Perspectives on molecular mechanisms of post-translational modification and their functional influence on certain diseases
DOI:
https://doi.org/10.5564/pib.v39i1.3143Keywords:
protein modification, protein-protein interaction, disease, database of PTMsAbstract
Post-translational modification (PTM) is a vital biological process significantly impacting protein structure and function. It involves adding functional groups to the main and side chains during and after protein synthesis, thereby modifying their structure and function. PTMs are essential in shaping proteins into their final, functional, and three-dimensional forms. While numerous PTMs are still under active investigation and exploration. Herewith, we briefly overview some of the most prevalent PTMs, elucidate their associated functions, and establish connections between PTMs and a diverse range of diseases. Notably, we elucidate the profound influence of PTMs on neurodegenerative diseases and cancer, and provide a deep understanding of their many effects. Lastly, it considers a concise overview of PTM computational methods and databases, shedding light on the cutting-edge techniques and resources used to analyze and explore post-translational modifications.
Трансляцийн дараах өөрчлөлтийн молекул механизм ба түүний зарим өвчлөлд үзүүлэх нөлөө
Хураангуй. Трансляцийн дараах өөрчлөлт (ТДӨ) нь уургийн нийлэгжлийн үед, эсвэл нийлэгжлийн дараа уургийн гол болон хажуугийн гинжинд функциональ бүлэг нэмэх замаар уургийн бүтэц болон үйл ажиллагаанд нөлөөлдөг биологийн чухал үйл ажиллагааны нэг юм. Маш олон тооны ТДӨ-үүд судлагдсаар байгаа бөгөөд энэхүү тойм өгүүлэлд бид хамгийн түгээмэл арван ТДӨ-үүд болон тэдгээрийн үйл ажиллагааны талаар авч үзэв. Үүнээс гадна ТДӨ нь төрөл бүрийн өвчин, эмгэгтэй холбоотой байдгаас түгээмэл тохиолддог тархи, мэдрэлийн эмгэгүүд болон хавдрын биологийн үйл ажиллагаанд ТДӨ хэрхэн нөлөөлж байгаа талаар, түүнчлэн ТДӨ-ийн судалгааны аргууд болон мэдээллийн сангийн тухай тоймлон танилцуулав.
Түлхүүр үгс: уургийн өөрчлөлт, уураг-уургийн харилцан үйлчлэл, ТДӨ-ийн мэдээллийн сан
Downloads
208
References
P. Vellosillo and P. Minguez, “A global map of associations between types of protein posttranslational modifications and human genetic diseases,” iScience, vol. 24, no. 8, p. 102917, 2021, https://doi.org/10.1016/j.isci.2021.102917.
H. Ryšlavá, V. Hýsková, D. Kavan, and O. Vaněk, “Effect of posttranslational modifications on enzyme function and assembly,” J. Proteomics, vol. 92, pp. 80–109, Apr. 2013, https://doi.org/10.1016/j.jprot.2013.03.025.
S. Zhao et al., “Regulation of cellular metabolism by protein lysine acetylation.,” Science, vol. 327, no. 5968, pp. 1000–1004, Feb. 2010, https://doi.org/10.1126/science.1179689.
N. Blom, T. Sicheritz-Pontén, R. Gupta, S. Gammeltoft, and S. Brunak, “Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence.,” Proteomics, vol. 4, no. 6, pp. 1633–1649, Jun. 2004, https://doi.org/10.1002/pmic.200300771.
F. Sacco, L. Perfetto, L. Castagnoli, and G. Cesareni, “The human phosphatase interactome: An intricate family portrait,” FEBS Lett., vol. 586, no. 17, pp. 2732–2739, Aug. 2012, https://doi.org/10.1016/j.febslet.2012.05.008.
L. A. Pinna and M. Ruzzene, “How do protein kinases recognize their substrates?,” Biochim. Biophys. Acta - Mol. Cell Res., vol. 1314, no. 3, pp. 191–225, Dec. 1996, https://doi.org/10.1016/S0167-4889(96)00083-3.
