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Cited by 2Ubiquitin and proteasome pathwaysImmunotherapy and Immune ResponsesT-cell and B-cell Immunology

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Major histocompatibility class II in murine antigen presenting cells is modified with a branched K63 and K11-linked ubiquitin chain

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Liu, Haiyin, Francis, Lauren, Dagley, Laura F., Cobbold, Simon A., Webb, Andrew I., Komander, David, Villadangos, Jose A., Mintern, Justine D.·2025·Scientific Reports
DOI 10.1038/s41598-025-25817-4

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Abstract

Major histocompatibility class II (MHC II) is critical for adaptive immunity. MHC II intracellular trafficking and degradation is regulated by ubiquitination. Poly-ubiquitination (Ub) of MHC II directs it away from the plasma membrane and is a critical determinant of MHC II turnover. The MHC II Ub chain has not been characterized. Here, we describe the poly-Ub chain associated with MHC II in primary murine antigen presenting cells; conventional dendritic cells (cDCs) and B cells. Analysis was conducted for endogenous murine MHC II isoforms H2-A and H2-E immunoprecipitated from primary cells. We show that ubiquitination of both I-A and I-E expressed by cDCs and B cells is dependent on the E3 Ub ligase MARCH1. Using mass spectrometry Ub chain linkage analysis and innovative Ub "clipping" proteomics we comprehensively defined the features of the MHC II poly-Ub chain. This revealed the MARCH1-dependent poly-Ub chain associated with MHC II is composed of a branched chain with K11 and K63 Ub chain linkages. This is the first description of the Ub chain linkages and architecture associated with MARCH1-mediated ubiquitination of MHC II in primary antigen presenting cells. This is important because it creates possibilities for manipulation of MHC II function in adaptive immunity.

