Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) demonstrate unique abilities for continuous self-renewal and differentiation into all types of somatic cells. Understanding the mechanisms controlling these properties will facilitate an effective and safe introduction of ESCs and iPSCs into cell therapy. Recent data have underscored the importance of proteostasis in the maintenance of ESC function. The present review focuses on the role of ubiquitin-proteasome system (UPS), a key member of proteostasis network, in the regulation of pluripotency and differentiation of ESCs and iPSCs.
Similar content being viewed by others
REFERENCES
Abu-Dawud, R., Graffmann, N., Ferber, S., Wruck, W., and Adjaye, J., Pluripotent stem cells: induction and self-renewal, Philos. Trans. R. Soc. London, B, 2018, vol. 373, p. 20170213. https://doi.org/10.1098/rstb.2017.0213
Al Mamun, M.M., Khan, M.R., Zhu, Y., Zhang, Y., Zhou, S., Xu, R., Bukhari, I., Thorne, R.F., Li, J., and Zhang, X.D., Stub1 maintains proteostasis of master transcription factors in embryonic stem cells, Cell Rep., 2022, vol. 39, p. 110919. https://doi.org/10.1016/j.celrep.2022.110919
Alekseenko, Z., Dias, J.M., Adler, A.F., Kozhevniko-va, M., van Lunteren, J.A., Nolbrant, S., Jeggari, A., Vasylovska, S., Yoshitake, T., and Kehr, J., Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery, Nat. Commun., 2022, vol. 13, p. 1. https://doi.org/10.1038/s41467-022-30777-8
Babaie, Y., Herwig, R., Greber, B., Brink, T.C., Wruck, W., Groth, D., Lehrach, H., Burdon, T., and Adjaye, J., Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells, Stem Cells, 2007, vol. 25, p. 500. https://doi.org/10.1634/stemcells.2006-0426
Baharvand, H., Hajheidari, M., Ashtiani, S.K., and Salekdeh, G.H., Proteomic signature of human embryonic stem cells, Proteomics, 2006, vol. 6, p. 3544. https://doi.org/10.1002/pmic.200500844
Bai, M., Zhao, X., Sahara, K., Ohte, Y., Hirano, Y., Kaneko, T., Yashiroda, H., and Murata, S., Assembly mechanisms of specialized core particles of the proteasome, Biomolecules, 2014, vol. 4, p. 662. https://doi.org/10.3390/biom4030662
Beckwith, R., Estrin, E., Worden, E.J., and Martin, A., Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase, Nat. Struct. Mol. Biol., 2013, vol. 20, p. 1164. https://doi.org/10.1038/nsmb.2659
Behbahan, I.S., Duan, Y., Lam, A., Khoobyari, S., Ma, X., Ahuja, T.P., and Zern, M.A., New approaches in the differentiation of human embryonic stem cells and induced pluripotent stem cells toward hepatocytes, Stem Cell Rev. Rep., 2011, vol. 7, p. 748. https://doi.org/10.1007/s12015-010-9216-4
Bernstein, B.E., Mikkelsen, T.S., Xie, X., Kamal, M., Huebert, D.J., Cuff, J., Fry, B., Meissner, A., Wernig, M., and Plath, K., A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, 2006, vol. 125, p. 315. https://doi.org/10.1016/j.cell.2006.02.041
Biancotti, J.C., Narwani, K., Buehler, N., Mandefro, B., Golan-Lev, T., Yanuka, O., Clark, A., Hill, D., Benvenisty, N., and Lavon, N., Human embryonic stem cells as models for aneuploid chromosomal syndromes, Stem Cells, 2010, vol. 28, p. 1530. https://doi.org/10.1002/stem.483
Blondelle, J., Shapiro, P., Domenighetti, A.A., and Lange, S., Cullin E3 ligase activity is required for myoblast differentiation, J. Mol. Biol., 2017, vol. 429, p. 1045. https://doi.org/10.1016/j.jmb.2017.02.012
Buckley, S.M., Aranda-Orgilles, B., Strikoudis, A., Apostolou, E., Loizou, E., Moran-Crusio, K., Farnsworth, C.L., Koller, A.A., Dasgupta, R., Silva, J.C., Stadtfeld, M., Hochedlinger, K., Chen, E.I., and Aifantis, I., Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system, Cell Stem Cell, 2012, vol. 11, p. 783. https://doi.org/10.1016/j.stem.2012.09.011
