Abstract
Histone proteins and their diverse array of post-translational modifications have been subject to exquisite evolutionary conservation in eukaryotes. Accordingly, the factors that control the deposition, removal, and interpretation of histone modifications are themselves deeply conserved, with many strongly impacting development and disease in humans. Of these modifications, lysine methylation has in recent years emerged as a prevalent modification occurring on histone proteins. However, although numerous lysine methyltransferase and demethylase enzymes have been extensively characterized with respect to their ability to control methylation at specific histone residues, their known targets have been rapidly expanding to include the methylation of non-histone proteins as well. These findings extend the role of lysine methylation well-beyond the established histone code and its role in epigenetic regulation. To date, this lysine methylation has been found to directly regulate protein sub-cellular localization, protein-protein interactions, and has also been found to interplay with other post-translational modifications. As a result, lysine methylation is now known to coordinate protein function and be a key driving of a growing list of cellular signaling events, including apoptosis, DNA damage repair, protein translation, cell growth, and signal transduction among others. This chapter will provide insight into the role of protein lysine methylation and its role in regulating protein function and its impact on human development and disease.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Accari SL, Fisher PR (2015) Emerging roles of JmjC domain-containing proteins. Int Rev Cell Mol Biol 319:165–220
Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA 51:786–794
Ambler R, Rees M (1959) Epsilon-N-methyl-lysine in bacterial flagellar protein. Nature 184:56–57
Anderson D, Koch CA, Grey L et al (1990) Binding of SH2 domains of phospholipase C gamma 1, GAP, and Src to activated growth factor receptors. Science 250:979–982
Arrowsmith CH, Bountra C, Fish PV et al (2012) Epigenetic protein families: a new frontier for drug discovery. Nat Rev Drug Discov 11:384–400
Baek SH, Kim K (2016) Regulation of HIF-1α stability by lysine methylation. BMB Rep 49:245–246
Barbier M, Owings JP, MartÃnez-Ramos I et al (2013) Lysine trimethylation of EF-Tu mimics platelet-activating factor to initiate Pseudomonas aeruginosa pneumonia. MBio 4:e00207–e00213
Biet F, de Melo Marques MA, Grayon M et al (2007) Mycobacterium smegmatis produces an HBHA homologue which is not involved in epithelial adherence. Microbes Infect 9:175–182
Biggar KK, Li SS (2015) Non-histone protein methylation as a regulator of cellular signalling and function. Nat Rev Mol Cell Biol 16:5–17
Brahms H, Meheus L, de Brabandere V et al (2001) Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B’ and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA 7:1531–1542
Cao XJ, Garcia BA (2016) Global proteomics analysis of protein lysine methylation. Curr Protoc Protein Sci 86:24.8.1–24.8.19
Cao XJ, Arnaudo AM, Garcia BA (2013) Large-scale global identification of protein lysine methylation in vivo. Epigenetics 8:477–485
Carlson SM, Gozani O (2016) Nonhistone lysine methylation in the regulation of cancer pathways. Cold Spring Harb Perspect Med 6:11
Carlson SM, Moore KE, Green EM et al (2014) Proteome-wide enrichment of proteins modified by lysine methylation. Nat Protoc 9:37–50
Casciello F, Windloch K, Gannon F et al (2015) Functional role of G9a histone methyltransferase in cancer. Front Immunol 6:487
Chao CC, Wu SL, Ching WM (2004) Using LC-MS with de novo software to fully characterize the multiple methylations of lysine residues in a recombinant fragment of an outer membrane protein from a virulent strain of Rickettsia prowazekii. Biochim Biophys Acta 1702:145–152
