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Control of protein stability by post-translational modifications

Author

Listed:
  • Ji Min Lee

    (Korea Advanced Institute of Science and Technology)

  • Henrik M. Hammarén

    (European Molecular Biology Laboratory)

  • Mikhail M. Savitski

    (European Molecular Biology Laboratory)

  • Sung Hee Baek

    (Seoul National University)

Abstract

Post-translational modifications (PTMs) can occur on specific amino acids localized within regulatory domains of target proteins, which control a protein’s stability. These regions, called degrons, are often controlled by PTMs, which act as signals to expedite protein degradation (PTM-activated degrons) or to forestall degradation and stabilize a protein (PTM-inactivated degrons). We summarize current knowledge of the regulation of protein stability by various PTMs. We aim to display the variety and breadth of known mechanisms of regulation as well as highlight common themes in PTM-regulated degrons to enhance potential for identifying novel drug targets where druggable targets are currently lacking.

Suggested Citation

  • Ji Min Lee & Henrik M. Hammarén & Mikhail M. Savitski & Sung Hee Baek, 2023. "Control of protein stability by post-translational modifications," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-35795-8
    DOI: 10.1038/s41467-023-35795-8
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    as
    1. Feng Leng & Jiekai Yu & Chunxiao Zhang & Salvador Alejo & Nam Hoang & Hong Sun & Fei Lu & Hui Zhang, 2018. "Methylated DNMT1 and E2F1 are targeted for proteolysis by L3MBTL3 and CRL4DCAF5 ubiquitin ligase," Nature Communications, Nature, vol. 9(1), pages 1-17, December.
    2. Sergei Chuikov & Julia K. Kurash & Jonathan R. Wilson & Bing Xiao & Neil Justin & Gleb S. Ivanov & Kristine McKinney & Paul Tempst & Carol Prives & Steven J. Gamblin & Nickolai A. Barlev & Danny Reinb, 2004. "Regulation of p53 activity through lysine methylation," Nature, Nature, vol. 432(7015), pages 353-360, November.
    3. Laura D. Gallego & Maren Schneider & Chitvan Mittal & Anete Romanauska & Ricardo M. Gudino Carrillo & Tobias Schubert & B. Franklin Pugh & Alwin Köhler, 2020. "Phase separation directs ubiquitination of gene-body nucleosomes," Nature, Nature, vol. 579(7800), pages 592-597, March.
    4. Rajneesh Pathania & Sabarish Ramachandran & Selvakumar Elangovan & Ravi Padia & Pengyi Yang & Senthilkumar Cinghu & Rajalakshmi Veeranan-Karmegam & Pachiappan Arjunan & Jaya P. Gnana-Prakasam & Fulzel, 2015. "DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis," Nature Communications, Nature, vol. 6(1), pages 1-11, November.
    5. Tarig Bashir & N. Valerio Dorrello & Virginia Amador & Daniele Guardavaccaro & Michele Pagano, 2004. "Control of the SCFSkp2–Cks1 ubiquitin ligase by the APC/CCdh1 ubiquitin ligase," Nature, Nature, vol. 428(6979), pages 190-193, March.
    6. Björn Schwanhäusser & Dorothea Busse & Na Li & Gunnar Dittmar & Johannes Schuchhardt & Jana Wolf & Wei Chen & Matthias Selbach, 2011. "Global quantification of mammalian gene expression control," Nature, Nature, vol. 473(7347), pages 337-342, May.
    7. Toby Mathieson & Holger Franken & Jan Kosinski & Nils Kurzawa & Nico Zinn & Gavain Sweetman & Daniel Poeckel & Vikram S. Ratnu & Maike Schramm & Isabelle Becher & Michael Steidel & Kyung-Min Noh & Gio, 2018. "Systematic analysis of protein turnover in primary cells," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    8. Wenyi Wei & Nagi G. Ayad & Yong Wan & Guo-Jun Zhang & Marc W. Kirschner & William G. Kaelin, 2004. "Degradation of the SCF component Skp2 in cell-cycle phase G1 by the anaphase-promoting complex," Nature, Nature, vol. 428(6979), pages 194-198, March.
    9. Manas K. Santra & Narendra Wajapeyee & Michael R. Green, 2009. "F-box protein FBXO31 mediates cyclin D1 degradation to induce G1 arrest after DNA damage," Nature, Nature, vol. 459(7247), pages 722-725, June.
    10. Xin Liu & Ling Wang & Kehao Zhao & Paul R. Thompson & Yousang Hwang & Ronen Marmorstein & Philip A. Cole, 2008. "The structural basis of protein acetylation by the p300/CBP transcriptional coactivator," Nature, Nature, vol. 451(7180), pages 846-850, February.
    11. Takaaki Tsunematsu & Yoshihiro Takihara & Naozumi Ishimaru & Michele Pagano & Takashi Takata & Yasusei Kudo, 2013. "Aurora-A controls pre-replicative complex assembly and DNA replication by stabilizing geminin in mitosis," Nature Communications, Nature, vol. 4(1), pages 1-11, October.
    12. Mainak Guharoy & Pallab Bhowmick & Mohamed Sallam & Peter Tompa, 2016. "Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system," Nature Communications, Nature, vol. 7(1), pages 1-13, April.
    13. Alaji Bah & Robert M. Vernon & Zeba Siddiqui & Mickaël Krzeminski & Ranjith Muhandiram & Charlie Zhao & Nahum Sonenberg & Lewis E. Kay & Julie D. Forman-Kay, 2015. "Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch," Nature, Nature, vol. 519(7541), pages 106-109, March.
    14. J. Wade Harper & Eric J. Bennett, 2016. "Proteome complexity and the forces that drive proteome imbalance," Nature, Nature, vol. 537(7620), pages 328-338, September.
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