Articoli di riviste: "Histone acylation"

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Xiao, Yanhui, Wenjing Li, Hui Yang, Lulu Pan, Liwei Zhang, Lu Lu, Jiwei Chen et al. "HBO1 is a versatile histone acyltransferase critical for promoter histone acylations". Nucleic Acids Research 49, n. 14 (14 luglio 2021): 8037–59. http://dx.doi.org/10.1093/nar/gkab607.

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Abstract Recent studies demonstrate that histones are subjected to a series of short-chain fatty acid modifications that is known as histone acylations. However, the enzymes responsible for histone acylations in vivo are not well characterized. Here, we report that HBO1 is a versatile histone acyltransferase that catalyzes not only histone acetylation but also propionylation, butyrylation and crotonylation both in vivo and in vitro and does so in a JADE or BRPF family scaffold protein-dependent manner. We show that the minimal HBO1/BRPF2 complex can accommodate acetyl-CoA, propionyl-CoA, butyryl-CoA and crotonyl-CoA. Comparison of CBP and HBO1 reveals that they catalyze histone acylations at overlapping as well as distinct sites, with HBO1 being the key enzyme for H3K14 acylations. Genome-wide chromatin immunoprecipitation assay demonstrates that HBO1 is highly enriched at and contributes to bulk histone acylations on the transcriptional start sites of active transcribed genes. HBO1 promoter intensity highly correlates with the level of promoter histone acylation, but has no significant correlation with level of transcription. We also show that HBO1 is associated with a subset of DNA replication origins. Collectively our study establishes HBO1 as a versatile histone acyltransferase that links histone acylations to promoter acylations and selection of DNA replication origins.

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Yan, Kezhi, Justine Rousseau, Keren Machol, Laura A. Cross, Katherine E. Agre, Cynthia Forster Gibson, Anne Goverde et al. "Deficient histone H3 propionylation by BRPF1-KAT6 complexes in neurodevelopmental disorders and cancer". Science Advances 6, n. 4 (gennaio 2020): eaax0021. http://dx.doi.org/10.1126/sciadv.aax0021.

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Lysine acetyltransferase 6A (KAT6A) and its paralog KAT6B form stoichiometric complexes with bromodomain- and PHD finger-containing protein 1 (BRPF1) for acetylation of histone H3 at lysine 23 (H3K23). We report that these complexes also catalyze H3K23 propionylation in vitro and in vivo. Immunofluorescence microscopy and ATAC-See revealed the association of this modification with active chromatin. Brpf1 deletion obliterates the acylation in mouse embryos and fibroblasts. Moreover, we identify BRPF1 variants in 12 previously unidentified cases of syndromic intellectual disability and demonstrate that these cases and known BRPF1 variants impair H3K23 propionylation. Cardiac anomalies are present in a subset of the cases. H3K23 acylation is also impaired by cancer-derived somatic BRPF1 mutations. Valproate, vorinostat, propionate and butyrate promote H3K23 acylation. These results reveal the dual functionality of BRPF1-KAT6 complexes, shed light on mechanisms underlying related developmental disorders and various cancers, and suggest mutation-based therapy for medical conditions with deficient histone acylation.

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Neja, Sultan, Wan Mohaiza Dashwood, Roderick H. Dashwood e Praveen Rajendran. "Histone Acyl Code in Precision Oncology: Mechanistic Insights from Dietary and Metabolic Factors". Nutrients 16, n. 3 (30 gennaio 2024): 396. http://dx.doi.org/10.3390/nu16030396.

