Цитология, 2023, T. 65, № 3, стр. 232-245

Убиквитин-протеасомная система в регуляции клеточной плюрипотентности и дифференцировки

У. И. Поденкова 1, И. В. Зубарев 1, А. Н. Томилин 1, А. С. Цимоха 1*

1 Институт цитологии РАН
194064 Санкт-Петербург, Россия

* E-mail: atsimokha@incras.ru

Поступила в редакцию 30.11.2022
После доработки 05.12.2022
Принята к публикации 05.12.2022

Аннотация

Эмбриональные стволовые клетки (ЭСК) и индуцированные плюрипотентные стволовые клетки (иПСК) демонстрируют уникальную способность к непрерывному самообновлению и дифференцировке во все типы соматических клеток. Понимание механизмов, контролирующих эти свойства, приблизит к эффективному и безопасному использованию ЭСК и иПСК в клеточной терапии. Недавние совокупные данные подчеркнули важность протеостаза в поддержании функции ЭСК. Настоящий обзор посвящен роли убиквитин-протеасомной системы (УПС) – ключевого участника сети протеостаза – в регуляции плюрипотентности и дифференцировки ЭСК и иПСК.

Ключевые слова: деубиквитиназы, дифференцировка, плюрипотентность, протеасома, убиквитин-лигазы, убиквитин-протеасомная система, эмбриональные стволовые клетки

Список литературы

  1. Гордеев М.Н., Бахмет Е.И., Томилин А.Н. 2021. Динамика плюрипотентности в эмбриогенезе и в культуре. Онтогенез. Т. 52. № 6. С. 429. (Gordeev M., Bakhmet E., Tomilin A. 2021. Pluripotency dynamics during embryogenesis and in cell culture. Russ. J. Dev. Biol. V. 52. № 6. P. 379.)https://doi.org/10.1134/S1062360421060059

  2. Селенина А.В., Цимоха А.С., Томилин А.Н. 2017. Протеасомы в регуляции белкового гомеостаза плюрипотентных стволовых клеток. Acta Naturae. Т. 9. № 3. С. 42. (Selenina A.V., Tsimokha A.S., Tomilin A.N. 2017. Proteasomes in protein homeostasis of pluripotent stem cells. Acta Naturae. V. 9. № 3. P. 42.)

  3. Abu-Dawud R., Graffmann N., Ferber S., Wruck W., Adjaye J. 2018. Pluripotent stem cells: induction and self-renewal. Philos. Trans. R. Soc. Lond. B Biol. Sci. V. 373. P. 20170213. https://doi.org/10.1098/rstb.2017.0213

  4. Al Mamun M.M., Khan M.R., Zhu Y., Zhang Y., Zhou S., Xu R., Bukhari I., Thorne R.F., Li J., Zhang X.D. 2022. Stub1 maintains proteostasis of master transcription factors in embryonic stem cells. Cell Rep. V. 39. P. 110919. https://doi.org/10.1016/j.celrep.2022.110919

  5. Alekseenko Z., Dias J.M., Adler A.F., Kozhevnikova M., van Lunteren J.A., Nolbrant S., Jeggari A., Vasylovska S., Yoshitake T., Kehr J. 2022. Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery. Nature Commun. V.13. P. 1. https://doi.org/10.1038/s41467-022-30777-8

  6. Babaie Y., Herwig R., Greber B., Brink T.C., Wruck W., Groth D., Lehrach H., Burdon T., Adjaye J. 2007. Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells. Stem Cells. V. 25. P. 500. https://doi.org/10.1634/stemcells.2006-0426

  7. Baharvand H., Hajheidari M., Ashtiani S.K., Salekdeh G.H. 2006. Proteomic signature of human embryonic stem cells. Proteomics. V. 6. P. 3544. https://doi.org/10.1002/pmic.200500844

  8. Bai M., Zhao X., Sahara K., Ohte Y., Hirano Y., Kaneko T., Yashiroda H., Murata S. 2014. Assembly mechanisms of specialized core particles of the proteasome. Biomolecules. V. 4. P. 662. https://doi.org/10.3390/biom4030662

  9. Beckwith R., Estrin E., Worden E.J., Martin A. 2013. Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase. Nat. Struct. Mol. Biol. V. 20. P. 1164. https://doi.org/10.1038/nsmb.2659

  10. Behbahan I.S., Duan Y., Lam A., Khoobyari S., Ma X., Ahuja T.P., Zern M.A. 2011. New approaches in the differentiation of human embryonic stem cells and induced pluripotent stem cells toward hepatocytes. Stem Cell Rev. Rep. V. 7. P. 748. https://doi.org/10.1007/s12015-010-9216-4