G. Manning, G. D. Plowman, T. Hunter, and S. Sudarsanam, “Evolution of protein kinase signaling from yeast to man,” Trends Biochem. Sci., vol. 27, no. 10, pp. 514–520, Oct. 2002, https://doi.org/10.1016/S0968-0004(02)02179-5.
F. Ardito, M. Giuliani, D. Perrone, G. Troiano, and L. Lo Muzio, “The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review),” Int. J. Mol. Med., vol. 40, no. 2, pp. 271–280, Aug. 2017, https://doi.org/10.3892/ijmm.2017.3036.
P. Cohen, “The origins of protein phosphorylation,” Nat. Cell Biol., vol. 4, no. 5, pp. E127–E130, May 2002, https://doi.org/10.1038/ncb0502-e127.
S. Ramazi and J. Zahiri, “Posttranslational modifications in proteins: resources, tools and prediction methods.,” Database (Oxford)., vol. 2021, Apr. 2021, https://doi.org/10.1093/database/baab012.
G. A. Khoury, R. C. Baliban, and C. A. Floudas, “Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database,” Sci. Rep., vol. 1, no. 1, p. 90, Sep. 2011, https://doi.org/10.1038/srep00090.
T. Bilbrough, E. Piemontese, and O. Seitz, “Dissecting the role of protein phosphorylation: a chemical biology toolbox,” Chem. Soc. Rev., vol. 51, no. 13, pp. 5691–5730, 2022, https://doi.org/10.1039/D1CS00991E.
A. Drazic, L. M. Myklebust, R. Ree, and T. Arnesen, “The world of protein acetylation,” Biochim. Biophys. Acta - Proteins Proteomics, vol. 1864, no. 10, pp. 1372–1401, Oct. 2016, https://doi.org/10.1016/j.bbapap.2016.06.007.
T. Y. Lee, J. B. K. Hsu, F. M. Lin, W. C. Chang, P. C. Hsu, and H. D. Huang, “N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites,” J. Comput. Chem., vol. 31, no. 15, pp. 2759–2771, Nov. 2010, https://doi.org/10.1002/jcc.21569.
J. Hollebeke, P. Van Damme, and K. Gevaert, “N-terminal acetylation and other functions of N α -acetyltransferases,” bchm, vol. 393, no. 4, pp. 291–298, Apr. 2012, https://doi.org/10.1515/hsz-2011-0228.
S. Thao, C.-S. Chen, H. Zhu, and J. C. Escalante-Semerena, “Nε−Lysine Acetylation of a Bacterial Transcription Factor Inhibits Its DNA-Binding Activity,” PLoS One, vol. 5, no. 12, p. e15123, Dec. 2010, https://doi.org/10.1371/journal.pone.0015123.
X. Yang and S. Grégoire, “Metabolism, cytoskeleton and cellular signalling in the grip of protein N ϵ ‐ and O‐acetylation,” EMBO Rep., vol. 8, no. 6, pp. 556–562, Jun. 2007, https://doi.org/10.1038/sj.embor.7400977.
C. Xia, Y. Tao, M. Li, T. Che, and J. Qu, “Protein acetylation and deacetylation: An important regulatory modification in gene transcription (Review),” Exp. Ther. Med., Jul. 2020, https://doi.org/10.3892/etm.2020.9073.
T. Narita, B. T. Weinert, and C. Choudhary, “Functions and mechanisms of non-histone protein acetylation,” Nat. Rev. Mol. Cell Biol., vol. 20, no. 3, pp. 156–174, Mar. 2019, https://doi.org/10.1038/s41580-018-0081-3.
B. Suresh, J. Lee, H. Kim, and S. Ramakrishna, “Regulation of pluripotency and differentiation by deubiquitinating enzymes.,” Cell Death Differ., vol. 23, no. 8, pp. 1257–1264, Aug. 2016, https://doi.org/10.1038/cdd.2016.53.
M. Sun and X. Zhang, “Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture.,” Cell Biosci., vol. 12, no. 1, p. 126, Aug. 2022, https://doi.org/10.1186/s13578-022-00870-y.
M. Rape, “Ubiquitylation at the crossroads of development and disease.,” Nat. Rev. Mol. Cell Biol., vol. 19, no. 1, pp. 59–70, Jan. 2018, https://doi.org/10.1038/nrm.2017.83.