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Cancer etiology involves complex interactions between genetic and non-genetic factors, with epigenetic mechanisms serving as key regulators at multiple stages of pathogenesis. Poor dietary habits contribute to cancer predisposition by impacting DNA methylation patterns, non-coding RNA expression, and histone epigenetic landscapes. Histone post-translational modifications (PTMs), including acyl marks, act as a molecular code and play a crucial role in translating changes in cellular metabolism into enduring patterns of gene expression. As cancer cells undergo metabolic reprogramming to support rapid growth and proliferation, nuanced roles have emerged for dietary- and metabolism-derived histone acylation changes in cancer progression. Specific types and mechanisms of histone acylation, beyond the standard acetylation marks, shed light on how dietary metabolites reshape the gut microbiome, influencing the dynamics of histone acyl repertoires. Given the reversible nature of histone PTMs, the corresponding acyl readers, writers, and erasers are discussed in this review in the context of cancer prevention and treatment. The evolving ‘acyl code’ provides for improved biomarker assessment and clinical validation in cancer diagnosis and prognosis.

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Soffers, Jelly H. M., Xuanying Li, Susan M. Abmayr e Jerry L. Workman. "Reading and Interpreting the Histone Acylation Code". Genomics, Proteomics & Bioinformatics 14, n. 6 (dicembre 2016): 329–32. http://dx.doi.org/10.1016/j.gpb.2016.12.001.

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Klein, Brianna J., Johayra Simithy, Xiaolu Wang, JaeWoo Ahn, Forest H. Andrews, Yi Zhang, Jacques Côté, Xiaobing Shi, Benjamin A. Garcia e Tatiana G. Kutateladze. "Recognition of Histone H3K14 Acylation by MORF". Structure 25, n. 4 (aprile 2017): 650–54. http://dx.doi.org/10.1016/j.str.2017.02.003.

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Khan, Abid, Joseph B. Bridgers e Brian D. Strahl. "Expanding the Reader Landscape of Histone Acylation". Structure 25, n. 4 (aprile 2017): 571–73. http://dx.doi.org/10.1016/j.str.2017.03.010.

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Jo, Chanhee, Seokjae Park, Sungjoon Oh, Jinmi Choi, Eun-Kyoung Kim, Hong-Duk Youn e Eun-Jung Cho. "Histone acylation marks respond to metabolic perturbations and enable cellular adaptation". Experimental & Molecular Medicine 52, n. 12 (dicembre 2020): 2005–19. http://dx.doi.org/10.1038/s12276-020-00539-x.

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AbstractAcetylation is the most studied histone acyl modification and has been recognized as a fundamental player in metabolic gene regulation, whereas other short-chain acyl modifications have only been recently identified, and little is known about their dynamics or molecular functions at the intersection of metabolism and epigenetic gene regulation. In this study, we aimed to understand the link between nonacetyl histone acyl modification, metabolic transcriptional regulation, and cellular adaptation. Using antibodies specific for butyrylated, propionylated, and crotonylated H3K23, we analyzed dynamic changes of H3K23 acylation upon various metabolic challenges. Here, we show that H3K23 modifications were highly responsive and reversibly regulated by nutrient availability. These modifications were commonly downregulated by the depletion of glucose and recovered based on glucose or fatty acid availability. Depletion of metabolic enzymes, namely, ATP citrate lyase, carnitine acetyltransferase, and acetyl-CoA synthetase, which are involved in Ac-CoA synthesis, resulted in global loss of H3K23 butyrylation, crotonylation, propionylation, and acetylation, with a profound impact on gene expression and cellular metabolic states. Our data indicate that Ac-CoA/CoA and central metabolic inputs are important for the maintenance of histone acylation. Additionally, genome-wide analysis revealed that acyl modifications are associated with gene activation. Our study shows that histone acylation acts as an immediate and reversible metabolic sensor enabling cellular adaptation to metabolic stress by reprogramming gene expression.

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Zheng, Lanlan, Chen Li, Xueping Ma, Hanlin Zhou, Yuan Liu, Ping Wang, Huilan Yang et al. "Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation". Nucleic Acids Research 49, n. 13 (24 giugno 2021): 7347–60. http://dx.doi.org/10.1093/nar/gkab536.