  11. Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wernig M., Plath K. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. V. 125. P. 315. https://doi.org/10.1016/j.cell.2006.02.041

  12. Biancotti J.C., Narwani K., Buehler N., Mandefro B., Golan-Lev T., Yanuka O., Clark A., Hill D., Benvenisty N., Lavon N. 2010. Human embryonic stem cells as models for aneuploid chromosomal syndromes. Stem Cells. V. 28. P. 1530. https://doi.org/10.1002/stem.483

  13. Blondelle J., Shapiro P., Domenighetti A.A., Lange S. 2017. Cullin E3 ligase activity is required for myoblast differentiation. J. Mol. Biol. V. 429. P. 1045. https://doi.org/10.1016/j.jmb.2017.02.012

  14. 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., Aifantis I. 2012. Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell. V. 11. P. 783. https://doi.org/10.1016/j.stem.2012.09.011

  15. Budenholzer L., Cheng C.L., Li Y., Hochstrasser M. 2017. Proteasome Structure and Assembly. J. Mol. Biol. V. 429. P. 3500. https://doi.org/10.1016/j.jmb.2017.05.027

  16. Bustos F., Segarra-Fas A., Chaugule V.K., Brandenburg L., Branigan E., Toth R., Macartney T., Knebel A., Hay R.T., Walden H. 2018. RNF12 X-linked intellectual disability mutations disrupt E3 ligase activity and neural differentiation. Cell Rep. V. 23. P. 1599. https://doi.org/10.1016/j.celrep.2018.04.022

  17. Cao F., Lin S., Xie X., Ray P., Patel M., Zhang X., Drukker M., Dylla S.J., Connolly A.J., Chen X. 2006. In vivo visualization of embryonic stem cell survival, proliferation, and migration after cardiac delivery. Circulation. V. 113. P. 1005. https://doi.org/10.1161/CIRCULATIONAHA.105.588954

  18. Cascio P., Hilton C., Kisselev A.F., Rock K.L., Goldberg A.L. 2001. 26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide. EMBO J. V. 20. P. 2357. https://doi.org/10.1093/emboj/20.10.2357

  19. Choi J., Baek K.H. 2018. Cellular functions of stem cell factors mediated by the ubiquitin-proteasome system. Cell. Mol. Life Sci. V. 75. P. 1947. https://doi.org/10.1007/s00018-018-2770-7

  20. Ciechanover A., Kwon Y.T. 2015. Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies. Exp. Mol. Med. V. 47. P. e147. https://doi.org/10.1038/emm.2014.117

  21. Cui Z., Hwang S.M., Gomes A.V. 2014. Identification of the immunoproteasome as a novel regulator of skeletal muscle differentiation. Mol. Cell. Biol. V. 34. P. 96. https://doi.org/10.1128/MCB.00622-13

  22. Dahlmann B. 2005. Proteasomes. Essays Biochem. V. 41. P. 31. https://doi.org/10.1042/EB0410031

  23. de Napoles M., Mermoud J.E., Wakao R., Tang Y.A., Endoh M., Appanah R., Nesterova T.B., Silva J., Otte A.P., Vidal M. 2004. Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev. Cell. V. 7. P. 663. https://doi.org/10.1016/j.devcel.2004.10.005

  24. Diefenbacher M.E., Chakraborty A., Blake S.M., Mitter R., Popov N., Eilers M., Behrens A. 2015. Usp28 counteracts Fbw7 in intestinal homeostasis and cancer. Cancer Res. V. 75. P. 1181. https://doi.org/10.1158/0008-5472.CAN-14-1726

  25. Dieudonne F.-X., Sévère N., Biosse-Duplan M., Weng J.-J., Su Y., Marie P.J. 2013. Promotion of osteoblast differentiation in mesenchymal cells through Cbl-mediated control of STAT5 activity. Stem Cells. V. 31. P. 1340. https://doi.org/10.1002/stem.1380

  26. Drews O., Taegtmeyer H. 2014. Targeting the ubiquitin-proteasome system in heart disease: the basis for new therapeutic strategies. Antioxid. Redox. Signal. V. 21. P. 2322. https://doi.org/10.1089/ars.2013.5823

  27. Du Z., He F., Yu Z., Bowerman B., Bao Z. 2015. E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis. Dev. Biol. V. 398. P. 267. https://doi.org/10.1016/j.ydbio.2014.12.009