Budenholzer, L., Cheng, C.L., Li, Y., and Hochstrasser, M., Proteasome structure and assembly, J. Mol. Biol., 2017, vol. 429, p. 3500. https://doi.org/10.1016/j.jmb.2017.05.027
Bustos, F., Segarra-Fas, A., Chaugule, V.K., Brandenburg, L., Branigan, E., Toth, R., Macartney, T., Knebel, A., Hay, R.T., and Walden, H., RNF12 X-linked intellectual disability mutations disrupt E3 ligase activity and neural differentiation, Cell Rep., 2018, vol. 23, p. 1599. https://doi.org/10.1016/j.celrep.2018.04.022
Cao, F., Lin, S., Xie, X., Ray, P., Patel, M., Zhang, X., Drukker, M., Dylla, S.J., Connolly, A.J., and Chen, X., In vivo visualization of embryonic stem cell survival, proliferation, and migration after cardiac delivery, Circulation, 2006, vol. 113, p. 1005. https://doi.org/10.1161/CIRCULATIONAHA.105.588954
Cascio, P., Hilton, C., Kisselev, A.F., Rock, K.L., and Goldberg, A.L., 26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide, EMBO J., 2001, vol. 20, p. 2357. https://doi.org/10.1093/emboj/20.10.2357
Choi, J. and Baek, K.H., Cellular functions of stem cell factors mediated by the ubiquitin-proteasome system, Cell. Mol. Life Sci., 2018, vol. 75, p. 1947. https://doi.org/10.1007/s00018-018-2770-7
Ciechanover, A. and Kwon, Y.T., Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies, Exp. Mol. Med., 2015, vol. 47, p. e147. https://doi.org/10.1038/emm.2014.117
Cui, Z., Hwang, S.M., and Gomes, A.V., Identification of the immunoproteasome as a novel regulator of skeletal muscle differentiation, Mol. Cell. Biol., 2014, vol. 34, p. 96. https://doi.org/10.1128/MCB.00622-13
Dahlmann, B., Proteasomes, Essays Biochem., 2005, vol. 41, p. 31. https://doi.org/10.1042/EB0410031
de Napoles, M., Mermoud, J.E., Wakao, R., Tang, Y.A., Endoh, M., Appanah, R., Nesterova, T.B., Silva, J., Otte, A.P., and Vidal, M., Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation, Dev. Cell, 2004, vol. 7, p. 663. https://doi.org/10.1016/j.devcel.2004.10.005
Diefenbacher, M.E., Chakraborty, A., Blake, S.M., Mitter, R., Popov, N., Eilers, M., and Behrens, A., Usp28 counteracts Fbw7 in intestinal homeostasis and cancer, Cancer Res., 2015, vol. 75, p. 1181. https://doi.org/10.1158/0008-5472.CAN-14-1726
Dieudonne, F.-X., Sévère, N., Biosse-Duplan, M., Weng, J.-J., Su, Y., and Marie, P.J., Promotion of osteoblast differentiation in mesenchymal cells through Cbl-mediated control of STAT5 activity, Stem Cells, 2013, vol. 31, p. 1340. https://doi.org/10.1002/stem.1380
Drews, O. and Taegtmeyer, H., Targeting the ubiquitin-proteasome system in heart disease: the basis for new therapeutic strategies, Antioxid. Redox. Signal., 2014, vol. 21, p. 2322. https://doi.org/10.1089/ars.2013.5823
Du, Z., He, F., Yu, Z., Bowerman, B., and Bao, Z., E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis, Dev. Biol., 2015, vol. 398, p. 267. https://doi.org/10.1016/j.ydbio.2014.12.009
Dutta, D., Sharma, V., Mutsuddi, M., and Mukherjee, A., Regulation of Notch signaling by E3 ubiquitin ligases, FEBS J., 2021, vol. 289, p. 937. https://doi.org/10.1111/febs.15792
Endoh, M., Endo, T.A., Endoh, T., Fujimura, Y.-I., Ohara, O., Toyoda, T., Otte, A.P., Okano, M., Brockdorff, N., and Vidal, M., Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity, Development, 2008, vol. 135, p. 1513. https://doi.org/10.1242/dev.014340
Fabre, B., Lambour, T., Garrigues, L., Amalric, F., Vigneron, N., Menneteau, T., Stella, A., Monsarrat, B., Van den Eynde, B., and Burlet-Schiltz, O., Deciphering preferential interactions within supramolecular protein complexes: the proteasome case, Mol. Syst. Biol., 2015, vol. 11, p. 771. https://doi.org/10.15252/msb.20145497