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Abstract Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation whose prevalence and function in plants remain unclear. Here, we identified 41 Khib sites on histones in Arabidopsis thaliana, which did not overlap with frequently modified N-tail lysines (e.g. H3K4, H3K9 and H4K8). Chromatin immunoprecipitation-sequencing (ChIP-seq) assays revealed histone Khib in 35% of protein-coding genes. Most Khib peaks were located in genic regions, and they were highly enriched at the transcription start sites. Histone Khib is highly correlated with acetylation (ac), particularly H3K23ac, which it largely resembles in its genomic and genic distribution. Notably, co-enrichment of histone Khib and H3K23ac correlates with high gene expression levels. Metabolic profiling, transcriptome analyses, and ChIP-qPCR revealed that histone Khib and H3K23ac are co-enriched on genes involved in starch and sucrose metabolism, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis, and help fine-tune plant response to dark-induced starvation. These findings suggest that Khib and H3K23ac may act in concert to promote high levels of gene transcription and regulate cellular metabolism to facilitate plant adaption to stress. Finally, HDA6 and HDA9 are involved in removing histone Khib. Our findings reveal Khib as a conserved yet unique plant histone mark acting with lysine acetylation in transcription-associated epigenomic processes.

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Zhao, Dan, Yuanyuan Li, Xiaozhe Xiong, Zhonglei Chen e Haitao Li. "YEATS Domain—A Histone Acylation Reader in Health and Disease". Journal of Molecular Biology 429, n. 13 (giugno 2017): 1994–2002. http://dx.doi.org/10.1016/j.jmb.2017.03.010.

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Sharma, Deepika, Swati Sharma e Preeti Chauhan. "Acetylation of Histone and Modification of Gene Expression via HDAC Inhibitors Affects the Obesity". Biomedical and Pharmacology Journal 14, n. 1 (28 marzo 2021): 153–61. http://dx.doi.org/10.13005/bpj/2110.

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Obesity is due to imbalance between energy intake and energy expenditure. Adipose tissues are the main site for the fat storage as well as for dissipation. There are two types of adipose tissues: white adipose tissue, which store fat as triglyceride, brown adipose tissue, which burns the fat into energy through the thermogenesis due to uncoupling protein1 present in inner mitochondrial membrane. Histone acylation causes changes in the chromatin structure without causing any change in the deoxyribonucleic acidsequence and thus regulate gene expression.Histonedeacetylase causes the deacylation of histone and interfere with function of histone. Thus histonedeacetylase inhibitors alter the expression of thermogenic gene encoding uncoupling protein 1, peroxisome proliferator activated receptor γ and also causes browning or beiging of white adipose tissue and increases the energy expenditure.

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Yuan, Zhao-Di, Wei-Ning Zhu, Ke-Zhi Liu, Zhan-Peng Huang e Yan-Chuang Han. "Small Molecule Epigenetic Modulators in Pure Chemical Cell Fate Conversion". Stem Cells International 2020 (20 ottobre 2020): 1–12. http://dx.doi.org/10.1155/2020/8890917.

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Although innovative technologies for somatic cell reprogramming and transdifferentiation provide new strategies for the research of translational medicine, including disease modeling, drug screening, artificial organ development, and cell therapy, recipient safety remains a concern due to the use of exogenous transcription factors during induction. To resolve this problem, new induction approaches containing clinically applicable small molecules have been explored. Small molecule epigenetic modulators such as DNA methylation writer inhibitors, histone methylation writer inhibitors, histone acylation reader inhibitors, and histone acetylation eraser inhibitors could overcome epigenetic barriers during cell fate conversion. In the past few years, significant progress has been made in reprogramming and transdifferentiation of somatic cells with small molecule approaches. In the present review, we systematically discuss recent achievements of pure chemical reprogramming and transdifferentiation.