  28. Dutta D., Sharma V., Mutsuddi M., Mukherjee A. 2021. Regulation of Notch signaling by E3 ubiquitin ligases. FEBS J. V. 289. P. 937. https://doi.org/10.1111/febs.15792

  29. Endoh M., Endo T.A., Endoh T., Fujimura Y.-I., Ohara O., Toyoda T., Otte A.P., Okano M., Brockdorff N., Vidal M. 2008. Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity. Development. V. 135. P. 1513. https://doi.org/10.1242/dev.014340

  30. Fabre B., Lambour T., Garrigues L., Amalric F., Vigneron N., Menneteau T., Stella A., Monsarrat B., Van den Eynde B., Burlet-Schiltz O. 2015. Deciphering preferential interactions within supramolecular protein complexes: the proteasome case. Mol. Syst. Biol. V. 11. P. 771. https://doi.org/10.15252/msb.20145497

  31. Fang L., Zhang L., Wei W., Jin X., Wang P., Tong Y., Li J., Du J.X., Wong J. 2014. A methylation-phosphorylation switch determines Sox2 stability and function in ESC maintenance or differentiation. Mol. Cell. V. 55. P. 537. https://doi.org/10.1016/j.molcel.2014.06.018

  32. 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. 1998. Unified nomenclature for subunits of the Saccharomyces cerevisiae proteasome regulatory particle. Trends Biochem. Sci. V. 23. P. 244. https://doi.org/10.1016/s0968-0004(98)01222-5

  33. Fort P., Kajava A.V., Delsuc F., Coux O. 2015. Evolution of proteasome regulators in eukaryotes. Genome Biol. Evol. V. 7. P. 1363. https://doi.org/10.1093/gbe/evv068

  34. Fu X. 2014. The immunogenicity of cells derived from induced pluripotent stem cells. Cell. Mol. Immunol. V. 11. P. 14. https://doi.org/10.1038/cmi.2013.60

  35. 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., Oren M. 2012. RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation. Mol. Cell. V. 46. P. 662. https://doi.org/10.1016/j.molcel.2012.05.023

  36. Fujikawa T., Oh S.-H., Pi L., Hatch H.M., Shupe T., Petersen B.E. 2005. Teratoma formation leads to failure of treatment for type I diabetes using embryonic stem cell-derived insulin-producing cells. Am. J. Pathol. V. 166. P. 1781. https://doi.org/10.1016/S0002-9440(10)62488-1

  37. Gao C., Xiao G., Hu J. 2014. Regulation of Wnt/β-catenin signaling by posttranslational modifications. Cell Biosci. V. 4. P. 13. https://doi.org/10.1186/2045-3701-4-13

  38. Gao J., Buckley S.M., Cimmino L., Guillamot M., Strikoudis A., Cang Y., Goff S.P., Aifantis I. 2015. The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis. Elife. V. 4. P. e07539. https://doi.org/10.7554/eLife.07539

  39. Glickman M.H., Rubin D.M., Coux O., Wefes I., Pfeifer G., Cjeka Z., Baumeister W., Fried V. A., Finley D. 1998. A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3. Cell. V. 94. P. 615. https://doi.org/10.1016/s0092-8674(00)81603-7

  40. Groll M., Bajorek M., Kohler A., Moroder L., Rubin D.M., Huber R., Glickman M.H., Finley D. 2000. A gated channel into the proteasome core particle. Nat. Struct. Biol. V. 7. P. 1062. https://doi.org/10.1038/80992

  41. Groll M., Bochtler M., Brandstetter H., Clausen T., Huber R. 2005. Molecular machines for protein degradation. Chembiochem. V. 6. P. 222. https://doi.org/10.1002/cbic.200400313

  42. Groll M., Ditzel L., Lowe J., Stock D., Bochtler M., Bartunik H.D., Huber R. 1997. Structure of 20S proteasome from yeast at 2.4 A resolution. Nature. V. 386. P. 463. https://doi.org/10.1038/386463a0

  43. Hatakeyama S. 2012. Ubiquitin-mediated regulation of JAK-STAT signaling in embryonic stem cells. JAKSTAT. V. 1. P. 168. https://doi.org/10.4161/jkst.21560

  44. Hayashi K., de Sousa Lopes S.M.C., Tang F., Surani M.A. 2008. Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states. Cell Stem Cell. V. 3. P. 391. https://doi.org/10.1016/j.stem.2008.07.027