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  1. Komander, D. & Rape, M. The Ubiquitin Code. in Annual Review of Biochemistry, pp 203–229. (2012). · DOI · Paper page
  2. Haakonsen, D. L. & Rape, M. Branching out: improved signaling by heterotypic ubiquitin chains. Trends Cell. Biol. 29, 704–716 (2019). · DOI
  3. French, M. E., Koehler, C. F. & Hunter, T. Emerging functions of branched ubiquitin chains. Cell. Discov. 7, 6 (2021). · DOI
  4. Liu, H., Mintern, J. D. & Villadangos, J. A. MARCH ligases in immunity. Curr. Opin. Immunol. 58, 38–43 (2019). · DOI
  5. Liu, H. et al. Ubiquitin ligase MARCH 8 cooperates with CD83 to control surface MHC II expression in thymic epithelium and CD4 T cell selection. J. Exp. Med. 213, 1695–1703 (2016). · DOI
  6. von Rohrscheidt, J. et al. Thymic CD4 T cell selection requires Attenuation of March8-mediated MHCII turnover in cortical epithelial cells through CD83. J. Exp. Med. 213, 1685–1694 (2016). · DOI
  7. Schriek, P. et al. Marginal zone B cells acquire dendritic cell functions by trogocytosis. Science 375, eabf7470 (2022). · DOI
  8. Bandola-Simon, J. & Roche, P. A. Regulation of MHC class II and CD86 expression by March-I in immunity and disease. Curr. Opin. Immunol. 82, 102325 (2023). · DOI
  9. Bannard, O. et al. Ubiquitin-mediated fluctuations in MHC class II facilitate efficient germinal center B cell responses. J. Exp. Med. 213, 993–1009 (2016). · DOI
  10. Wilson, K. R. et al. MARCH1-mediated ubiquitination of MHC II impacts the MHC I antigen presentation pathway. PloS One. 13, e0200540–e0200540 (2018). · DOI
  11. Wilson, K. R. et al. MHC class II ubiquitination regulates dendritic cell function and immunity. J. Immunol. 207, 2255–2264 (2021). · DOI
  12. Walseng, E. et al. Ubiquitination regulates MHC class II-peptide complex retention and degradation in dendritic cells. Proc. Natl. Acad. Sci. 107, 20465–20470 (2010). · DOI
  13. Cho, K. J., Walseng, E., Ishido, S. & Roche, P. A. Ubiquitination by March-I prevents MHC class II recycling and promotes MHC class II turnover in antigen-presenting cells. Proc. Natl. Acad. Sci. U S A. 112, 10449–10454 (2015). · DOI
  14. Ohmura-Hoshino, M. et al. Requirement of MARCH-I-Mediated MHC II ubiquitination for the maintenance of conventional dendritic cells. J. Immunol. 183, 6893–6897 (2009). · DOI
  15. Kim, H. J. et al. Ubiquitination of MHC class II by March-I regulates dendritic cell fitness. J. Immunol. 206, 494–504 (2021). · DOI
  16. Oh, J. et al. MARCH1-mediated MHCII ubiquitination promotes dendritic cell selection of natural regulatory T cells. J. Exp. Med. 210, 1069–1077 (2013). · DOI
  17. Liu, H. et al. Ubiquitination of MHC class II is required for development of regulatory but not conventional CD4(+) T cells. J. Immunol. 205, 1207–1216 (2020). · DOI
  18. Ishikawa, R., Kajikawa, M. & Ishido, S. Loss of MHC II ubiquitination inhibits the activation and differentiation of CD4 T cells. Int. Immunol. 26, 283–289 (2014). · DOI
  19. Mathis, D. J., Benoist, C., Williams, V. E. 2, Kanter, M., McDevitt, H. O. & nd, Several mechanisms can account for defective E alpha gene expression in different mouse haplotypes. Proc. Natl. Acad. Sci. U S A. 80, 273–277 (1983). · DOI
  20. Harton, J., Jin, L., Hahn, A. & Drake, J. Immunological Functions of the Membrane Proximal Region of MHC Class II Molecules. F1000Res 5 (2016). · DOI
  21. Villadangos, J. A., Riese, R. J., Peters, C., Chapman, H. A. & Ploegh, H. L. Degradation of mouse invariant chain: roles of cathepsins S and D and the influence of major histocompatibility complex polymorphism. J. Exp. Med. 186, 549–560 (1997). · DOI
  22. Liu, H. et al. Ubiquitin-like protein 3 (UBL3) is required for MARCH ubiquitination of major histocompatibility complex class II and CD86. Nat. Commun. 13, 1934 (2022). · DOI
  23. Dodd, R. B. et al. Solution structure of the kaposi’s sarcoma-associated herpesvirus K3 N-terminal domain reveals a novel E2-binding C4HC3-type RING domain. J. Biol. Chem. 279, 53840–53847 (2004). · DOI
  24. Duncan, L. M. et al. Lysine-63-linked ubiquitination is required for endolysosomal degradation of class I molecules. EMBO J. 25, 1635–1645 (2006). · DOI
  25. Boname, J. M. et al. Efficient internalization of MHC I requires lysine-11 and lysine-63 mixed linkage Polyubiquitin chains. Traffic 11, 210–220 (2010). · DOI
  26. Katherine, E. et al. The Mechanism of Linkage-Specific Ubiquitin Chain Elongation by a Single-Subunit E2. Cell 144, 769–781 (2011). · DOI
  27. Steiner, Q. G. et al. In vivo transformation of mouse conventional CD8α + dendritic cells leads to progressive multisystem histiocytosis. Blood 111, 2073–2082 (2008). · DOI
  28. Hospenthal, M. K., Mevissen, T. E. T. & Komander, D. Deubiquitinase-based analysis of ubiquitin chain architecture using ubiquitin chain restriction (UbiCRest). Nat. Protoc. 10, 349–361 (2015). · DOI
  29. Kirkpatrick, D. S. et al. Quantitative analysis of in vitro ubiquitinated Cyclin B1 reveals complex chain topology. Nat. Cell Biol. 8, 700–710 (2006). · DOI
  30. Shin, J. S. et al. Surface expression of MHC class II in dendritic cells is controlled by regulated ubiquitination. Nature 444, 115–118 (2006). · DOI
  31. van Niel, G. et al. Dendritic cells regulate exposure of MHC class II at their plasma membrane by oligoubiquitination. Immunity 25, 885–894 (2006). · DOI
  32. Fuertes Marraco, S. A. et al. Novel murine dendritic cell lines: a powerful auxiliary tool for dendritic cell research. Front. Immunol. 3, 331–331 (2012). · DOI
  33. Ma, J. K., Platt, M. Y., Eastham-Anderson, J., Shin, J. S. & Mellman, I. MHC class II distribution in dendritic cells and B cells is determined by ubiquitin chain length. Proc. Natl. Acad. Sci. 109, 8820–8827 (2012). · DOI
  34. Alix, E. et al. The tumour suppressor TMEM127 is a Nedd4-Family E3 ligase adaptor required by Salmonella sted to ubiquitinate and degrade MHC class II molecules. Cell. Host Microbe. 28, 54–68 (2020). e57. · DOI
  35. Meyer, H. J. & Rape, M. Enhanced protein degradation by branched ubiquitin chains. Cell 157, 910–921 (2014). · DOI
  36. Ohtake, F., Saeki, Y., Ishido, S., Kanno, J. & Tanaka, K. The K48-K63 branched ubiquitin chain regulates NF-kappaB signaling. Mol. Cell. 64, 251–266 (2016). · DOI
  37. Matsuki, Y. et al. Novel regulation of MHC class II function in B cells. EMBO J. 26, 846–854 (2007). · DOI
  38. Kontgen, F., Suss, G., Stewart, C., Steinmetz, M. & Bluethmann, H. Targeted disruption of the MHC class II Aa gene in C57BL/6 mice. Int. Immunol. 5, 957–964 (1993). · DOI
  39. Doench, J. G. et al. Optimized SgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016). · DOI · Paper page
  40. Brinkman, E. K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 42, e168 (2014). · DOI · Paper page
  41. Wisniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample Preparation method for proteome analysis. Nat. Methods. 6, 359–362 (2009). · DOI · Paper page
  42. Schilling, B. et al. Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol. Cell. Proteom. 11, 202–214 (2012). · DOI
  43. Perez-Riverol, Y. et al. The PRIDE database at 20 years: 2025 update. Nucleic Acids Res. 53, D543–D553 (2025). · DOI

Metadata

Authors
Liu, H., Francis, L., Dagley, L. F., Cobbold, S. A., Webb, A. I., Komander, D., Villadangos, J. A., & Mintern, J. D.
Affiliations
The University of Melbourne (AU)
Corresponding author
Mintern, Justine D.
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2025-11-25
Volume
15
Issue
1
Pages
41884-41884
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-025-25817-4
OpenAlex
W4416666706
Cited by
2
References
1
Citations by year
2026: 2
FWCI
0.60
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by-nc-nd)
  • Research Square (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by-nc-nd)
Funders
  • NHMRC, Australia
  • Australian Research Council
  • Human Frontier Science Program
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
  • Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
  • Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
Keywords
MHC class II, ubiquitination, polyubiquitin chains, K63-linked ubiquitin, branched ubiquitin chains, MARCH1, E3 ubiquitin ligase, antigen-presenting cells, myeloid dendritic cells, B cells, I-A, I-E, adaptive immunity
MeSH terms
Animals, Antigen-Presenting Cells, Histocompatibility Antigens Class II, B-Lymphocytes, Dendritic Cells, Mice, Inbred C57BL, Ubiquitin, Ubiquitin-Protein Ligases, Mice, Ubiquitination

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