Chao CC, Zhang Z, Wang H et al (2008) Serological reactivity and biochemical characterization of methylated and unmethylated forms of a recombinant protein fragment derived from outer membrane protein B of Rickettsia typhi. Clin Vaccine Immunol 15:684–690
Chen Y, Zhu WG (2016) Biological function and regulation of histone and non-histone lysine methylation in response to DNA damage. Acta Biochim Biophys Sin 48:603–616
Chen H, Xue Y, Huang N et al (2006a) MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res 34:W249–W253
Chen Z, Zang J, Whetstine J et al (2006b) Structural insights into histone demethylation by JMJD2 family members. Cell 125:691–702
Chen L, Vasilatos SN, Qin Y et al (2017) Functional characterization of lysine-specific demethylase 2 (LSD2/KDM1B) in breast cancer progression. Oncotarget 8:81737–81753
Cho HS, Hayami S, Toyokawa G et al (2012) RB1 methylation by SMYD2 enhances cell cycle progression through an increase of RB1 phosphorylation. Neoplasia 14:476–486
Chuikov S, Kurash JK, Wilson JR et al (2004) Regulation of p53 activity through lysine methylation. Nature 432:353–360
Ciccia A, Elledge SJ (2010) The DNA damage response: making it safe to play with knives. Mol Cell 40:179–204
Clarke SG (2013) Protein methylation at the surface and buried deep: thinking outside the histone box. Trends Biochem Sci 38:243–252
Cloutier P, Lavallée-Adam M, Faubert D et al (2014) Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin. J Proteome 100:115–124
D’Oto A, Tian QW, Davidoff AM et al (2016) Histone demethylases and their roles in cancer epigenetics. J Med Oncol Ther 1:34
Debler EW, Jain K, Warmack RA et al (2016) A glutamate/aspartate switch controls product specificity in a protein arginine methyltransferase. Proc Natl Acad Sci USA 113:2068–2073
Delogu G, Chiacchio T, Vanini V et al (2011) Methylated HBHA produced in M. smegmatis discriminates between active and non-active TB disease among the QFT-IT-responders. Eur Respir J 38:1901
Dhami GK, Liu H, Galka M et al (2013) Dynamic methylation of Numb by Set8 regulates its binding to p53 and apoptosis. Mol Cell 50:565–576
Duan G, Walther D (2015) The roles of post-translational modifications in the context of protein interaction networks. PLoS Comput Biol 11:1–23
Dulev S, Tkach J, Lin S et al (2014) SET8 methyltransferase activity during the DNA double-strand break response is required for recruitment of 53BP1. EMBO Rep 15(11):1163–1174
Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8:286–298
Falnes PØ, Jakobsson ME, Davydova E et al (2016) Protein lysine methylation by seven-β-strand methyltransferases. Biochem J 473:1995–2009
Fang R, Chen F, Dong Z et al (2013) LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell 49:558–570
Freitag M (2017) Histone methylation by SET domain proteins in fungi. Annu Rev Microbiol 71:413–439
Gayatri S, Bedford MT (2014) Readers of histone methylarginine marks. Biochim Biophys Acta 1839:702–710
Greer EL, Shi Y (2012) Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 13:343–357
Guo A, Gu H, Zhou J et al (2014) Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol Cell Proteomics 13:372–387
Hamamoto R, Silva FP, Tsuge M et al (2006) Enhanced SMYD3 expression is essential for the growth of breast cancer cells. Cancer Sci 97:113–118
Hamamoto R, Saloura V, Nakamura Y (2015) Critical roles of non-histone protein lysine methylation in human tumorigenesis. Nat Rev Cancer 15:110–124
Helin K, Dhanak D (2013) Chromatin proteins and modifications as drug targets. Nature 502:480–488
Horton JR, Upadhyay AK, Qi HH et al (2010) Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol 17:38–43
Hou H, Yu H (2010) Structural insights into histone lysine demethylation. Curr Opin Struct Biol 20:739–748