  45. He M., Zhou Z., Shah A.A., Zou H., Tao J., Chen Q., Wan Y. 2016. The emerging role of deubiquitinating enzymes in genomic integrity, diseases, and therapeutics. Cell Biosci. V. 6. P. 62. https://doi.org/10.1186/s13578-016-0127-1

  46. Hernebring M., Brolen G., Aguilaniu H., Semb H., Nystrom T. 2006. Elimination of damaged proteins during differentiation of embryonic stem cells. Proc. Natl. Acad. Sci. USA. V. 103. P. 7700. https://doi.org/10.1073/pnas.0510944103

  47. Hernebring M., Fredriksson A., Liljevald M., Cvijovic M., Norrman K., Wiseman J., Semb H., Nystrom T. 2013. Removal of damaged proteins during ES cell fate specification requires the proteasome activator PA28. Sci. Rep. V. 3. P. 1381. https://doi.org/10.1038/srep01381

  48. Hershko A., Ciechanover A. 1992. The ubiquitin system for protein degradation. Annu. Rev. Biochem. V. 61. P. 761. https://doi.org/10.1146/annurev.bi.61.070192.003553

  49. Hershko A., Ciechanover A. 1998. The ubiquitin system. Annu. Rev. Biochem. V. 67. P. 425. https://doi.org/10.1146/annurev.biochem.67.1.425

  50. Inoue D., Aihara H., Sato T., Mizusaki H., Doiguchi M., Higashi M., Imamura Y., Yoneda M., Miyanishi T., Fujii S. 2015. Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation. Sci. Rep. V. 5. P. 16567. https://doi.org/10.1038/srep16567

  51. Jiang T.X., Zhao M., Qiu X.B. 2018. Substrate receptors of proteasomes. Biol. Rev. Camb. Philos. Soc. V. 93. P. 1765. https://doi.org/10.1111/brv.12419

  52. Jing X., Infante J., Nachtman R.G., Jurecic R. 2008. E3 ligase FLRF (Rnf41) regulates differentiation of hematopoietic progenitors by governing steady-state levels of cytokine and retinoic acid receptors. Exp. Hematol. V. 36. P. 1110. https://doi.org/10.1016/j.exphem.2008.04.001

  53. Kammerl I.E., Dann A., Mossina A., Brech D., Lukas C., Vosyka O., Nathan P., Conlon T.M., Wagner D.E., Overkleeft H.S. 2016. Impairment of immunoproteasome function by cigarette smoke and in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. V. 193. P. 1230. https://doi.org/10.1164/rccm.201506-1122OC

  54. 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., Jung S.K. 2014. ERK1 phosphorylates Nanog to regulate protein stability and stem cell self-renewal. Stem Cell Res. V. 13. P. 1. https://doi.org/10.1016/j.scr.2014.04.001

  55. Konstantinova I.M., Tsimokha A.S., Mittenberg A.G. 2008. Role of proteasomes in cellular regulation. Int. Rev. Cell. Mol. Biol. V. 267. P. 59. https://doi.org/10.1016/S1937-6448(08)00602-3

  56. Li S., Xiao F., Zhang J., Sun X., Wang H., Zeng Y., Hu J., Tang F., Gu J., Zhao Y., Jin Y., Liao B. 2018. Disruption of OCT4 ubiquitination increases OCT4 protein stability and ASH2L-B-mediated H3K4 methylation promoting pluripotency acquisition. Stem Cell Reports. V. 11. P. 973. https://doi.org/10.1016/j.stemcr.2018.09.001

  57. Liao B., Zhong X., Xu H., Xiao F., Fang Z., Gu J., Chen Y., Zhao Y., Jin Y. 2013. Itch, an E3 ligase of Oct4, is required for embryonic stem cell self-renewal and pluripotency induction. J. Cell. Physiol. V. 228. P. 1443. https://doi.org/10.1002/jcp.24297

  58. Liu X., Yao Y., Ding H., Han C., Chen Y., Zhang Y., Wang C., Zhang X., Zhang Y., Zhai Y. 2016. USP21 deubiquitylates Nanog to regulate protein stability and stem cell pluripotency. Signal Transduct. Target. Ther. V. 1. P. 16024. https://doi.org/10.1038/sigtrans.2016.24

  59. Liu Y.-J., Nakamura T., Nakano T. 2012. Essential role of DPPA3 for chromatin condensation in mouse oocytogenesis. Biol. Reprod. V. 86. P. 40. https://doi.org/10.1095/biolreprod.111.095018

