PTMs in Conversation: Activity and Function of Deubiquitinating Enzymes Regulated Via Post-translational Modifications

Overview

Journal Cell Biochem Biophys

Specialties Biochemistry
Biophysics
Cell Biology

Date 2011 Apr 12

PMID 21480003

Citations 44

Authors

Benedikt M Kessler

Mariola J Edelmann

Affiliations

Soon will be listed here.

Abstract

Deubiquitinating enzymes (DUBs) constitute a diverse protein family and their impact on numerous biological and pathological processes has now been widely appreciated. Many DUB functions have to be tightly controlled within the cell, and this can be achieved in several ways, such as substrate-induced conformational changes, binding to adaptor proteins, proteolytic cleavage, and post-translational modifications (PTMs). This review is focused on the role of PTMs including monoubiquitination, sumoylation, acetylation, and phosphorylation as characterized and putative regulative factors of DUB function. Although this aspect of DUB functionality has not been yet thoroughly studied, PTMs represent a versatile and reversible method of controlling the role of DUBs in biological processes. In several cases PTMs might constitute a feedback mechanism insuring proper functioning of the ubiquitin proteasome system and other DUB-related pathways.

Citing Articles

XGBoost-enhanced ensemble model using discriminative hybrid features for the prediction of sumoylation sites.

Khan S, Noor S, Javed T, Naseem A, Aslam F, AlQahtani S BioData Min. 2025; 18(1):12.

PMID: 39901279 PMC: 11792219. DOI: 10.1186/s13040-024-00415-8.

PSSM-Sumo: deep learning based intelligent model for prediction of sumoylation sites using discriminative features.

Khan S, AlQahtani S, Noor S, Ahmad N BMC Bioinformatics. 2024; 25(1):284.

PMID: 39215231 PMC: 11363370. DOI: 10.1186/s12859-024-05917-0.

Phosphorylation-dependent deubiquitinase OTUD3 regulates YY1 stability and promotes colorectal cancer progression.

Wu L, Zhou Z, Yu Y, Cheng C, Zhou S, Yan Y Cell Death Dis. 2024; 15(2):137.

PMID: 38351178 PMC: 10864350. DOI: 10.1038/s41419-024-06526-8.

Phosphorylation of USP27X by GSK3β maintains the stability and oncogenic functions of CBX2.

Xing Y, Ba-Tu J, Dong C, Cao X, Li B, Jia X Cell Death Dis. 2023; 14(11):782.

PMID: 38030604 PMC: 10687032. DOI: 10.1038/s41419-023-06304-y.

Enhancing Sumoylation Site Prediction: A Deep Neural Network with Discriminative Features.

Khan S, Khan M, Iqbal N, Dilshad N, Almufareh M, Alsubaie N Life (Basel). 2023; 13(11).

PMID: 38004293 PMC: 10672286. DOI: 10.3390/life13112153.

References

Nijman S, Luna-Vargas M, Velds A, Brummelkamp T, Dirac A, Sixma T . A genomic and functional inventory of deubiquitinating enzymes. Cell. 2005; 123(5):773-86. DOI: 10.1016/j.cell.2005.11.007. View

Shen C, Ye Y, Robertson S, Lau A, Mak D, Chou M . Calcium/calmodulin regulates ubiquitination of the ubiquitin-specific protease TRE17/USP6. J Biol Chem. 2005; 280(43):35967-73. DOI: 10.1074/jbc.M505220200. View

Oliveira A, Hsi B, Weremowicz S, Rosenberg A, Dal Cin P, Joseph N . USP6 (Tre2) fusion oncogenes in aneurysmal bone cyst. Cancer Res. 2004; 64(6):1920-3. DOI: 10.1158/0008-5472.can-03-2827. View

Boone D, Turer E, Lee E, Ahmad R, Wheeler M, Tsui C . The ubiquitin-modifying enzyme A20 is required for termination of Toll-like receptor responses. Nat Immunol. 2004; 5(10):1052-60. DOI: 10.1038/ni1110. View