Hu LL, Li Z, Wang K et al (2011) Prediction and analysis of protein methylarginine and methyllysine based on Multisequence features. Biopolymers 95:763–771
Huang J, Perez-Burgos L, Placek BJ et al (2006) Repression of p53 activity by Smyd2-mediated methylation. Nature 444:629–632
Huang J, Sengupta R, Espejo AB et al (2007) p53 is regulated by the lysine demethylase LSD1. Nature 449:105–108
Huang J, Dorsey J, Chuikov S et al (2010) G9a and Glp methylate lysine 373 in the tumor suppressor p53. J Biol Chem 285:9636–9641
Hyun K, Jeon J, Park K et al (2017) Writing, erasing and reading histone lysine methylations. Exp Mol Med 49:e324
Jakobsson ME, Moen A, Bousset L et al (2013) Identification and characterization of a novel human methyltransferase modulating Hsp70 function through lysine methylation. J Biol Chem 288:27752–27763
Jørgensen S, Elvers I, Trelle MB et al (2007) The histone methyltransferase SET8 is required for S-phase progression. J Cell Biol 179:1337–1345
Kernstock S, Davydova E, Jakobsson M et al (2012) Lysine methylation of VCP by a member of a novel human protein methyltransferase family. Nat Commun 3:1038
Kim S, Paik WK (1965) Studies on the origin of epsilon-N-methyl-L-lysine in protein. J Biol Chem 240:4629–4634
Kim Y, Nam HJ, Lee J et al (2016a) Methylation-dependent regulation of HIF-1α stability restricts retinal and tumour angiogenesis. Nat Commun 7:10347
Kim JH, Yoo BC, Yang WS et al (2016b) The role of protein arginine methyltransferases in inflammatory responses. Mediat Inflamm 2016:4028353
Klose RJ, Kallin EM, Zhang Y (2006) JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 7:715–727
Kooistra SM, Helin K (2012) Molecular mechanisms and potential functions of histone demethylases. Nat Rev Mol Cell Biol 13:297–311
Kunizaki M, Hamamoto R, Silva FP et al (2007) The lysine 831 of vascular endothelial growth factor receptor 1 is a novel target of methylation by SMYD3. Cancer Res 67:10759–10765
Lachner M, O’Carroll D, Rea S et al (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410:116–120
Lanouette S, Mongeon V, Figeys D et al (2014) The functional diversity of protein lysine methylation. Mol Syst Biol 10:724
Lee JY, Park JH, Choi HJ et al (2017) LSD1 demethylates HIF1α to inhibit hydroxylation and ubiquitin-mediated degradation in tumor angiogenesis. Oncogene 36:5512–5521
Liu H, Galka M, Mori E et al (2013) A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response. Mol Cell 50:723–735
Liu X, Chen Z, Xu C et al (2015) Repression of hypoxia-inducible factor α signaling by Set7-mediated methylation. Nucleic Acids Res 43:5081–5098
Liu Y, Wang Y, Chen C et al (2017) LSD1 binds to HPV16 E7 and promotes the epithelial-mesenchymal transition in cervical cancer by demethylating histones at the Vimentin promoter. Oncotarget 8:11329–11342
Lu X, Simon MD, Chodaparambil JV et al (2008) The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat Struct Mol Biol 15:1122–1124
Marabelli C, Marrocco B, Mattevi A (2016) The growing structural and functional complexity of the LSD1/KDM1A histone demethylase. Curr Opin Struct Biol 41:135–144
Mazur PK, Reynoird N, Khatri P et al (2014) SMYD3 links lysine methylation of MAP 3K2 to Ras-driven cancer. Nature 510:283–287
Murray K (1964) The occurrence of epsilon-N-methyl lysine in histones. Biochemistry 3:10–15
Nagasawa S, Sedukhina AS, Nakagawa Y et al (2015) LSD1 overexpression is associated with poor prognosis in basal-like breast cancer, and sensitivity to PARP inhibition. PLoS One 10:e0118002
Ng SS, Kavanagh KL, McDonough M et al (2007) Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature 448:87–91
Ng SS, Yue WW, Oppermann U et al (2009) Dynamic protein methylation in chromatin biology. Cell Mol Life Sci 66:407–422