Fang, L., Zhang, L., Wei, W., Jin, X., Wang, P., Tong, Y., Li, J., Du, J.X., and Wong, J., A methylation-phosphorylation switch determines Sox2 stability and function in ESC maintenance or differentiation, Mol. Cell, 2014, vol. 55, p. 537. https://doi.org/10.1016/j.molcel.2014.06.018
Finley, D., Tanaka, K., Mann, C., Feldmann, H., Hochstrasser, M., Vierstra, R., Johnston, S., Hampton, R., Haber, J., McCusker, J., Silver, P., Frontali, L., Thorsness, P., Varshavsky, A., Byers, B., et al., Unified nomenclature for subunits of the Saccharomyces cerevisiae proteasome regulatory particle, Trends Biochem. Sci., 1998, vol. 23, p. 244. https://doi.org/10.1016/s0968-0004(98)01222-5
Fort, P., Kajava, A.V., Delsuc, F., and Coux, O., Evolution of proteasome regulators in eukaryotes, Genome Biol. Evol., 2015, vol. 7, p. 1363. https://doi.org/10.1093/gbe/evv068
Fu, X., The immunogenicity of cells derived from induced pluripotent stem cells, Cell. Mol. Immunol., 2014, vol. 11, p. 14. https://doi.org/10.1038/cmi.2013.60
Fuchs, G., Shema, E., Vesterman, R., Kotler, E., Wolchinsky, Z., Wilder, S., Golomb, L., Pribluda, A., Zhang, F., Haj-Yahya, M., Feldmesser, E., Brik, A., Yu, X., Hanna, J., Aberdam, D., Domany, E., and Oren, M., RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation, Mol. Cell, 2012, vol. 46, p. 662. https://doi.org/10.1016/j.molcel.2012.05.023
Fujikawa, T., Oh, S.-H., Pi, L., Hatch, H.M., Shupe, T., and Petersen, B.E., Teratoma formation leads to failure of treatment for type I diabetes using embryonic stem cell-derived insulin-producing cells. Am. J. Pathol, 2005., vol. 166, p. 1781. https://doi.org/10.1016/S0002-9440(10)62488-1
Gao, C., Xiao, G., and Hu, J., Regulation of Wnt/β-catenin signaling by posttranslational modifications. Cell Biosci., 2014, vol. 4, p. 13. https://doi.org/10.1186/2045-3701-4-13
Gao, J., Buckley, S.M., Cimmino, L., Guillamot, M., Strikoudis, A., Cang, Y., Goff, S.P., and Aifantis, I., The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis, Elife, 2015, vol. 4, p. e07539. https://doi.org/10.7554/eLife.07539
Glickman, M.H., Rubin, D.M., Coux, O., Wefes, I., Pfeifer, G., Cjeka, Z., Baumeister, W., Fried, V.A., and Finley, D., A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3, Cell, 1998, vol. 94, p. 615. https://doi.org/10.1016/s0092-8674(00)81603-7
Gordeev, M., Bakhmet, E., and Tomilin, A., Pluripotency dynamics during embryogenesis and in cell culture, Russ. J. Dev. Biol., 2021, vol. 52, no. 6, p. 379. https://doi.org/10.1134/S1062360421060059
Groll, M., Bajorek, M., Kohler, A., Moroder, L., Rubin, D.M., Huber, R., Glickman, M.H., and Finley, D., A gated channel into the proteasome core particle, Nat. Struct. Biol., 2000, vol. 7, p. 1062. https://doi.org/10.1038/80992
Groll, M., Bochtler, M., Brandstetter, H., Clausen, T., and Huber, R., Molecular machines for protein degradation, ChemBioChem, 2005, vol. 6, p. 222. https://doi.org/10.1002/cbic.200400313
Groll, M., Ditzel, L., Lowe, J., Stock, D., Bochtler, M., Bartunik, H.D., and Huber, R., Structure of 20S proteasome from yeast at 2.4 A resolution, Nature, 1997, vol. 386, p. 463. https://doi.org/10.1038/386463a0
Hatakeyama, S., Ubiquitin-mediated regulation of JAK-STAT signaling in embryonic stem cells, JAKSTAT, 2012, vol. 1, p. 168. https://doi.org/10.4161/jkst.21560
Hayashi, K., de Sousa Lopes, S.M.C., Tang, F., and Surani, M.A., Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states, Cell Stem Cell, 2008, vol. 3, p. 391. https://doi.org/10.1016/j.stem.2008.07.027
He, M., Zhou, Z., Shah, A.A., Zou, H., Tao, J., Chen, Q., and Wan, Y., The emerging role of deubiquitinating enzymes in genomic integrity, diseases, and therapeutics, Cell Biosci., 2016, vol. 6, p. 62. https://doi.org/10.1186/s13578-016-0127-1