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Cao, Ji, Lei Sun, Pornpun Aramsangtienchai, Nicole A. Spiegelman, Xiaoyu Zhang, Weishan Huang, Edward Seto e Hening Lin. "HDAC11 regulates type I interferon signaling through defatty-acylation of SHMT2". Proceedings of the National Academy of Sciences 116, n. 12 (28 febbraio 2019): 5487–92. http://dx.doi.org/10.1073/pnas.1815365116.

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The smallest histone deacetylase (HDAC) and the only class IV HDAC member, HDAC11, is reported to regulate immune activation and tumorigenesis, yet its biochemical function is largely unknown. Here we identify HDAC11 as an efficient lysine defatty-acylase that is >10,000-fold more efficient than its deacetylase activity. Through proteomics studies, we hypothesized and later biochemically validated SHMT2 as a defatty-acylation substrate of HDAC11. HDAC11-catalyzed defatty-acylation did not affect the enzymatic activity of SHMT2. Instead, it affects the ability of SHMT2 to regulate type I IFN receptor ubiquitination and cell surface level. Correspondingly, HDAC11 depletion increased type I IFN signaling in both cell culture and mice. This study not only demonstrates that HDAC11 has an activity that is much more efficient than the corresponding deacetylase activity, but also expands the physiological functions of HDAC11 and protein lysine fatty acylation, which opens up opportunities to develop HDAC11-specific inhibitors as therapeutics to modulate immune responses.

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Gao, Mengqing, Jin Wang, Sophie Rousseaux, Minjia Tan, Lulu Pan, Lijun Peng, Sisi Wang et al. "Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution". Cell Reports 36, n. 4 (luglio 2021): 109460. http://dx.doi.org/10.1016/j.celrep.2021.109460.

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Zubrytski, Dzmitry M., Gábor Zoltán Elek, Margus Lopp e Dzmitry G. Kananovich. "Generation of Mixed Anhydrides via Oxidative Fragmentation of Tertiary Cyclopropanols with Phenyliodine(III) Dicarboxylates". Molecules 26, n. 1 (30 dicembre 2020): 140. http://dx.doi.org/10.3390/molecules26010140.

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Oxidative fragmentation of tertiary cyclopropanols with phenyliodine(III) dicarboxylates in aprotic solvents (dichloromethane, chloroform, toluene) produces mixed anhydrides. The fragmentation reaction is especially facile with phenyliodine(III) reagents bearing electron-withdrawing carboxylate ligands (trifluoroacetyl, 2,4,6-trichlorobenzoyl, 3-nitrobenzoyl), and affords 95−98% yields of the corresponding mixed anhydride products. The latter can be straightforwardly applied for the acylation of various nitrogen, oxygen and sulfur-centered nucleophiles (primary and secondary amines, hydroxylamines, primary alcohols, phenols, thiols). Intramolecular acylation yielding macrocyclic lactones can also be performed. The developed transformation has bolstered the synthetic utility of cyclopropanols as pluripotent intermediates in diversity-oriented synthesis of bioactive natural products and their synthetic congeners. For example, it was successfully applied for the last-stage modification of a cyclic peptide to produce a precursor of a known histone deacetylase inhibitor.

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Christott, Thomas, James Bennett, Carmen Coxon, Octovia Monteiro, Charline Giroud, Viktor Beke, Suet Ling Felce et al. "Discovery of a Selective Inhibitor for the YEATS Domains of ENL/AF9". SLAS DISCOVERY: Advancing the Science of Drug Discovery 24, n. 2 (25 ottobre 2018): 133–41. http://dx.doi.org/10.1177/2472555218809904.