Nishioka K, Rice JC, Sarma K et al (2002) PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell 9:1201–1213
Petrossian TC, Clarke SG (2009a) Bioinformatic identification of novel methyltransferases. Epigenomics 1:163–175
Petrossian TC, Clarke SG (2009b) Multiple motif scanning to identify methyltransferases from the yeast proteome. Mol Cell Proteomics 8:1516–1526
Poulard C, Rambaud J, Hussein N et al (2014) JMJD6 regulates ERα methylation on arginine. PLoS One 9:e87982
Qiu WR, Xiao X, Lin WZ et al (2014) iMethyl-PseAAC: identification of protein methylation sites via a pseudo amino acid composition approach. Biomed Res Int 2014:947416
Scoumanne A, Chen X (2008) Protein methylation: a new regulator of the p53 tumor suppressor. Histol Histopathol 23:1143–1149
Shao J, Xu D, Tsai SN et al (2009) Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PLoS One 4:e4920
Shi Y, Lan F, Matson C et al (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941–953
Shi X, Kachirskaia I, Yamaguchi H et al (2007) Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol Cell 27:636–646
Shi SP, Qiu JD, Sun XY et al (2012) PMeS: prediction of methylation sites based on enhanced feature encoding scheme. PLoS One 7:e38772
Shi Y, Guo Y, Hu Y et al (2015) Position-specific prediction of methylation sites from sequence conservation based on information theory. Sci Rep 5:12403
Shien DM, Lee TY, Chang WC et al (2009) Incorporating structural characteristics for identification of protein methylation sites. J Comput Chem 30:1532–1543
Singer MS, Kahana A, Wolf AJ et al (1998) Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150:613–632
Smith BC, Denu JM (2009) Chemical mechanisms of histone lysine and arginine modifications. Biochim Biophys Acta 1789:45–57
Spillantini MG, Schmidt ML, Lee VM et al (1997) Alpha-synuclein in Lewy bodies. Nature 388:839–840
Stocker B, McDonough MA (1961) Gene determining presence or absence of [varepsilon]-N-methyl-lysine in Salmonella flagellar protein. Nature 189:556–558
Walport LJ, Hopkinson RJ, Chowdhury R et al (2016) Arginine demethylation is catalysed by a subset of JmjC histone lysine demethylases. Nat Commun 7:11974
West LE, Gozani O (2011) Regulation of p53 function by lysine methylation. Epigenomics 3:363–369
West LE, Roy S, Lachmi-Weiner K et al (2010) The MBT repeats of L3MBTL1 link SET8-mediated p53 methylation at lysine 382 to target gene repression. J Biol Chem 285:37725–37732
Wu Z, Connolly J, Biggar KK (2017) Beyond histones: the expanding roles of lysine methylation. FEBS J 284:2732–2744
Xie Q, Hao Y, Tao L et al (2012) Lysine methylation of FOXO3 regulates oxidative stress-induced neuronal cell death. EMBO Rep 13:371–377
Yang Y, Hu L, Wang P et al (2010) Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell Res 20:886
Yang SJ, Park YS, Cho JH et al (2017) Regulation of hypoxia responses by flavin adenine dinucleotide-dependent modulation of HIF-1α protein stability. EMBO J 36:1011–1028
Zhang X, Zhou L, Cheng X (2000) Crystal structure of the conserved core of protein arginine methyltransferase PRMT3. EMBO J 19:3509–3519
Zhu W (2012) Methylation of FoxO3 regulates neuronal cell death. Acta Pharmacol Sin 33:577
Acknowledgements
This work was supported by an NSERC discovery grant to K.K. Biggar.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Adhikary, H., Bakos, O., Biggar, K.K. (2019). The Role of Protein Lysine Methylation in the Regulation of Protein Function: Looking Beyond the Histone Code. In: Jurga, S., Barciszewski, J. (eds) The DNA, RNA, and Histone Methylomes. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-030-14792-1_18
Download citation
DOI: https://doi.org/10.1007/978-3-030-14792-1_18
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-14791-4
Online ISBN: 978-3-030-14792-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)