Hernebring, M., Brolen, G., Aguilaniu, H., Semb, H., and Nystrom, T., Elimination of damaged proteins during differentiation of embryonic stem cells, Proc. Natl. Acad. Sci. U. S. A., 2006, vol. 103, p. 7700. https://doi.org/10.1073/pnas.0510944103
Hernebring, M., Fredriksson, A., Liljevald, M., Cvijovic, M., Norrman, K., Wiseman, J., Semb, H., and Nystrom, T., Removal of damaged proteins during ES cell fate specification requires the proteasome activator PA28, Sci. Rep., 2013, vol. 3, p. 1381. https://doi.org/10.1038/srep01381
Hershko, A. and Ciechanover, A., The ubiquitin system for protein degradation, Annu. Rev. Biochem., 1992, vol. 61, p. 761. https://doi.org/10.1146/annurev.bi.61.070192.003553
Hershko, A. and Ciechanover, A., The ubiquitin system, Annu. Rev. Biochem., 1998, vol. 67, p. 425. https://doi.org/10.1146/annurev.biochem.67.1.425
Inoue, D., Aihara, H., Sato, T., Mizusaki, H., Doiguchi, M., Higashi, M., Imamura, Y., Yoneda, M., Miyanishi, T., and Fujii, S., Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation, Sci. Rep., 2015, vol. 5, p. 16567. https://doi.org/10.1038/srep16567
Jiang, T.X., Zhao, M., and Qiu, X.B., Substrate receptors of proteasomes, Biol. Rev. Camb. Philos. Soc., 2018, vol. 93, p. 1765. https://doi.org/10.1111/brv.12419
Jing, X., Infante, J., Nachtman, R.G., and Jurecic, R., E3 ligase FLRF (Rnf41) regulates differentiation of hematopoietic progenitors by governing steady-state levels of cytokine and retinoic acid receptors, Exp. Hematol., 2008, vol. 36, p. 1110. https://doi.org/10.1016/j.exphem.2008.04.001
Kammerl, I.E., Dann, A., Mossina, A., Brech, D., Lukas, C., Vosyka, O., Nathan, P., Conlon, T.M., Wagner, D.E., and Overkleeft, H.S., Impairment of immunoproteasome function by cigarette smoke and in chronic obstructive pulmonary disease, Am. J. Respir. Crit. Care Med., 2016, vol. 193, p. 1230. https://doi.org/10.1164/rccm.201506-1122OC
Kim, S.-H., Kim, M.O., Cho, Y.-Y., Yao, K., Kim, D.J., Jeong, C.-H., Yu, D.H., Bae, K.B., Cho, E.J., and Jung, S.K., ERK1 phosphorylates Nanog to regulate protein stability and stem cell self-renewal, Stem Cell Res., 2014, vol. 13, p. 1. https://doi.org/10.1016/j.scr.2014.04.001
Konstantinova, I.M., Tsimokha, A.S., and Mittenberg, A.G., Role of proteasomes in cellular regulation, Int. Rev. Cell. Mol. Biol., 2008, vol. 267, p. 59. https://doi.org/10.1016/S1937-6448(08)00602-3
Li, S., Xiao, F., Zhang, J., Sun, X., Wang, H., Zeng, Y., Hu, J., Tang, F., Gu, J., Zhao, Y., Jin, Y., and Liao, B., Disruption of OCT4 ubiquitination increases OCT4 protein stability and ASH2L-B-mediated H3K4 methylation promoting pluripotency acquisition, Stem Cell Rep., 2018, vol. 11, p. 973. https://doi.org/10.1016/j.stemcr.2018.09.001
Liao, B., Zhong ,X., Xu, H., Xiao, F., Fang, Z., Gu, J., Chen, Y., Zhao, Y., and Jin, Y. Itch, an E3 ligase of Oct4, is required for embryonic stem cell self-renewal and pluripotency induction. J. Cell. Physiol., 2013., vol. 228, p. 1443. https://doi.org/10.1002/jcp.24297
Liu, X., Yao, Y., Ding, H., Han, C., Chen, Y., Zhang, Y., Wang, C., Zhang, X., Zhang, Y., and Zhai, Y., USP21 de-ubiquitylates Nanog to regulate protein stability and stem cell pluripotency, Signal Transduct. Target. Ther., 2016, vol. 1, p. 16024. https://doi.org/10.1038/sigtrans.2016.24
Liu, Y.-J., Nakamura, T., and Nakano, T., Essential role of DPPA3 for chromatin condensation in mouse oocytogenesis, Biol. Reprod., 2012, vol. 86, p. 40. https://doi.org/10.1095/biolreprod.111.095018
Liu, Y., Xu, H.W., Wang, L., Li, S.Y., Zhao, C.J., Hao, J., Li, Q.Y., Zhao, T.T., Wu, W., and Wang, Y., Human embryonic stem cell-derived retinal pigment epithelium transplants as a potential treatment for wet age-related macular degeneration, Cell Discov., 2018, vol. 4, p. 50. https://doi.org/10.1038/s41421-018-0053-y