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Eleven-nineteen leukemia (ENL) contains an epigenetic reader domain (YEATS domain) that recognizes lysine acylation on histone 3 and facilitates transcription initiation and elongation through its interactions with the super elongation complex (SEC) and the histone methyl transferase DOT1L. Although it has been known for its role as a fusion protein in mixed lineage leukemia (MLL), overexpression of native ENL, and thus dysregulation of downstream genes in acute myeloid leukemia (AML), has recently been implicated as a driver of disease that is reliant on the epigenetic reader activity of the YEATS domain. We developed a peptide displacement assay (histone 3 tail with acylated lysine) and screened a small-molecule library totaling more than 24,000 compounds for their propensity to disrupt the YEATS domain–histone peptide binding. Among these, we identified a first-in-class dual inhibitor of ENL ( Kd = 745 ± 45 nM) and its paralog AF9 ( Kd = 523 ± 53 nM) and performed “SAR by catalog” with the aim of starting the development of a chemical probe for ENL.

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Etier, Aurelie, Fabien Dumetz, Sylvain Chéreau e Nadia Ponts. "Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism". Toxins 14, n. 5 (29 aprile 2022): 317. http://dx.doi.org/10.3390/toxins14050317.

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Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.

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Ponnan, Prija, Ajit Kumar, Prabhjot Singh, Prachi Gupta, Rini Joshi, Marco Gaspari, Luciano Saso et al. "Comparison of Protein Acetyltransferase Action of CRTAase with the Prototypes of HAT". Scientific World Journal 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/578956.

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Our laboratory is credited for the discovery of enzymatic acetylation of protein, a phenomenon unknown till we identified an enzyme termed acetoxy drug: protein transacetylase (TAase), catalyzing the transfer of acetyl group from polyphenolic acetates to receptor proteins (RP). Later, TAase was identified as calreticulin (CR), an endoplasmic reticulum luminal protein. CR was termed calreticulin transacetylase (CRTAase). Our persistent study revealed that CR like other families of histone acetyltransferases (HATs) such as p300, Rtt109, PCAF, and ESA1, undergoes autoacetylation. The autoacetylated CR was characterized as a stable intermediate in CRTAase catalyzed protein acetylation, and similar was the case with ESA1. The autoacetylation of CR like that of HATs was found to enhance protein-protein interaction. CR like HAT-1, CBP, and p300 mediated the acylation of RP utilizing acetyl CoA and propionyl CoA as the substrates. The similarities between CRTAase and HATs in mediating protein acylation are highlighted in this review.

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Joshi, Joha, Micah J. McCauley, Allison Cross, Michael Morse, Mattew C. Amato, Nicole A. Becker, Ioulia F. Rouzina, Louis J. Maher e Mark C. Williams. "Acylation of key sites in the histone octamer core destabilizes nucleosome arrays". Biophysical Journal 121, n. 3 (febbraio 2022): 210a. http://dx.doi.org/10.1016/j.bpj.2021.11.1675.

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Amamoto, Yoshifumi, Yuki Aoi, Nozomu Nagashima, Hiroki Suto, Daisuke Yoshidome, Yasuhiro Arimura, Akihisa Osakabe et al. "Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin". Journal of the American Chemical Society 139, n. 22 (23 maggio 2017): 7568–76. http://dx.doi.org/10.1021/jacs.7b02138.

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Zhao, Yuqin, Shuailin Hao, Wenchi Wu, Youhang Li, Kaiping Hou, Yu Liu, Wei Cui, Xingzhi Xu e Hailong Wang. "Lysine Crotonylation: An Emerging Player in DNA Damage Response". Biomolecules 12, n. 10 (5 ottobre 2022): 1428. http://dx.doi.org/10.3390/biom12101428.

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The DNA damage response (DDR) system plays an important role in maintaining genome stability and preventing related diseases. The DDR network comprises many proteins and posttranslational modifications (PTMs) to proteins, which work in a coordinated manner to counteract various genotoxic stresses. Lysine crotonylation (Kcr) is a newly identified PTM occurring in both core histone and non-histone proteins in various organisms. This novel PTM is classified as a reversible acylation modification, which is regulated by a variety of acylases and deacylases and the intracellular crotonyl-CoA substrate concentration. Recent studies suggest that Kcr links cellular metabolism with gene regulation and is involved in numerous cellular processes. In this review, we summarize the regulatory mechanisms of Kcr and its functions in DDR, including its involvement in double-strand break (DSB)-induced transcriptional repression, DSB repair, and the DNA replication stress response.

