Introduction
Protein post-translational modifications (PTMs) have emerged as crucial regulators of diverse biological pathways, contributing to the complexity of cellular processes. Mass spectrometry-based proteomics has been instrumental in uncovering novel histone PTMs, with lysine acetylation being extensively studied. However, lysine crotonylation, a recently discovered PTM, stands out due to its unique structural and functional distinctions from acetylation. Recent advancements in mass spectrometry techniques have unveiled the prevalence of lysine crotonylation on non-histone proteins, implicating its involvement in various biological processes such as chromatin remodeling, metabolism, cell cycle regulation, and cellular organization.
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The Discovery of Lysine Crotonylation
In 2011, Tan et al. pioneered lysine crotonylation discovery using mass spectrometry-based proteomics. Their integrated approach, involving propionylation, OFFGEL peptide separation, and LTQ Orbitrap Velos mass spectrometer, unveiled 28 crotonylated human histone peptides. They developed an anti-crotonyl-lysine antibody, validating 19 crotonylation marks in HeLa cells through D4-crotonate labeling. This groundbreaking study marked the inception of lysine crotonylation research, propelling a swift expansion of its modification landscape.
Fig. 1 Illustrations of histone crotonylation sites in human (Wan J., et al. 2019).
The Mechanism of Lysine Crotonylation
The dynamic landscape of lysine crotonylation, spanning from histones to non-histone proteins, underscores its regulatory significance in diverse cellular processes. The identification of writers, erasers, and readers sheds light on the intricate mechanisms governing this emerging post-translational modification, offering potential insights into its physiological and pathological roles.
Writers of Lysine Crotonylation
Dynamic regulation of lysine crotonylation involves a balance between crotonyltransferases, termed "writers," and decrotonylases. Histone acetyltransferases (HATs), belonging to the p300/CBP, GNAT, and MYST families, exhibit histone crotonyltransferase (HCT) activities. Notably, p300 has dual HAT and HCT functions, with histone crotonylation stimulating transcription more effectively than acetylation. Other writers, such as MOF, extend the understanding of crotonylation beyond histones, catalyzing crotonylation on non-histone proteins like NPM1 and DDX5.
Erasers of Lysine Crotonylation
Histone deacetylases (HDACs) have been identified as histone decrotonylases (HDCRs), or "erasers," capable of removing lysine crotonylation. The NAD-dependent sirtuin family (class III) and the zinc-dependent Rpd3/Hda1 family (classes I, II, and IV) constitute the major families of lysine decrotonylases. Studies have shown HDAC3, Sirt1, Sirt2, and Sirt3 as active HDCRs, with HDAC1 and HDAC3 participating in the decrotonylation of non-histone proteins like NPM1.
Readers of Lysine Crotonylation
Three major classes of acetylation and non-acetyl acylation readers-double PHD finger (DPF), bromodomain, and YEATS-recognize histone crotonylation. These readers act as docking marks to recruit downstream effectors. Experimental evidence suggests specific binding affinities between YEATS domains and crotonyl-lysine, highlighting their role in recognizing crotonylation marks. Moreover, various studies have demonstrated the importance of DPF domains and bromodomains in maintaining a high affinity for crotonylation at specific lysine residues.
Functional Roles of Lysine Crotonylation
Regulation of Gene Transcription
Histone crotonylation has been implicated in the regulation of gene transcription, specifically marking enhancers and transcription starting sites of active genes. Changes in cellular crotonyl-CoA concentration were correlated with alterations in histone crotonylation levels flanking regulatory elements, emphasizing its role in transcriptional activation.
Regulation of Acute Kidney Injury
Studies on acute kidney injury (AKI) revealed an increased histone crotonylation level in affected kidney tissue. Crotonate administration, which elevated histone crotonylation, was associated with increased expression of PGC-1α and sirtuin-3, suggesting a potential therapeutic avenue for AKI.
Regulation of Spermatogenesis
Histone crotonylation levels during spermatogenesis are dynamically regulated, with CDYL acting as a crotonyl-CoA hydratase. The association of histone crotonylation with sex chromosome-linked genes in round spermatids suggests its involvement in this unique epigenetic event.
Regulation of Depression
Decreased histone crotonylation in the medial prefrontal cortex of rodents exposed to chronic social defeat stress links crotonylation to depressive behaviors. CDYL-mediated histone crotonylation appears to modulate VGF transcription, providing insights into the molecular basis of stress-induced depression.
Regulation of Telomere Maintenance
Crotonylation-induced activation of Zscan4 and increased T-SCE levels contribute to telomere maintenance. Crotonic acid-induced histone crotonylation enhances chemically induced pluripotent stem cells (CiPSC) clone formation, suggesting a role in stem cell biology.
Regulation of HIV Latency
Histone crotonylation, regulated by ACSS2, influences HIV replication and latency. ACSS2-mediated histone crotonylation disruption leads to latent HIV reactivation, highlighting a potential link between histone crotonylation and viral latency.
Regulation of Cancer
Lysine crotonylation levels exhibit tissue-specific patterns in various cancers, suggesting a role in cancer progression. The involvement of lysine crotonylation in hepatoma cell motility and proliferation indicates its potential as a therapeutic target in cancer.
In summary, lysine crotonylation, a unique post-translational modification, intricately governs diverse biological pathways. Its functional roles in gene transcription, acute kidney injury, spermatogenesis, depression, telomere maintenance, HIV latency, and cancer emphasize its physiological and pathological importance. Lysine crotonylation stands out as a dynamic regulator in cellular processes, presenting promising therapeutic possibilities for diverse conditions.
References
- Wan J., et al. Functions and mechanisms of lysine crotonylation. Journal of Cellular and Molecular Medicine. 2019, 23(11): 7163-7169.
- Jiang G., et al. Protein lysine crotonylation: past, present, perspective. Cell Death & Disease. 2021, 12(7): 703.
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