J. Murn and Y. Shi, “The winding path of protein methylation research: milestones and new frontiers.,” Nat. Rev. Mol. Cell Biol., vol. 18, no. 8, pp. 517–527, Aug. 2017, https://doi.org/10.1038/nrm.2017.35.
D. Y. Lee, C. Teyssier, B. D. Strahl, and M. R. Stallcup, “Role of protein methylation in regulation of transcription.,” Endocr. Rev., vol. 26, no. 2, pp. 147–170, Apr. 2005, https://doi.org/10.1210/er.2004-0008.
F. L. Zhang and P. J. Casey, “Protein prenylation: molecular mechanisms and functional consequences.,” Annu. Rev. Biochem., vol. 65, pp. 241–269, 1996, https://doi.org/10.1146/annurev.bi.65.070196.001325.
N. Xu, N. Shen, X. Wang, S. Jiang, B. Xue, and C. Li, “Protein prenylation and human diseases: a balance of protein farnesylation and geranylgeranylation.,” Sci. China. Life Sci., vol. 58, no. 4, pp. 328–335, Apr. 2015, https://doi.org/10.1007/s11427-015-4836-1.
C. C. Palsuledesai and M. D. Distefano, “Protein prenylation: enzymes, therapeutics, and biotechnology applications.,” ACS Chem. Biol., vol. 10, no. 1, pp. 51–62, Jan. 2015, https://doi.org/10.1021/cb500791f.
A. Jeong, K. F. Suazo, W. G. Wood, M. D. Distefano, and L. Li, “Isoprenoids and protein prenylation: implications in the pathogenesis and therapeutic intervention of Alzheimer’s disease.,” Crit. Rev. Biochem. Mol. Biol., vol. 53, no. 3, pp. 279–310, Jun. 2018, https://doi.org/10.1080/10409238.2018.1458070.
S. Jentsch and I. Psakhye, “Control of Nuclear Activities by Substrate-Selective and Protein-Group SUMOylation,” Annu. Rev. Genet., vol. 47, no. 1, pp. 167–186, Nov. 2013, https://doi.org/10.1146/annurev-genet-111212-133453.
Y.-S. Yang, C.-C. Wang, B.-H. Chen, Y.-H. Hou, K.-S. Hung, and Y.-C. Mao, “Tyrosine sulfation as a protein post-translational modification.,” Molecules, vol. 20, no. 2, pp. 2138–2164, Jan. 2015, https://doi.org/10.3390/molecules20022138.
K. L. Moore, “Protein tyrosine sulfation: a critical posttranslation modification in plants and animals.,” Proc. Natl. Acad. Sci. U. S. A., vol. 106, no. 35, pp. 14741–14742, Sep. 2009, https://doi.org/10.1073/pnas.0908376106.
K. Ohtsubo and J. D. Marth, “Glycosylation in Cellular Mechanisms of Health and Disease,” Cell, vol. 126, no. 5, pp. 855–867, 2006, https://doi.org/10.1016/j.cell.2006.08.019.
P. Messner, “Prokaryotic Protein Glycosylation Is Rapidly Expanding from ‘Curiosity’ to ‘Ubiquity,’” ChemBioChem, vol. 10, no. 13, pp. 2151–2154, Sep. 2009, https://doi.org/10.1002/cbic.200900388.
K. Loaeza-Reyes et al., “An Overview of Glycosylation and its Impact on Cardiovascular Health and Disease,” Front. Mol. Biosci., vol. 8, Nov. 2021, https://doi.org/10.3389/fmolb.2021.751637.
C. Reily, T. J. Stewart, M. B. Renfrow, and J. Novak, “Glycosylation in health and disease.,” Nat. Rev. Nephrol., vol. 15, no. 6, pp. 346–366, Jun. 2019, https://doi.org/10.1038/s41581-019-0129-4.
H. G. Lee, A. A. Lemmon, and C. D. Lima, “SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.,” Proc. Natl. Acad. Sci. U. S. A., vol. 120, no. 1, p. e2213703120, Jan. 2023, https://doi.org/10.1073/pnas.2213703120.
