PDF
Abstract
Histone post-translational modifications (HPTMs) are essential for chromatin structure, transcriptional regulation, and DNA repair. Lysine succinylation (Ksuc), a recently identified HPTM, involves the addition of succinyl groups to lysine residues, altering their chemical environment and impacting histone-DNA interactions. This review provides a detailed account of histone lysine succinylation, focusing on its research history, specific modification sites, and regulatory mechanisms. Succinylation primarily occurs at the globular domain and C-terminal regions of histones, with key sites such as H3K79 and H3K122 extensively being studied. Succinyl-CoA serves as the donor molecule for this modification, with enzymatic pathways involving KAT2A, HAT1, and p300, as well as non-enzymatic pathways influenced by metabolic intermediates. Desuccinylation is regulated by enzymes such as sirtuin family and HDAC family members. Histone lysine succinylation enhances chromatin accessibility, promotes gene transcription, and facilitates DNA damage repair. Additionally, this modification is implicated in the progression of diseases such as cancer and hepatitis B virus (HBV) infection, highlighting its potential as a therapeutic target. By exploring the interplay between histone succinylation and cellular metabolism, this review underscores the significance of this novel modification in epigenetic regulation and disease development.
Lead Contact: Jinke Gu.
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
Keywords
Histone
/
Succinylation
/
Desuccinylation
/
Chromatin dynamics
/
Disease
Cite this article
Download citation ▾
Minghui Zhang, Huacai Peng, Zhouzhu Liang, Jinke Gu.
Histone lysine succinylation: a comprehensive review of enzymatic pathways and disease associations.
Genome Instability & Disease, 2025, 6(3): 250-260 DOI:10.1007/s42764-025-00148-w
| [1] |
AlarconC, WicksteedB, PrentkiM, CorkeyBE, RhodesCJ. Succinate is a preferential metabolic stimulus-coupling signal for glucose-induced proinsulin biosynthesis translation. Diabetes, 2002, 51: 2496-2504
|
| [2] |
AliH, et al.. Peroxisomes attenuate cytotoxicity of very long-chain fatty acids. Biochimica Et Biophysica Acta, Molecular and Cell Biology of Lipids, 2023, 1868159259
|
| [3] |
AnandC, SantoshiM, SinghPR, NagarajaV. Rv0802c is an acyltransferase that succinylates and acetylates Mycobacterium tuberculosis nucleoid-associated protein HU. Microbiology (Reading), 2021, 1671
|
| [4] |
AntonenkovVD, HiltunenJK. Transfer of metabolites across the peroxisomal membrane. Biochimica Et Biophysica Acta, 2012, 1822: 1374-1386
|
| [5] |
AudagnottoM, Dal PeraroM. Protein post-translational modifications: In silico prediction tools and molecular modeling. Computational and Structural Biotechnology Journal, 2017, 15: 307-319
|
| [6] |
CaiY, et al.. Identification of new subunits of the multiprotein mammalian TRRAP/TIP60-containing histone acetyltransferase complex. Journal of Biological Chemistry, 2003, 278: 42733-42736
|
| [7] |
CarageaC, SinapovJ, SilvescuA, DobbsD, HonavarV. Glycosylation site prediction using ensembles of support vector machine classifiers. BMC Bioinformatics, 2007, 8438
|
| [8] |
ChenS, et al.. Histone H3K36me3 mediates the genomic instability of Benzo[a]pyrene in human bronchial epithelial cells. Environmental Pollution, 2024, 346123564
|
| [9] |
ChinopoulosC. The mystery of extramitochondrial proteins lysine succinylation. International Journal of Molecular Sciences, 2021, 221
|
| [10] |