Mattout, A. and Meshorer, E., Chromatin plasticity and genome organization in pluripotent embryonic stem cells, Curr. Opin. Cell Biol., 2010, vol. 22, p. 334. https://doi.org/10.1016/j.ceb.2010.02.001
Meiners, S., Keller, I.E., Semren, N., and Caniard, A., Regulation of the proteasome: evaluating the lung proteasome as a new therapeutic target, Antioxid. Redox. Signal., 2014, vol. 21, p. 2364. https://doi.org/10.1089/ars.2013.5798
Meiners, S., Ludwig, A., Stangl, V., and Stangl, K., Proteasome inhibitors: poisons and remedies, Med. Res. Rev., 2008, vol. 28, p. 309. https://doi.org/10.1002/med.20111
Meshorer, E. and Misteli, T., Chromatin in pluripotent embryonic stem cells and differentiation, Nat. Rev. Mol. Cell Biol., 2006, vol. 7, p. 540. https://doi.org/10.1038/nrm1938
Miyazono, K., TGF-β signaling by Smad proteins, Cytokine Growth Factor Rev., 2000, vol. 11, p. 15. https://doi.org/10.1016/s1359-6101(99)00025-8
Morozov, A.V. and Karpov, V.L., Biological consequences of structural and functional proteasome diversity, Heliyon, 2018, vol. 4, p. e00894. https://doi.org/10.1016/j.heliyon.2018.e00894
Murata, S., Takahama, Y., and Tanaka, K., Thymoproteasome: probable role in generating positively selecting peptides, Curr. Opin. Immunol., 2008, vol. 20, p. 192. https://doi.org/10.1016/j.coi.2008.03.002
Nakagawa, T., Kajitani, T., Togo, S., Masuko, N., Ohdan, H., Hishikawa, Y., Koji, T., Matsuyama, T., Ikura, T., and Muramatsu, M., Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation, Genes Dev., 2008, vol. 22, p. 37. https://doi.org/10.1101/gad.1609708
Nakamura, T., Arai, Y., Umehara, H., Masuhara, M., Kimura, T., Taniguchi, H., Sekimoto, T., Ikawa, M., Yoneda, Y., and Okabe, M., PGC7/Stella protects against DNA demethylation in early embryogenesis, Nat. Cell Biol., 2007, vol. 9, p. 64. https://doi.org/10.1038/ncb1519
Nakamura, T., Liu, Y.-J., Nakashima, H., Umehara, H., Inoue, K., Matoba, S., Tachibana, M., Ogura, A., Shinkai, Y., and Nakano, T., PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos, Nature, 2012, vol. 486, p. 415. https://doi.org/10.1038/nature11093
Nandi, D., Tahiliani, P., Kumar, A., and Chandu, D., The ubiquitin-proteasome system, J. Biosci., 2006, vol. 31, p. 137. https://doi.org/10.1007/BF02705243
Ng, H.-H. and Surani, M.A., The transcriptional and signalling networks of pluripotency, Nat. Cell Biol., 2011, vol. 13, p. 490. https://doi.org/10.1038/ncb0511-490
Nguyen, D.T.T., Richter, D., Michel, G., Mitschka, S., Kolanus, W., Cuevas, E., and Wulczyn, F.G., The ubiquitin ligase LIN41/TRIM71 targets p53 to antagonize cell death and differentiation pathways during stem cell differentiation, Cell Death Differ., 2017, vol. 24, p. 1063. https://doi.org/10.1038/cdd.2017.54
Noormohammadi, A., Calculli, G., Gutierrez-Garcia, R., Khodakarami, A., Koyuncu, S., and Vilchez, D., Mechanisms of protein homeostasis (proteostasis) maintain stem cell identity in mammalian pluripotent stem cells, Cell. Mol. Life Sci., 2018, vol. 75, p. 275. https://doi.org/10.1007/s00018-017-2602-1
Okita, Y., Matsumoto, A., Yumimoto, K., Isoshita, R., and Nakayama, K.I., Increased efficiency in the generation of induced pluripotent stem cells by F bxw7 ablation, Genes Cells, 2012, vol. 17, p. 768. https://doi.org/10.1111/j.1365-2443.2012.01626.x
Okita, Y. and Nakayama, K.I., UPS delivers pluripotency, Cell Stem Cell, 2012, vol. 11, p. 728. https://doi.org/10.1016/j.stem.2012.11.009
Okumura, F., Matsunaga, Y., Katayama, Y., Nakayama, K.I., and Hatakeyama, S., TRIM8 modulates STAT3 activity through negative regulation of PIAS3, J. Cell Sci., 2010, vol. 123, p. 2238. https://doi.org/10.1242/jcs.068981