  60. Liu Y., Xu H.W., Wang L., Li S.Y., Zhao C.J., Hao J., Li Q.Y., Zhao T.T., Wu W., Wang Y. 2018. Human embryonic stem cell-derived retinal pigment epithelium transplants as a potential treatment for wet age-related macular degeneration. Cell Discov. V. 4. P. 50. https://doi.org/10.1038/s41421-018-0053-y

  61. Mattout A., Meshorer E. 2010. Chromatin plasticity and genome organization in pluripotent embryonic stem cells. Curr. Opin. Cell Biol. V. 22. P. 334. https://doi.org/10.1016/j.ceb.2010.02.001

  62. Meiners S., Keller I.E., Semren N., Caniard A. 2014. Regulation of the proteasome: evaluating the lung proteasome as a new therapeutic target. Antioxid. Redox. Signal. V. 21. P. 2364. https://doi.org/10.1089/ars.2013.5798

  63. Meiners S., Ludwig A., Stangl V., Stangl K. 2008. Proteasome inhibitors: poisons and remedies. Med. Res. Rev. V. 28. P. 309. https://doi.org/10.1002/med.20111

  64. Meshorer E., Misteli T. 2006. Chromatin in pluripotent embryonic stem cells and differentiation. Nat. Rev. Mol. Cell Biol. V. 7. P. 540. https://doi.org/10.1038/nrm1938

  65. Miyazono K. 2000. TGF-β signaling by Smad proteins. Cytokine Growth Factor Rev. V. 11. P. 15. https://doi.org/10.1016/s1359-6101(99)00025-8

  66. Morozov A.V., Karpov V.L. 2018. Biological consequences of structural and functional proteasome diversity. Heliyon. V. 4. P. e00894. https://doi.org/10.1016/j.heliyon.2018.e00894

  67. Murata S., Takahama Y., Tanaka K. 2008. Thymoproteasome: probable role in generating positively selecting peptides. Curr. Opin. Immunol. V. 20. P. 192. https://doi.org/10.1016/j.coi.2008.03.002

  68. Nakagawa T., Kajitani T., Togo S., Masuko N., Ohdan H., Hishikawa Y., Koji T., Matsuyama T., Ikura T., Muramatsu M. 2008. Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di-and trimethylation. Genes Dev. V. 22. P. 37. https://doi.org/10.1101/gad.1609708

  69. Nakamura T., Arai Y., Umehara H., Masuhara M., Kimura T., Taniguchi H., Sekimoto T., Ikawa M., Yoneda Y., Okabe M. 2007. PGC7/Stella protects against DNA demethylation in early embryogenesis. Nat. Cell Biol. V. 9. P. 64. https://doi.org/10.1038/ncb1519

  70. Nakamura T., Liu Y.-J., Nakashima H., Umehara H., Inoue K., Matoba S., Tachibana M., Ogura A., Shinkai Y., Nakano T. 2012. PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos. Nature. V. 486. P. 415. https://doi.org/10.1038/nature11093

  71. Nandi D., Tahiliani P., Kumar A., Chandu D. 2006. The ubiquitin-proteasome system. J. Biosci. V. 31. P. 137. https://doi.org/10.1007/BF02705243

  72. Ng H.-H., Surani M.A. 2011. The transcriptional and signalling networks of pluripotency. Nat. Cell Biol. V. 13. P. 490. https://doi.org/10.1038/ncb0511-490

  73. Nguyen D.T.T., Richter D., Michel G., Mitschka S., Kolanus W., Cuevas E., Wulczyn F.G. 2017. The ubiquitin ligase LIN41/TRIM71 targets p53 to antagonize cell death and differentiation pathways during stem cell differentiation. Cell Death Differ. V. 24. P. 1063. https://doi.org/10.1038/cdd.2017.54

  74. Noormohammadi A., Calculli G., Gutierrez-Garcia R., Khodakarami A., Koyuncu S., Vilchez D. 2018. Mechanisms of protein homeostasis (proteostasis) maintain stem cell identity in mammalian pluripotent stem cells. Cell. Mol. Life Sci. V. 75. P. 275. https://doi.org/10.1007/s00018-017-2602-1

  75. Okita Y., Matsumoto A., Yumimoto K., Isoshita R., Nakayama K.I. 2012. Increased efficiency in the generation of induced pluripotent stem cells by F bxw7 ablation. Genes Cells. V. 17. P. 768. https://doi.org/10.1111/j.1365-2443.2012.01626.x