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Xu, Huiwen, Maoyan Wu, Xiumei Ma, Wei Huang e Yong Xu. "Function and Mechanism of Novel Histone Posttranslational Modifications in Health and Disease". BioMed Research International 2021 (3 marzo 2021): 1–13. http://dx.doi.org/10.1155/2021/6635225.

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Histone posttranslational modifications (HPTMs) are crucial epigenetic mechanisms regulating various biological events. Different types of HPTMs characterize and shape functional chromatin states alone or in combination, and dedicated effector proteins selectively recognize these modifications for gene expression. The dysregulation of HPTM recognition events takes part in human diseases. With the application of mass spectrometry- (MS-) based proteomics, novel histone lysine acylation has been successively discovered, e.g., propionylation, butyrylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, malonylation, succinylation, crotonylation, glutarylation, and lactylation. These nine types of modifications expand the repertoire of HPTMs and regulate chromatin remodeling, gene expression, cell cycle, and cellular metabolism. Recent researches show that HPTMs have a close connection with the pathogenesis of cancer, metabolic diseases, neuropsychiatric disorders, infertility, kidney diseases, and acquired immunodeficiency syndrome (AIDS). This review focuses on the chemical structure, sites, functions of these novel HPTMs, and underlying mechanism in gene expression, providing a glimpse into their complex regulation in health and disease.

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Ourailidou, Maria E., Paul Dockerty, Martin Witte, Gerrit J. Poelarends e Frank J. Dekker. "Metabolic alkene labeling and in vitro detection of histone acylation via the aqueous oxidative Heck reaction". Organic & Biomolecular Chemistry 13, n. 12 (2015): 3648–53. http://dx.doi.org/10.1039/c4ob02502d.

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Varner, Erika L., Sophie Trefely, David Bartee, Eliana von Krusenstiern, Luke Izzo, Carmen Bekeova, Roddy S. O'Connor et al. "Quantification of lactoyl-CoA (lactyl-CoA) by liquid chromatography mass spectrometry in mammalian cells and tissues". Open Biology 10, n. 9 (settembre 2020): 200187. http://dx.doi.org/10.1098/rsob.200187.

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Lysine lactoylation is a recently described protein post-translational modification (PTM). However, the biochemical pathways responsible for this acylation remain unclear. Two metabolite-dependent mechanisms have been proposed: enzymatic histone lysine lactoylation derived from lactoyl-coenzyme A (lactoyl-CoA, also termed lactyl-CoA), and non-enzymatic lysine lactoylation resulting from acyl-transfer via lactoyl-glutathione. While the former has precedent in the form of enzyme-catalysed lysine acylation, the lactoyl-CoA metabolite has not been previously quantified in mammalian systems. Here, we use liquid chromatography–high-resolution mass spectrometry (LC-HRMS) together with a synthetic standard to detect and validate the presence of lactoyl-CoA in cell and tissue samples. Conducting a retrospective analysis of data from previously analysed samples revealed the presence of lactoyl-CoA in diverse cell and tissue contexts. In addition, we describe a biosynthetic route to generate 13 C 3 15 N 1 -isotopically labelled lactoyl-CoA, providing a co-eluting internal standard for analysis of this metabolite. We estimate lactoyl-CoA concentrations of 1.14 × 10 −8 pmol per cell in cell culture and 0.0172 pmol mg −1 tissue wet weight in mouse heart. These levels are similar to crotonyl-CoA, but between 20 and 350 times lower than predominant acyl-CoAs such as acetyl-, propionyl- and succinyl-CoA. Overall our studies provide the first quantitative measurements of lactoyl-CoA in metazoans, and provide a methodological foundation for the interrogation of this novel metabolite in biology and disease.