Osmulski, P.A., Hochstrasser, M., and Gaczynska, M., A tetrahedral transition state at the active sites of the 20S proteasome is coupled to opening of the alpha-ring channel, Structure, 2009, vol. 17, p. 1137. https://doi.org/10.1016/j.str.2009.06.011
Pak, C., Danko, T., Zhang, Y., Aoto, J., Anderson, G., Maxeiner, S., Yi, F., Wernig, M., and Südhof, T.C., Human neuropsychiatric disease modeling using conditional deletion reveals synaptic transmission defects caused by heterozygous mutations in NRXN1, Cell Stem Cell, 2015, vol. 17, p. 316. https://doi.org/10.1016/j.stem.2015.07.017
Pan, J., Deng, Q., Jiang, C., Wang, X., Niu, T., Li, H., Chen, T., Jin, J., Pan, W., Cai, X., Yang, X., Lu, M., Xiao, J., and Wang, P., USP37 directly deubiquitinates and stabilizes c-Myc in lung cancer, Oncogene, 2015, vol. 34, p. 3957. https://doi.org/10.1038/onc.2014.327
Pickering, A.M. and Davies, K.J., Degradation of damaged proteins: the main function of the 20S proteasome, Prog. Mol. Biol. Transl. Sci., 2012, vol. 109, p. 227. https://doi.org/10.1016/B978-0-12-397863-9.00006-7
Qian, M.X., Pang, Y., Liu, C.H., Haratake, K., Du, B.Y., Ji, D.Y., Wang, G.F., Zhu, Q.Q., Song, W., Yu, Y., Zhang, X.X., Huang, H.T., Miao, S., Chen, L.B., Zhang, Z.H., Liang, Y.N., et al., Acetylation-mediated proteasomal degradation of core histones during DNA repair and spermatogenesis, Cell, 2013, vol. 153, p. 1012. https://doi.org/10.1016/j.cell.2013.04.032
Rezania, A., Bruin, J.E., Arora, P., Rubin, A., Batushansky, I., Asadi, A., O’dwyer, S., Quiskamp, N., Mojibian, M., and Albrecht, T., Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells, Nat. Biotechnol., 2014, vol. 32, p. 1121. https://doi.org/10.1038/nbt.3033
Sang, H., Wang, D., Zhao, S., Zhang, J., Zhang, Y., Xu, J., Chen, X., Nie, Y., Zhang, K., and Zhang, S., Dppa3 is critical for Lin28a-regulated ES cells naïve–primed state conversion, J. Mol. Cell Biol., 2019, vol. 11, p. 474. https://doi.org/10.1093/jmcb/mjy069
Saretzki, G., Armstrong, L., Leake, A., Lako, M., and von Zglinicki, T., Stress defense in murine embryonic stem cells is superior to that of various differentiated murine cells, Stem Cells, 2004, vol. 22, p. 962. https://doi.org/10.1634/stemcells.22-6-962
Saric, T., Chang, S.-C., Hattori, A., York, I.A., Mar-kant, S., Rock, K.L., Tsujimoto, M., and Goldberg, A.L., An IFN-γ-induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I-presented peptides, Nat. Immunol., 2002, vol. 3, p. 1169. https://doi.org/10.1038/ni859
Sato, N., Sanjuan, I.M., Heke, M., Uchida, M., Naef, F., and Brivanlou, A.H., Molecular signature of human embryonic stem cells and its comparison with the mouse, Dev. Biol., 2003, vol. 260, p. 404. https://doi.org/10.1016/s0012-1606(03)00256-2
Schuldiner, M., Eiges, R., Eden, A., Yanuka, O., Itskovitz-Eldor, J., Goldstein, R.S., and Benvenisty, N., Induced neuronal differentiation of human embryonic stem cells, Brain Res., 2001, vol. 913, p. 201. https://doi.org/10.1016/s0006-8993(01)02776-7
Schwartz, S.D., Regillo, C.D., Lam, B.L., Eliott, D., Rosenfeld, P.J., Gregori, N.Z., Hubschman, J.-P., Davis, J.L., Heilwell, G., and Spirn, M., Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies, Lancet, 2015, vol. 385, p. 509. https://doi.org/10.1016/S0140-6736(14)61376-3
Seemuller, E., Lupas, A., Stock, D., Lowe, J., Huber, R., and Baumeister, W., Proteasome from Thermoplasma acidophilum: a threonine protease, Science, 1995, vol. 268, p. 579. https://doi.org/10.1126/science.7725107
Selenina, A.V., Tsimokha, A.S., and Tomilin, A.N., Proteasomes in protein homeostasis of pluripotent stem cells, Acta Naturae, 2017, vol. 9, no. 3, p. 42.