Z.-J. Han, Y.-H. Feng, B.-H. Gu, Y.-M. Li, and H. Chen, “The post-translational modification, SUMOylation, and cancer (Review).,” Int. J. Oncol., vol. 52, no. 4, pp. 1081–1094, Apr. 2018, https://doi.org/10.3892/ijo.2018.4280.
Y. Wang and M. Dasso, “SUMOylation and deSUMOylation at a glance.,” J. Cell Sci., vol. 122, no. Pt 23, pp. 4249–4252, Dec. 2009, https://doi.org/10.1242/jcs.050542.
X. Yang, V. Chatterjee, Y. Ma, E. Zheng, and S. Y. Yuan, “Protein Palmitoylation in Leukocyte Signaling and Function.,” Front. cell Dev. Biol., vol. 8, p. 600368, 2020, https://doi.org/10.3389/fcell.2020.600368.
J. E. Smotrys and M. E. Linder, “Palmitoylation of intracellular signaling proteins: regulation and function.,” Annu. Rev. Biochem., vol. 73, pp. 559–587, 2004, https://doi.org/10.1146/annurev.biochem.73.011303.073954.
M. Qu, X. Zhou, X. Wang, and H. Li, “Lipid-induced S-palmitoylation as a Vital Regulator of Cell Signaling and Disease Development.,” Int. J. Biol. Sci., vol. 17, no. 15, pp. 4223–4237, 2021, https://doi.org/10.7150/ijbs.64046.
X. Guan and C. A. Fierke, “Understanding Protein Palmitoylation: Biological Significance and Enzymology.,” Sci. China. Chem., vol. 54, no. 12, pp. 1888–1897, Dec. 2011, https://doi.org/10.1007/s11426-011-4428-2.
C. Aicart-Ramos, R. A. Valero, and I. Rodriguez-Crespo, “Protein palmitoylation and subcellular trafficking,” Biochim. Biophys. Acta - Biomembr., vol. 1808, no. 12, pp. 2981–2994, Dec. 2011, https://doi.org/10.1016/j.bbamem.2011.07.009.
B. Wang et al., “Protein N-myristoylation: functions and mechanisms in control of innate immunity,” Cell. Mol. Immunol., vol. 18, no. 4, pp. 878–888, 2021, https://doi.org/10.1038/s41423-021-00663-2.
H. Jiang, X. Zhang, X. Chen, P. Aramsangtienchai, Z. Tong, and H. Lin, “Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies.,” Chem. Rev., vol. 118, no. 3, pp. 919–988, Feb. 2018, https://doi.org/10.1021/acs.chemrev.6b00750.
Q. Chen, S. Yang, Y. Zhang, B. Li, H. Xu, and S. Zuo, “Identification of MAD2L1 as a Potential Biomarker in Hepatocellular Carcinoma via Comprehensive Bioinformatics Analysis,” Biomed Res. Int., vol. 2022, https://doi.org/10.1155/2022/9868022.
C. A. Ross and M. A. Poirier, “Opinion: What is the role of protein aggregation in neurodegeneration?,” Nat. Rev. Mol. Cell Biol., vol. 6, no. 11, pp. 891–898, Nov. 2005, https://doi.org/10.1038/nrm1742.
T. N. Shamsi, T. Athar, R. Parveen, and S. Fatima, “A review on protein misfolding, aggregation and strategies to prevent related ailments.,” Int. J. Biol. Macromol., vol. 105, no. Pt 1, pp. 993–1000, Dec. 2017, https://doi.org/10.1016/j.ijbiomac.2017.07.116.
S. N. Thomas et al., “Dual modification of Alzheimer’s disease PHF-tau protein by lysine methylation and ubiquitylation: a mass spectrometry approach.,” Acta Neuropathol., vol. 123, no. 1, pp. 105–117, Jan. 2012, https://doi.org/10.1007/s00401-011-0893-0.
H. Trzeciakiewicz et al., “A Dual Pathogenic Mechanism Links Tau Acetylation to Sporadic Tauopathy.,” Sci. Rep., vol. 7, p. 44102, Mar. 2017, https://doi.org/10.1038/srep44102.