  76. Okita Y., Nakayama K.I. 2012. UPS delivers pluripotency. Cell Stem Cell. V. 11. P. 728. https://doi.org/10.1016/j.stem.2012.11.009

  77. Okumura F., Matsunaga Y., Katayama Y., Nakayama K.I., Hatakeyama S. 2010. TRIM8 modulates STAT3 activity through negative regulation of PIAS3. J. Cell Sci. V. 123. P. 2238. https://doi.org/10.1242/jcs.068981

  78. Osmulski P.A., Hochstrasser M., Gaczynska M. 2009. A tetrahedral transition state at the active sites of the 20S proteasome is coupled to opening of the alpha-ring channel. Structure. V. 17. P. 1137. https://doi.org/10.1016/j.str.2009.06.011

  79. Pak C., Danko T., Zhang Y., Aoto J., Anderson G., Maxeiner S., Yi F., Wernig M., Südhof T.C. 2015. Human neuropsychiatric disease modeling using conditional deletion reveals synaptic transmission defects caused by heterozygous mutations in NRXN1. Cell Stem Cell. V. 17. P. 316. https://doi.org/10.1016/j.stem.2015.07.017

  80. 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., Wang P. 2015. USP37 directly deubiquitinates and stabilizes c-Myc in lung cancer. Oncogene. V. 34. P. 3957. https://doi.org/10.1038/onc.2014.327

  81. Pickering A.M., Davies K.J. 2012. Degradation of damaged proteins: the main function of the 20S proteasome. Prog. Mol. Biol. Transl. Sci. V. 109. P. 227. https://doi.org/10.1016/B978-0-12-397863-9.00006-7

  82. 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. 2013. Acetylation-mediated proteasomal degradation of core histones during DNA repair and spermatogenesis. Cell. V. 153. P. 1012. https://doi.org/10.1016/j.cell.2013.04.032

  83. Rezania A., Bruin J.E., Arora P., Rubin A., Batushansky I., Asadi A., O’dwyer S., Quiskamp N., Mojibian M., Albrecht T. 2014. Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells. Nat. Biotechnol. V. 32. P. 1121. https://doi.org/10.1038/nbt.3033

  84. Sang H., Wang D., Zhao S., Zhang J., Zhang Y., Xu J., Chen X., Nie Y., Zhang K., Zhang S. 2019. Dppa3 is critical for Lin28a-regulated ES cells naïve–primed state conversion. J. Mol. Cell Biol. V. 11. P. 474. https://doi.org/10.1093/jmcb/mjy069

  85. Saretzki G., Armstrong L., Leake A., Lako M., von Zglinicki T. 2004. Stress defense in murine embryonic stem cells is superior to that of various differentiated murine cells. Stem Cells. V. 22. P. 962. https://doi.org/10.1634/stemcells.22-6-962

  86. Saric T., Chang S.-C., Hattori A., York I.A., Markant S., Rock K.L., Tsujimoto M., Goldberg A.L. 2002. An IFN-γ–induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I–presented peptides. Nat. Immunol. V. 3. P. 1169. https://doi.org/10.1038/ni859

  87. Sato N., Sanjuan I.M., Heke M., Uchida M., Naef F., Brivanlou A.H. 2003. Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev. Biol. V. 260. P. 404. https://doi.org/10.1016/s0012-1606(03)00256-2

  88. Schuldiner M., Eiges R., Eden A., Yanuka O., Itskovitz-Eldor J., Goldstein R.S., Benvenisty N. 2001. Induced neuronal differentiation of human embryonic stem cells. Brain Res. V. 913. P. 201. https://doi.org/10.1016/s0006-8993(01)02776-7

  89. 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., Spirn M. 2015. 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. V. 385. P. 509. https://doi.org/10.1016/S0140-6736(14)61376-3

  90. Seemuller E., Lupas A., Stock D., Lowe J., Huber R., Baumeister W. 1995. Proteasome from Thermoplasma acidophilum: a threonine protease. Science. V. 268. P. 579. https://doi.org/10.1126/science.7725107

  91. Sinenko S.A., Starkova T.Y., Kuzmin A.A., Tomilin A.N. 2021. Physiological signaling functions of reactive oxygen species in stem cells: From flies to man. Front. Cell Dev. Biol. V. 9. P. 714370. https://doi.org/10.3389/fcell.2021.714370

  92. Smalle J., Vierstra R.D. 2004. The ubiquitin 26S proteasome proteolytic pathway. Annu. Rev. Plant Biol. V. 55. P. 555. https://doi.org/10.1146/annurev.arplant.55.031903.141801