Sinenko, S.A., Starkova, T.Y., Kuzmin, A.A., and Tomilin, A.N., Physiological signaling functions of reactive oxygen species in stem cells: from flies to man, Front. Cell Dev. Biol., 2021, vol. 9, p. 714370. https://doi.org/10.3389/fcell.2021.714370
Smalle, J. and Vierstra, R.D., The ubiquitin 26S proteasome proteolytic pathway, Annu. Rev. Plant Biol., 2004, vol. 55, p. 555. https://doi.org/10.1146/annurev.arplant.55.031903.141801
Stadtmueller, B.M. and Hill, C.P., Proteasome activators, Mol. Cell, 2011, vol. 41, p. 8. https://doi.org/10.1016/j.molcel.2010.12.020
Sun, X.X., He, X., Yin, L., Komada, M., Sears, R.C., and Dai, M.S., The nucleolar ubiquitin-specific protease USP36 deubiquitinates and stabilizes c-Myc, Proc. Natl. Acad. Sci. U. S. A., 2015, vol. 112, p. 3734. https://doi.org/10.1073/pnas.1411713112
Suresh, B., Lee, J., Kim, K.S., and Ramakrishna, S., The importance of ubiquitination and deubiquitination in cellular reprogramming, Stem Cells Int., 2016, vol. 2016, p. 6705927. https://doi.org/10.1155/2016/6705927
Takahashi, K. and Yamanaka, S., Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 2006, vol. 126, p. 663. https://doi.org/10.1016/j.cell.2006.07.024
Thomson, J.A., Itskovitz-Eldor, J., Shapiro, S.S., Waknitz, M.A., Swiergiel, J.J., Marshall, V.S., and Jones, J.M., Embryonic stem cell lines derived from human blastocysts, Science, 1998, vol. 282, p. 1145. https://doi.org/10.1126/science.282.5391.1145
Uechi, H., Hamazaki, J., and Murata, S., Characterization of the testis-specific proteasome subunit alpha4s in mammals, J. Biol. Chem., 2014, vol. 289, p. 12365. https://doi.org/10.1074/jbc.M114.558866
Urbach, A. and Benvenisty, N., Studying early lethality of 45, XO (Turner’s syndrome) embryos using human embryonic stem cells. PLoS One, 2009., vol. 4, p. e4175. https://doi.org/10.1371/journal.pone.0004175
Uyama, M., Sato, M.M., Kawanami, M., and Tamura, M., Regulation of osteoblastic differentiation by the proteasome inhibitor bortezomib, Genes Cells, 2012, vol. 17, p. 548. https://doi.org/10.1111/j.1365-2443.2012.01611.x
van der Stoop, P., Boutsma, E.A., Hulsman, D., Noback, S., Heimerikx, M., Kerkhoven, R.M., Voncken, J.W., Wessels, L.F., and van Lohuizen, M., Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells, PLoS One, 2008, vol. 3, p. e2235. https://doi.org/10.1371/journal.pone.0002235
Verma, R., Aravind, L., Oania, R., McDonald, W.H., Yates, J.R., 3rd, Koonin, E.V., and Deshaies, R.J., Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome, Science, 2002, vol. 298, p. 611. https://doi.org/10.1126/science.1075898
Vilchez, D., Boyer, L., Lutz, M., Merkwirth, C., Morantte, I., Tse, C., Spencer, B., Page, L., Masliah, E., Berggren, W.T., Gage, F.H., and Dillin, A., FOXO4 is necessary for neural differentiation of human embryonic stem cells, Aging Cell, 2013, vol. 12, p. 518. https://doi.org/10.1111/acel.12067
Vilchez, D., Boyer, L., Morantte, I., Lutz, M., Merkwirth, C., Joyce, D., Spencer, B., Page, L., Masliah, E., Berggren, W.T., Gage, F.H., and Dillin, A., Increased proteasome activity in human embryonic stem cells is regulated by PSMD11, Nature, 2012a, vol. 489, p. 304. https://doi.org/10.1038/nature11468
Vilchez, D., Morantte, I., Liu, Z., Douglas, P.M., Merkwirth, C., Rodrigues, A.P., Manning, G., and Dillin, A., RPN-6 determines C. elegans longevity under proteotoxic stress conditions, Nature, 2012b, vol. 489, p. 263. https://doi.org/10.1038/nature11315
Voutsadakis, I.A., The ubiquitin–proteasome system and signal transduction pathways regulating epithelial mesenchymal transition of cancer, J. Biomed. Sci., 2012, vol. 19, p. 67. https://doi.org/10.1186/1423-0127-19-67
Wang, D., Bu, F., and Zhang, W., The role of ubiquitination in regulating embryonic stem cell maintenance and cancer development, Int. J. Mol. Sci., 2019, vol. 20, p. 2667. https://doi.org/10.3390/ijms20112667
Wang, X., Meul, T., and Meiners, S., Exploring the proteasome system: a novel concept of proteasome inhibition and regulation, Pharmacol. Ther., 2020, vol. 211, p. 107526. https://doi.org/10.1016/j.pharmthera.2020.107526
Watanabe, M., Takahashi, H., Saeki, Y., Ozaki, T., Itoh, S., Suzuki, M., Mizushima, W., Tanaka, K., and Hata-keyama, S., The E3 ubiquitin ligase TRIM23 regulates adipocyte differentiation via stabilization of the adipogenic activator PPARγ, Elife, 2015, vol. 4, p. e05615. https://doi.org/10.7554/eLife.05615