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Liu, Yuexia, Yizhou Li, Juntong Liang, Zhuwen Sun e Chao Sun. "Non-Histone Lysine Crotonylation Is Involved in the Regulation of White Fat Browning". International Journal of Molecular Sciences 23, n. 21 (22 ottobre 2022): 12733. http://dx.doi.org/10.3390/ijms232112733.

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Lysine crotonylation modification is a novel acylation modification that is similar to acetylation modification. Studies have found that protein acetylation plays an important regulatory part in the occurrence and prevention of obesity and is involved in the regulation of glucose metabolism, tricarboxylic acid cycle, white fat browning and fatty acid metabolism. Therefore, we speculate that protein crotonylation may also play a more vital role in regulating the browning of white fat. To verify this conjecture, we identified 7254 crotonyl modification sites and 1629 modified proteins in iWAT of white fat browning model mice by affinity enrichment and liquid chromatography–mass spectrometry (LC-MS/MS). We selected five representative proteins in the metabolic process, namely glycerol-3-phosphate dehydrogenase 1 (GPD1), fatty acid binding protein 4 (FABP4), adenylate kinase 2 (AK2), triosephosphate isomerase 1 (TPI1) and NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 8 (NDUFA8). Through qPCR, Western blotting, immunofluorescence staining, Oil Red O staining and HE staining, we demonstrated that GPD1 and FABP4 inhibited white fat browning, while AK2, TPI1 and NDUFA8 promoted white fat browning. GPD1 and FABP4 proteins were downregulated by crotonylation modification, while AK2, TPI1 and NDUFA8 proteins were upregulated by crotonylation modification. Further detection found that the crotonylation modification of GPD1, FABP4, AK2, TPI1 and NDUFA8 promoted white fat browning, which was consistent with the sequencing results. These results indicate that the protein crotonylation is involved in regulating white fat browning, which is of great significance for controlling obesity and treating obesity-related diseases.

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Wilson, John P., Anuradha S. Raghavan, Yu-Ying Yang, Guillaume Charron e Howard C. Hang. "Proteomic Analysis of Fatty-acylated Proteins in Mammalian Cells with Chemical Reporters RevealsS-Acylation of Histone H3 Variants". Molecular & Cellular Proteomics 10, n. 3 (14 novembre 2010): M110.001198. http://dx.doi.org/10.1074/mcp.m110.001198.

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Barnes, Claire E., David M. English e Shaun M. Cowley. "Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription". Essays in Biochemistry 63, n. 1 (aprile 2019): 97–107. http://dx.doi.org/10.1042/ebc20180061.

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Abstract Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.

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Deng, Yijun, Christina Ng DiMarco, Tanya Vakhilt, Marco Jonas, Jaclyn White, Dennis Arefyev, Ramachandar Tokala et al. "Process Development of the Soft Histone Deacetylate Enzyme Inhibitor SHP-141: Acylation of Methyl Paraben and Suberyl Hydroxamic Acid Formation". Organic Process Research & Development 20, n. 10 (28 settembre 2016): 1812–20. http://dx.doi.org/10.1021/acs.oprd.6b00280.

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Brewster, Richard C., e Alison N. Hulme. "Halomethyl-Triazoles for Rapid, Site-Selective Protein Modification". Molecules 26, n. 18 (8 settembre 2021): 5461. http://dx.doi.org/10.3390/molecules26185461.

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Post-translational modifications (PTMs) are used by organisms to control protein structure and function after protein translation, but their study is complicated and their roles are not often well understood as PTMs are difficult to introduce onto proteins selectively. Designing reagents that are both good mimics of PTMs, but also only modify select amino acid residues in proteins is challenging. Frequently, both a chemical warhead and linker are used, creating a product that is a misrepresentation of the natural modification. We have previously shown that biotin-chloromethyl-triazole is an effective reagent for cysteine modification to give S-Lys derivatives where the triazole is a good mimic of natural lysine acylation. Here, we demonstrate both how the reactivity of the alkylating reagents can be increased and how the range of triazole PTM mimics can be expanded. These new iodomethyl-triazole reagents are able to modify a cysteine residue on a histone protein with excellent selectivity in 30 min to give PTM mimics of acylated lysine side-chains. Studies on the more complicated, folded protein SCP-2L showed promising reactivity, but also suggested the halomethyl-triazoles are potent alkylators of methionine residues.