  93. Stadtmueller B.M., Hill C.P. 2011. Proteasome activators. Mol. Cell. V. 41. P. 8. https://doi.org/10.1016/j.molcel.2010.12.020

  94. Sun X.X., He X., Yin L., Komada M., Sears R.C., Dai M.S. 2015. The nucleolar ubiquitin-specific protease USP36 deubiquitinates and stabilizes c-Myc. Proc. Natl. Acad. Sci. USA. V. 112. P. 3734. https://doi.org/10.1073/pnas.1411713112

  95. Suresh B., Lee J., Kim K.S., Ramakrishna S. 2016. The importance of ubiquitination and deubiquitination in cellular reprogramming. Stem Cells Int. V. 2016. P. 6705927. https://doi.org/10.1155/2016/6705927

  96. Takahashi K., Yamanaka S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. V. 126. P. 663. https://doi.org/10.1016/j.cell.2006.07.024

  97. Thomson J.A., Itskovitz-Eldor J., Shapiro S.S., Waknitz M.A., Swiergiel J.J., Marshall V.S., Jones J.M. 1998. Embryonic stem cell lines derived from human blastocysts. Science. V. 282. P. 1145. https://doi.org/10.1126/science.282.5391.1145

  98. Uechi H., Hamazaki J., Murata S. 2014. Characterization of the testis-specific proteasome subunit alpha4s in mammals. J. Biol. Chem. V. 289. P. 12365. https://doi.org/10.1074/jbc.M114.558866

  99. Urbach A., Benvenisty N. 2009. Studying early lethality of 45, XO (Turner’s syndrome) embryos using human embryonic stem cells. PLoS One. V. 4. P. e4175. https://doi.org/10.1371/journal.pone.0004175

  100. Uyama M., Sato M.M., Kawanami M., Tamura M. 2012. Regulation of osteoblastic differentiation by the proteasome inhibitor bortezomib. Genes Cells. V. 17. P. 548. https://doi.org/10.1111/j.1365-2443.2012.01611.x

  101. van der Stoop P., Boutsma E.A., Hulsman D., Noback S., Heimerikx M., Kerkhoven R.M., Voncken J.W., Wessels L.F., van Lohuizen M. 2008. Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells. PLoS One. V. 3. P. e2235. https://doi.org/10.1371/journal.pone.0002235

  102. Verma R., Aravind L., Oania R., McDonald W.H., Yates J.R., 3rd, Koonin E.V., Deshaies R.J. 2002. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science. V. 298. P. 611. https://doi.org/10.1126/science.1075898

  103. Vilchez D., Boyer L., Lutz M., Merkwirth C., Morantte I., Tse C., Spencer B., Page L., Masliah E., Berggren W.T., Gage F.H., Dillin A. 2013. FOXO4 is necessary for neural differentiation of human embryonic stem cells. Aging Cell. V. 12. P. 518. https://doi.org/10.1111/acel.12067

  104. Vilchez D., Boyer L., Morantte I., Lutz M., Merkwirth C., Joyce D., Spencer B., Page L., Masliah E., Berggren W.T., Gage F.H., Dillin A. 2012a. Increased proteasome activity in human embryonic stem cells is regulated by PSMD11. Nature. V. 489. P. 304. https://doi.org/10.1038/nature11468

  105. Vilchez D., Morantte I., Liu Z., Douglas P.M., Merkwirth C., Rodrigues A.P., Manning G., Dillin A. 2012b. RPN-6 determines C. elegans longevity under proteotoxic stress conditions. Nature. V. 489. P. 263. https://doi.org/10.1038/nature11315

  106. Voutsadakis I.A. 2012. The ubiquitin–proteasome system and signal transduction pathways regulating epithelial mesenchymal transition of cancer. J. Biomed. Sci. V. 19. P. 67. https://doi.org/10.1186/1423-0127-19-67

  107. Wang D., Bu F., Zhang W. 2019. The role of ubiquitination in regulating embryonic stem cell maintenance and cancer development. Int. J. Mol. Sci. V. 20. P. 2667. https://doi.org/10.3390/ijms20112667

  108. Wang X., Meul T., Meiners S. 2020. Exploring the proteasome system: a novel concept of proteasome inhibition and regulation. Pharmacol. Ther. V. 211. P. 107526. https://doi.org/10.1016/j.pharmthera.2020.107526