ChoiS, et al.. Oxoglutarate dehydrogenase and acetyl-CoA acyltransferase 2 selectively associate with H2A.Z-occupied promoters and are required for histone modifications. Biochimica Et Biophysica Acta (BBA)—Gene Regulatory Mechanisms, 2019, 186219446
|
| [11] |
DaiX, et al.. H2A.Z represses gene expression by modulating promoter nucleosome structure and enhancer histone modifications in arabidopsis. Molecular Plant, 2017, 10: 1274-1292
|
| [12] |
De LucasJR, et al.. Functional characterization of residues within the carnitine/acylcarnitine translocase RX2PANAAXF distinct motif. Molecular Membrane Biology, 2008, 25: 152-163
|
| [13] |
Del MonteF, AgnettiG. Protein post-translational modifications and misfolding: New concepts in heart failure. Proteomics: Clinical Applications, 2014, 8: 534-542
|
| [14] |
DongX, WengZ. The correlation between histone modifications and gene expression. Epigenomics, 2013, 5: 113-116
|
| [15] |
DoyonY, SelleckW, LaneWS, TanS, CoteJ. Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Molecular and Cellular Biology, 2004, 24: 1884-1896
|
| [16] |
DuJ, et al.. Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science, 2011, 334: 806-809
|
| [17] |
FerdinandusseS, DenisS, Van RoermundCW, WandersRJ, DacremontG. Identification of the peroxisomal beta-oxidation enzymes involved in the degradation of long-chain dicarboxylic acids. Journal of Lipid Research, 2004, 45: 1104-1111
|
| [18] |
GaoX, et al.. Systematic analysis of lysine acetylome and succinylome reveals the correlation between modification of H2A.X complexes and DNA damage response in breast cancer. Oncol Reports, 2020, 43: 1819-1830
|
| [19] |
Gonzalez-RamirezM, et al.. Differential contribution to gene expression prediction of histone modifications at enhancers or promoters. PLoS Computational Biology, 2021, 17e1009368
|
| [20] |
HangT, et al.. Structural insights into the molecular mechanism underlying Sirt5-catalyzed desuccinylation of histone peptides. The Biochemical Journal, 2019, 476: 211-223
|
| [21] |
HuB, et al.. Lysine succinylation precisely controls normal erythropoiesis. Haematologica, 2024, 20241
|
| [22] |
HuangH, SabariBR, GarciaBA, AllisCD, ZhaoY. SnapShot: Histone modifications. Cell, 2014, 159: 458-458 e451
|
| [23] |
HuntMC, TillanderV, AlexsonSE. Regulation of peroxisomal lipid metabolism: The role of acyl-CoA and coenzyme A metabolizing enzymes. Biochimie, 2014, 98: 45-55
|
| [24] |
JinQ, et al.. Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO Journal, 2011, 30: 249-262
|
| [25] |
Jin, Y., et al. (2023). Resveratrol rescues cutaneous radiation-induced DNA damage via a novel AMPK/SIRT7/HMGB1 regulatory axis. Cell Death Dis, 13, 847.
|
| [26] |
JingY, et al.. Site-specific installation of succinyl lysine analog into histones reveals the effect of H2BK34 succinylation on nucleosome dynamics. Cell Chemical Biology, 2018, 25: 166-174 e167
|
| [27] |
JingY, et al.. Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility. Nucleic Acids Research, 2020, 48: 9538-9549
|
| [28] |
JingY, LiX, LiuZ, LiXD. Roles of negatively charged histone lysine acylations in regulating nucleosome structure and dynamics. Frontiers in Molecular Biosciences, 2022, 9899013
|
| [29] |
JingY, LiuZ, LiXD. Preparation of site-specific succinylated histone mimics to investigate its impact on nucleosome dynamics. Methods in Molecular Biology, 2022, 2530: 141-157
|
| [30] |
KafkiaE, et al.. Operation of a TCA cycle subnetwork in the mammalian nucleus. Science Advances, 2022, 8eabq5206
|
| [31] |
Kaypee, S., et al. (2023). Epigenetic Cancer Therapy (Second Edition). In S. G. Gray (Ed.) (pp. 459–505). Academic Press, Boston.
