for isg15, an antiviral ubiquitin-like protein. [Google Scholar]
  • 41.Thery F, Martina L, Asselman C, Zhang Y, Vessely M, Repo H, Sedeyn K, Moschonas GD, Bredow C, Teo QW, Zhang J, Leandro K, Eggermont D, De Sutter D, Boucher K, Hochepied T, Festjens N, Callewaert N, Saelens X, Dermaut B, Knobeloch KP, Beling A, Sanyal S, Radoshevich L, Eyckerman S, Impens F. Nat Commun. 2021;12:5772. doi: 10.1038/s41467-021-26061-w. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 42.Catic A, Fiebiger E, Korbel GA, Blom D, Galardy PJ, Ploegh HL. PLoS One. 2007;2:e679. doi: 10.1371/journal.pone.0000679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 43.Potter JL, Narasimhan J, Mende-Mueller L, Haas AL. J Biol Chem. 1999;274:25061–25068. doi: 10.1074/jbc.274.35.25061. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

11426_2022_1455_MOESM1_ESM.docx (1.7MB, docx)

Supplementary material, approximately 1.71 MB.

Articles from Science China. Chemistry are provided here courtesy of Nature Publishing Group

RESOURCES