Weitzman, M.D., Lilley, C.E., and Chaurushiya, M.S., Genomes in conflict: maintaining genome integrity during virus infection, Annu. Rev. Microbiol., 2010, vol. 64, p. 61. https://doi.org/10.1146/annurev.micro.112408.134016
Werner, A., Manford, A.G., and Rape, M., Ubiquitin-dependent regulation of stem cell biology, Trends Cell Biol., 2017, vol. 27, p. 568. https://doi.org/10.1016/j.tcb.2017.04.002
Xiao, N., Eto, D., Elly, C., Peng, G., Crotty, S., and Liu, Y.-C., The E3 ubiquitin ligase Itch is required for the differentiation of follicular helper T cells, Nat. Immunol., 2014, vol. 15, p. 657. https://doi.org/10.1038/ni.2912
Xu, H., Wang, W., Li, C., Yu, H., Yang, A., Wang, B., and Jin, Y., WWP2 promotes degradation of transcription factor OCT4 in human embryonic stem cells, Cell Res., 2009, vol. 19, p. 561. https://doi.org/10.1038/cr.2009.31
Yadav, D., Lee, J.Y., Puranik, N., Chauhan, P.S., Chavda, V., Jin, J.-O., and Lee, P.C., Modulating the ubiquitin–proteasome system: a therapeutic strategy for autoimmune diseases, Cells, 2022, vol. 11, p. 1093. https://doi.org/10.3390/cells11071093
Yao, T. and Cohen, R.E., A cryptic protease couples deubiquitination and degradation by the proteasome, Nature, 2002, vol. 419, p. 403. https://doi.org/10.1038/nature01071
Young, L.E., Fernandes, K., McEvoy, T.G., Butterwith, S.C., Gutierrez, C.G., Carolan, C., Broad-bent, P.J., Robinson, J.J., Wilmut, I., and Sinclair, K.D., Epigenetic change in IGF2R is associated with fetal overgrowth after sheep embryo culture, Nat. Genet., 2001, vol. 27, p. 153. https://doi.org/10.1038/84769
Young, R.A., Control of the embryonic stem cell state, Cell, 2011, vol. 144, p. 940. https://doi.org/10.1016/j.cell.2011.01.032
Zhang, F., Hu, Y., Huang, P., Toleman, C.A., Paterson, A.J., and Kudlow, J.E., Proteasome function is regulated by cyclic AMP-dependent protein kinase through phosphorylation of Rpt6, J. Biol. Chem., 2007, vol. 282, p. 22460. https://doi.org/10.1074/jbc.M702439200
Zhang, F. and Laiho, M., On and off: proteasome and TGF-beta signaling. Exp. Cell Res, 2003., vol. 291, p. 275. https://doi.org/10.1016/j.yexcr.2003.07.007
Zhang, X., Linder, S., and Bazzaro, M., Drug development targeting the ubiquitin–proteasome system (UPS) for the treatment of human cancers, Cancers, 2020., vol. 12, p. 902. https://doi.org/10.3390/cancers12040902
Zhang, Y., Ding, H., Wang, X., Wang, X., Wan, S., Xu, A., Gan, R., and Ye, S.-D., MK2 promotes Tfcp2l1 degradation via β-TrCP ubiquitin ligase to regulate mouse embryonic stem cell self-renewal, Cell Rep., 2021, vol. 37, p. 109949. https://doi.org/10.1016/j.celrep.2021.109949
Zhao, S., Zhang, C., Xu, J., Liu, S., Yu, L., Chen, S., Wen, H., Li, Z., and Liu, N., Dppa3 facilitates self-renewal of embryonic stem cells by stabilization of pluripotent factors, Stem Cell Res. Ther., 2022, vol. 13, p. 169. https://doi.org/10.1186/s13287-022-02846-8
Zhou, L., Mideros, S.X., Bao, L., Hanlon, R., Arredondo, F.D., Tripathy, S., Krampis, K., Jerauld, A., Evans, C., and St Martin, S.K., Infection and genotype remodel the entire soybean transcriptome, BMC Genomics, 2009, vol. 10, p. 49. https://doi.org/10.1186/1471-2164-10-49
Zhou, W., Zhu, P., Wang, J., Pascual, G., Ohgi, K.A., Lozach, J., Glass, C.K., and Rosenfeld, M.G., Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation, Mol. Cell, 2008, vol. 29, p. 69. https://doi.org/10.1016/j.molcel.2007.11.002
Funding
The work was performed with the financial support of Russian Science Foundation (grant no. 22-14-00390).
Author information
Authors and Affiliations
Contributions
U.I. Podenkova, I.V. Zubarev: writing the main part of the work, selection of literature (made an equal contribution to the preparation of the article). U.I. Podenkova and A.S. Tsimokha: preparation of illustrations. A.S. Tsimokha: selection of literature, writing a conclusion; A.N. Tomilin and A.S. Tsimokha: final edits.
Corresponding author
Ethics declarations
The authors declare that they have no conflicts of interest.
This paper does not contain information on any studies involving humans or animals performed by the authors.
Additional information
Abbreviations: PSCs—pluripotent stem cells; iPSCs—induced pluripotent stem cells; UPS—ubiquitin-proteasome system; ESCs—embryonic stem cells.
Rights and permissions
About this article
Cite this article
Podenkova, U.I., Zubarev, I.V., Tomilin, A.N. et al. Ubiquitin-Proteasome System in the Regulation of Cell Pluripotency and Differentiation. Cell Tiss. Biol. 17, 441–453 (2023). https://doi.org/10.1134/S1990519X23050103
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1990519X23050103