|
| [32] |
LeeJM, HammarenHM, SavitskiMM, BaekSH. Control of protein stability by post-translational modifications. Nature Communications, 2023, 14201
|
| [33] |
LiF, et al.. NADP (+)-IDH mutations promote hypersuccinylation that impairs mitochondria respiration and induces apoptosis resistance. Molecular Cell, 2015, 60: 661-675
|
| [34] |
LiJ, et al.. HDAC1/2/3 are major histone desuccinylases critical for promoter desuccinylation. Cell Discov, 2023, 985
|
| [35] |
LiL, et al.. SIRT7 is a histone desuccinylase that functionally links to chromatin compaction and genome stability. Nature Communications, 2016, 712235
|
| [36] |
LiQQ, et al.. Proteomic analysis of proteome and histone post-translational modifications in heat shock protein 90 inhibition-mediated bladder cancer therapeutics. Science and Reports, 2017, 7201
|
| [37] |
LiW, et al.. Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation. Nature Communications, 2022, 137414
|
| [38] |
LiX, et al.. Systematic identification of the lysine succinylation in the protozoan parasite Toxoplasma gondii. Journal of Proteome Research, 2014, 13: 6087-6095
|
| [39] |
LiuJ, ShangguanY, TangD, DaiY. Histone succinylation and its function on the nucleosome. Journal of Cellular and Molecular Medicine, 2021, 25: 7101-7109
|
| [40] |
LiuX, et al.. Dietary succinate supplementation to maternal mice improves fetal brown adipose tissue development and thermogenesis of female offspring. Journal of Nutritional Biochemistry, 2022, 100108908
|
| [41] |
Mehmel, M., et al. (2020). Nicotinamide Riboside—The Current State of Research and Therapeutic Uses. Nutrients, 12(6), 1616.
|
| [42] |
NardelliSC, et al.. The histone code of Toxoplasma gondii comprises conserved and unique posttranslational modifications. Mbio, 2013, 4: e00922-e1913
|
| [43] |
Natsume-KitataniY, MamitsukaH. Classification of promoters based on the combination of core promoter elements exhibits different histone modification patterns. PLoS ONE, 2016, 11e0151917
|
| [44] |
NieL, et al.. The landscape of histone modifications in a high-fat diet-induced obese (DIO) mouse model. Molecular and Cellular Proteomics, 2017, 16: 1324-1334
|
| [45] |
PaikWK, PearsonD, LeeHW, KimS. Nonenzymatic acetylation of histones with acetyl-CoA. Biochimica Et Biophysica Acta, 1970, 213: 513-522
|
| [46] |
PalmieriF. The mitochondrial transporter family (SLC25): Physiological and pathological implications. Pflugers Archiv: European Journal of Physiology, 2004, 447: 689-709
|
| [47] |
ParkJ, et al.. SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. Molecular Cell, 2013, 50: 919-930
|
| [48] |
PineiroM, HernandezF, PalacianE. Succinylation of histone amino groups facilitates transcription of nucleosomal cores. Biochimica Et Biophysica Acta, 1992, 1129: 183-187
|
| [49] |
PunziG, et al.. SLC25A10 biallelic mutations in intractable epileptic encephalopathy with complex I deficiency. Human Molecular Genetics, 2018, 27: 499-504
|
| [50] |
QinYP, et al.. KAT2A promotes hepatitis b virus transcription and replication through epigenetic regulation of cccDNA minichromosome. Frontiers in Microbiology, 2021, 12795388
|
| [51] |
RandoOJ. Global patterns of histone modifications. Current Opinion in Genetics and Development, 2007, 17: 94-99
|
| [52] |
RizzoC, et al.. Measurement of succinyl-carnitine and methylmalonyl-carnitine on dried blood spot by liquid chromatography-tandem mass spectrometry. Clinica Chimica Acta, 2014, 429: 30-33
|
| [53] |
RosenR, et al.. Probing the active site of homoserine trans-succinylase. FEBS Letters, 2004, 577: 386-392
|
| [54] |
RyslavaH, DoubnerovaV, KavanD, VanekO. Effect of posttranslational modifications on enzyme function and assembly. Journal of Proteomics, 2013, 92: 80-109
|
| [55] |
SealRL, et al.. A standardized nomenclature for mammalian histone genes. Epigenetics and Chromatin, 2022, 1534
|
| [56] |
SimithyJ, et al.. Characterization of histone acylations links chromatin modifications with metabolism. Nature Communications, 2017, 81141