  109. Watanabe M., Takahashi H., Saeki Y., Ozaki T., Itoh S., Suzuki M., Mizushima W., Tanaka K., Hatakeyama S. 2015. The E3 ubiquitin ligase TRIM23 regulates adipocyte differentiation via stabilization of the adipogenic activator PPARγ. Elife. V. 4. P. e05615. https://doi.org/10.7554/eLife.05615

  110. Weitzman M.D., Lilley C.E., Chaurushiya M.S. 2010. Genomes in conflict: maintaining genome integrity during virus infection. Annu. Rev. Microbiol. V. 64. P. 61. https://doi.org/10.1146/annurev.micro.112408.134016

  111. Werner A., Manford A.G., Rape M. 2017. Ubiquitin-dependent regulation of stem cell biology. Trends Cell Biol. V. 27. P. 568. https://doi.org/10.1016/j.tcb.2017.04.002

  112. Xiao N., Eto D., Elly C., Peng G., Crotty S., Liu Y.-C. 2014. The E3 ubiquitin ligase Itch is required for the differentiation of follicular helper T cells. Nat. Immunol. V. 15. P. 657. https://doi.org/10.1038/ni.2912

  113. Xu H., Wang W., Li C., Yu H., Yang A., Wang B., Jin Y. 2009. WWP2 promotes degradation of transcription factor OCT4 in human embryonic stem cells. Cell Res. V. 19. P. 561. https://doi.org/10.1038/cr.2009.31

  114. Yadav D., Lee J.Y., Puranik N., Chauhan P.S., Chavda V., Jin J.-O., Lee P.C. 2022. Modulating the ubiquitin–proteasome system: a therapeutic strategy for autoimmune diseases. Cells. V. 11. P. 1093. https://doi.org/10.3390/cells11071093

  115. Yao T., Cohen R.E. 2002. A cryptic protease couples deubiquitination and degradation by the proteasome. Nature. V. 419. P. 403. https://doi.org/10.1038/nature01071

  116. Young L.E., Fernandes K., McEvoy T.G., Butterwith S.C., Gutierrez C.G., Carolan C., Broadbent P.J., Robinson J.J., Wilmut I., Sinclair K.D. 2001. Epigenetic change in IGF2R is associated with fetal overgrowth after sheep embryo culture. Nat. Genet. V. 27. P. 153. https://doi.org/10.1038/84769

  117. Young R.A. 2011. Control of the embryonic stem cell state. Cell. V. 144. P. 940. https://doi.org/10.1016/j.cell.2011.01.032

  118. Zhang F., Hu Y., Huang P., Toleman C.A., Paterson A.J., Kudlow J.E. 2007. Proteasome function is regulated by cyclic AMP-dependent protein kinase through phosphorylation of Rpt6. J. Biol. Chem. V. 282. P. 22460. https://doi.org/10.1074/jbc.M702439200

  119. Zhang F., Laiho M. 2003. On and off: proteasome and TGF-beta signaling. Exp. Cell Res. V. 291. P. 275. https://doi.org/10.1016/j.yexcr.2003.07.007

  120. Zhang X., Linder S., Bazzaro M. 2020. Drug development targeting the ubiquitin–proteasome system (UPS) for the treatment of human cancers. Cancers. V. 12. P. 902. https://doi.org/10.3390/cancers12040902

  121. Zhang Y., Ding H., Wang X., Wang X., Wan S., Xu A., Gan R., Ye S.-D. 2021. MK2 promotes Tfcp2l1 degradation via β-TrCP ubiquitin ligase to regulate mouse embryonic stem cell self-renewal. Cell Rep. V. 37. P. 109949. https://doi.org/10.1016/j.celrep.2021.109949

  122. Zhao S., Zhang C., Xu J., Liu S., Yu L., Chen S., Wen H., Li Z., Liu N. 2022. Dppa3 facilitates self-renewal of embryonic stem cells by stabilization of pluripotent factors. Stem Cell Res. Ther. V. 13. P. 169. https://doi.org/10.1186/s13287-022-02846-8

  123. Zhou L., Mideros S.X., Bao L., Hanlon R., Arredondo F.D., Tripathy S., Krampis K., Jerauld A., Evans C., St Martin S.K. 2009. Infection and genotype remodel the entire soybean transcriptome. BMC Genomics. V. 10. P. 49. https://doi.org/10.1186/1471-2164-10-49

  124. Zhou W., Zhu P., Wang J., Pascual G., Ohgi K.A., Lozach J., Glass C.K., Rosenfeld M.G. 2008. Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation. Mol. Cell. V. 29. P. 69. https://doi.org/10.1016/j.molcel.2007.11.002

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