C. L. Hansen, M. O. A. Sommer, and S. R. Quake, “Systematic investigation of protein phase behavior with a microfluidic formulator.,” Proc. Natl. Acad. Sci. U. S. A., vol. 101, no. 40, pp. 14431–14436, Oct. 2004, https://doi.org/10.1073/pnas.0405847101.
K. S. McNaught, C. W. Olanow, B. Halliwell, O. Isacson, and P. Jenner, “Failure of the ubiquitin-proteasome system in Parkinson’s disease.,” Nat. Rev. Neurosci., vol. 2, no. 8, pp. 589–594, Aug. 2001, https://doi.org/10.1038/35086067.
H. Martini-Stoica, Y. Xu, A. Ballabio, and H. Zheng, “The Autophagy-Lysosomal Pathway in Neurodegeneration: A TFEB Perspective.,” Trends Neurosci., vol. 39, no. 4, pp. 221–234, Apr. 2016, https://doi.org/10.1016/j.tins.2016.02.002.
V. F. Langness, R. van der Kant, U. Das, L. Wang, R. D. S. Chaves, and L. S. B. Goldstein, “Cholesterol-lowering drugs reduce APP processing to Aβ by inducing APP dimerization.,” Mol. Biol. Cell, vol. 32, no. 3, pp. 247–259, Feb. 2021, https://doi.org/10.1091/mbc.E20-05-0345.
L. Chen, S. Liu, and Y. Tao, “Regulating tumor suppressor genes: post-translational modifications,” Signal Transduct. Target. Ther., vol. 5, no. 1, p. 90, 2020, https://doi.org/10.1038/s41392-020-0196-9.
Y. W. Wang, J. C. Zuo, C. Chen, and X. H. Li, “Post-translational modifications and immune responses in liver cancer,” Front. Immunol., vol. 14, no. July, pp. 1–7, 2023, https://doi.org/10.3389/fimmu.2023.1230465.
K. T. Bieging, S. S. Mello, and L. D. Attardi, “Unravelling mechanisms of p53-mediated tumour suppression,” Nat. Rev. Cancer, vol. 14, no. 5, pp. 359–370, May 2014, https://doi.org/10.1038/nrc3711.
F. Kruiswijk, C. F. Labuschagne, and K. H. Vousden, “p53 in survival, death and metabolic health: a lifeguard with a licence to kill.,” Nat. Rev. Mol. Cell Biol., vol. 16, no. 7, pp. 393–405, Jul. 2015, https://doi.org/10.1038/nrm4007.
C. Feng, L. Zhang, X. Chang, D. Qin, and T. Zhang, “Regulation of post-translational modification of PD-L1 and advances in tumor immunotherapy,” Front. Immunol., vol. 14, no. July, pp. 1–17, 2023, https://doi.org/10.3389/fimmu.2023.1230135.
A. M. Bode and Z. Dong, “Post-translational modification of p53 in tumorigenesis.,” Nat. Rev. Cancer, vol. 4, no. 10, pp. 793–805, Oct. 2004, https://doi.org/10.1038/nrc1455.
A. G. de Brevern and J. Rebehmed, “Current status of PTMs structural databases: applications, limitations and prospects.,” Amino Acids, vol. 54, no. 4, pp. 575–590, Apr. 2022, https://doi.org/10.1007/s00726-021-03119-z.
Z. Minic et al., “Phosphoproteomic Analysis of Breast Cancer-Derived Small Extracellular Vesicles Reveals Disease-Specific Phosphorylated Enzymes,” Biomedicines, vol. 10, no. 2, p. 408, Feb. 2022, https://doi.org/10.3390/biomedicines10020408.
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2023 Damdinbazar Dolgion
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Copyright on any research article in the Proceedings of the Institute of Biology is retained by the author(s).
The authors grant the Proceedings of the Institute of Biology license to publish the article and identify itself as the original publisher.
Articles in the Proceedings of the Institute of Biology are Open Access articles published under a Creative Commons Attribution-NonCommercial 4.0 International License - CC BY NC.
This license permits use, distribution and reproduction in any medium, provided the original work is properly cited.