|
| [57] |
SmestadJ, ErberL, ChenY, MaherLJIII. Chromatin succinylation correlates with active gene expression and is perturbed by defective TCA cycle metabolism. iScience, 2018, 2: 63-75
|
| [58] |
SoneK, et al.. Critical role of lysine 134 methylation on histone H2AX for gamma-H2AX production and DNA repair. Nature Communications, 2014, 55691
|
| [59] |
SongH, et al.. Histone post-translational modification and the DNA damage response. Genes and Diseases, 2023, 10: 1429-1444
|
| [60] |
SongMJ, et al.. Role of histone modification in chromatin-mediated transcriptional repression in protozoan parasite Trichomonas vaginalis. BMB Reports, 2024, 20241
|
| [61] |
TongY, et al.. KAT2A succinyltransferase activity-mediated 14-3-3zeta upregulation promotes beta-catenin stabilization-dependent glycolysis and proliferation of pancreatic carcinoma cells. Cancer Letters, 2020, 469: 1-10
|
| [62] |
VenkateshS, WorkmanJL. Histone exchange, chromatin structure and the regulation of transcription. Nature Reviews Molecular Cell Biology, 2015, 16: 178-189
|
| [63] |
WangY, et al.. KAT2A coupled with the alpha-KGDH complex acts as a histone H3 succinyltransferase. Nature, 2017, 552: 273-277
|
| [64] |
WangY, et al.. Identification of the YEATS domain of GAS41 as a pH-dependent reader of histone succinylation. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115: 2365-2370
|
| [65] |
WangY, GuoYR, XingD, TaoYJ, LuZ. Supramolecular assembly of KAT2A with succinyl-CoA for histone succinylation. Cell Discov, 2018, 447
|
| [66] |
WangZA, et al.. A versatile approach for site-specific lysine acylation in proteins. Angewandte Chemie (International Edition in English), 2017, 56: 1643-1647
|
| [67] |
WestinMA, HuntMC, AlexsonSE. The identification of a succinyl-CoA thioesterase suggests a novel pathway for succinate production in peroxisomes. Journal of Biological Chemistry, 2005, 280: 38125-38132
|
| [68] |
XieZ, et al.. Lysine succinylation and lysine malonylation in histones. Molecular and Cellular Proteomics, 2012, 11: 100-107
|
| [69] |
XuX, et al.. The first succinylome profile of Trichophyton rubrum reveals lysine succinylation on proteins involved in various key cellular processes. BMC Genomics, 2017, 18577
|
| [70] |
YangG, et al.. Histone acetyltransferase 1 is a succinyltransferase for histones and non-histones and promotes tumorigenesis. EMBO Reports, 2021, 22e50967
|
| [71] |
YangY, GibsonGE. Succinylation links metabolism to protein functions. Neurochemical Research, 2019, 44: 2346-2359
|
| [72] |
YangYH, WuSF, ZhuYP, YangJT, LiuJF. Global profiling of lysine succinylation in human lungs. Proteomics, 2022, 22e2100381
|
| [73] |
YuHB, et al.. SIRT7 restricts HBV transcription and replication through catalyzing desuccinylation of histone H3 associated with cccDNA minichromosome. Clinical Science (London, England), 2021, 135: 1505-1522
|
| [74] |
YuanY, et al.. IFN-alpha confers epigenetic regulation of HBV cccDNA minichromosome by modulating GCN5-mediated succinylation of histone H3K79 to clear HBV cccDNA. Clinical Epigenetics, 2020, 12135
|
| [75] |
ZhangJ, et al.. PARylated PDHE1alpha generates acetyl-CoA for local chromatin acetylation and DNA damage repair. Nature Structural and Molecular Biology, 2023, 30: 1719-1734
|
| [76] |
ZhangYJ, et al.. Current treatment strategies targeting histone deacetylase inhibitors in acute lymphocytic leukemia: a systematic review. Frontiers in Oncology, 2024, 141324859
|
| [77] |
Zorro ShahidianL, et al.. Succinylation of H3K122 destabilizes nucleosomes and enhances transcription. EMBO Reports, 2021, 22e51009
|
Funding
National Natural Science Foundation of China(32270832)
Basic and Applied Basic Research Foundation of Guangdong Province(2023B1515020039)
Shenzhen Science and Technology Innovation Program(RCYX20221008092904016)
Shenzhen University 2035 Program for Excellent Research(2022C012)
RIGHTS & PERMISSIONS
Shenzhen University School of Medicine; Fondazione Istituto FIRC di Oncologia Molecolare