Hu M, Li P, Li M, Li W, Yao T, Wu J . Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell. 2003; 111(7):1041-54. DOI: 10.1016/s0092-8674(02)01199-6. View

Reyes-Turcu F, Horton J, Mullally J, Heroux A, Cheng X, Wilkinson K . The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell. 2006; 124(6):1197-208. DOI: 10.1016/j.cell.2006.02.038. View

Reiley W, Zhang M, Wu X, Granger E, Sun S . Regulation of the deubiquitinating enzyme CYLD by IkappaB kinase gamma-dependent phosphorylation. Mol Cell Biol. 2005; 25(10):3886-95. PMC: 1087725. DOI: 10.1128/MCB.25.10.3886-3895.2005. View

Suresh B, Ramakrishna S, Lee H, Choi J, Kim J, Ahn W . K48- and K63-linked polyubiquitination of deubiquitinating enzyme USP44. Cell Biol Int. 2010; 34(8):799-808. DOI: 10.1042/CBI20090144. View

Edelmann M, Kramer H, Altun M, Kessler B . Post-translational modification of the deubiquitinating enzyme otubain 1 modulates active RhoA levels and susceptibility to Yersinia invasion. FEBS J. 2010; 277(11):2515-30. DOI: 10.1111/j.1742-4658.2010.07665.x. View

10.

Yuan J, Luo K, Zhang L, Cheville J, Lou Z . USP10 regulates p53 localization and stability by deubiquitinating p53. Cell. 2010; 140(3):384-96. PMC: 2820153. DOI: 10.1016/j.cell.2009.12.032. View

11.

Fernandez-Montalvan A, Bouwmeester T, Joberty G, Mader R, Mahnke M, Pierrat B . Biochemical characterization of USP7 reveals post-translational modification sites and structural requirements for substrate processing and subcellular localization. FEBS J. 2007; 274(16):4256-70. DOI: 10.1111/j.1742-4658.2007.05952.x. View

12.

Imami K, Sugiyama N, Kyono Y, Tomita M, Ishihama Y . Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column. Anal Sci. 2008; 24(1):161-6. DOI: 10.2116/analsci.24.161. View

13.

Molina H, Horn D, Tang N, Mathivanan S, Pandey A . Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A. 2007; 104(7):2199-204. PMC: 1794346. DOI: 10.1073/pnas.0611217104. View

14.

Sui S, Wang J, Yang B, Song L, Zhang J, Chen M . Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy. Proteomics. 2008; 8(10):2024-34. DOI: 10.1002/pmic.200700896. View

15.

Soares L, Seroogy C, Skrenta H, Anandasabapathy N, Lovelace P, Chung C . Two isoforms of otubain 1 regulate T cell anergy via GRAIL. Nat Immunol. 2003; 5(1):45-54. DOI: 10.1038/ni1017. View

16.

Tang L, Deng N, Wang L, Dai J, Wang Z, Jiang X . Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction. Mol Cell Proteomics. 2007; 6(11):1952-67. DOI: 10.1074/mcp.M700120-MCP200. View

17.

Matsuoka S, Ballif B, Smogorzewska A, McDonald 3rd E, Hurov K, Luo J . ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science. 2007; 316(5828):1160-6. DOI: 10.1126/science.1140321. View

18.

Cai J, Crotty T, Reichert E, Carraway 3rd K, Stafforini D, Topham M . Diacylglycerol kinase delta and protein kinase C(alpha) modulate epidermal growth factor receptor abundance and degradation through ubiquitin-specific protease 8. J Biol Chem. 2010; 285(10):6952-9. PMC: 2844144. DOI: 10.1074/jbc.M109.055731. View

19.

Singhal S, Taylor M, Baker R . Deubiquitylating enzymes and disease. BMC Biochem. 2008; 9 Suppl 1:S3. PMC: 2582804. DOI: 10.1186/1471-2091-9-S1-S3. View

20.

Zhang D, Zaugg K, Mak T, Elledge S . A role for the deubiquitinating enzyme USP28 in control of the DNA-damage response. Cell. 2006; 126(3):529-42. DOI: 10.1016/j.cell.2006.06.039. View