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Gan, Qing, Donge Tang, Qiang Yan, Jiejing Chen, Yong Xu, Wen Xue, Lu Xiao et al. "Differential Expression Study of Lysine Crotonylation and Proteome for Chronic Obstructive Pulmonary Disease Combined with Type II Respiratory Failure". Canadian Respiratory Journal 2021 (15 giugno 2021): 1–12. http://dx.doi.org/10.1155/2021/6652297.

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Introduction. The modification of lysine crotonylation (Kcr) is another biological function of histone in addition to modification of lysine acetylation (Kac), which may play a specific regulatory role in diseases. Objectives. This study compared the expression levels of Kcr and proteome between patients with chronic obstructive pulmonary disease (COPD) combined with type II respiratory failure (RF) to study the relationship between Kcr, proteome, and COPD. Methods. We tested the Kcr and proteome of COPD combined with type II RF and normal control (NC) using croton acylation enrichment technology and liquid chromatography tandem mass spectrometry (LC-MS/MS) with high resolution. Results. We found that 32 sites of 23 proteins were upregulated and 914 sites of 295 proteins were downregulated. We performed Kyoto Encyclopedia of Genes and Genomes (KEGG), protein domain, and Gene Ontology (GO) analysis on crotonylated protein. In proteomics research, we found that 190 proteins were upregulated and 151 proteins were downregulated. Among them, 90 proteins were both modified by differentially expressed crotonylation sites and differentially expressed in COPD combined with type II RF and NC. Conclusion. Differentially expressed crotonylation sites may be involved in the development of COPD combined with type II RF. 90 proteins modified by crotonylation and differentially expressed in COPD combined with type II RF can be used as markers for the study of the molecular pathogenesis of COPD combined with type II RF.

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Aleshin, V. A., D. A. Sibiryakina, A. V. Kazantsev, A. V. Graf e V. I. Bunik. "Acylation of the rat brain proteins is affected by the inhibition of pyruvate dehydrogenase <i>in vivo</i>". Биохимия 88, n. 1 (15 gennaio 2023): 147–63. http://dx.doi.org/10.31857/s0320972523010116.

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Organism adaptation to metabolic challenges requires coupling of metabolism to gene expression. In this regard, acylations of histones and metabolic proteins acquire significant interest. We hypothesize that adaptive response to inhibition of a key metabolic process, catalyzed by the acetyl-CoA-generating pyruvate dehydrogenase (PDH) complex, is mediated by changes in the protein acylations. The hypothesis is tested by intranasal administration to animals of PDH-specific inhibitors acetyl(methyl)phosphinate (AcMeP) or acetylphosphonate methyl ester (AcPMe), followed by the assessment of physiological parameters, brain protein acylation, and expression/phosphorylation of PDHA subunit. At the same dose, AcMeP, but not AcPMe, decreases acetylation and increases succinylation of the brain proteins with apparent molecular masses of 15-20 kDa. Regarding the proteins of 30-50 kDa, a strong inhibitor AcMeP affects acetylation only, while a less efficient AcPMe mostly increases succinylation. The unchanged succinylation of the 30-50 kDa proteins after the administration of AcMeP coincides with the upregulation of desuccinylase SIRT5. No significant differences between the levels of brain PDHA expression, PDHA phosphorylation, parameters of behavior or ECG are observed in the studied animal groups. The data indicate that the short-term inhibition of brain PDH affects acetylation and/or succinylation of the brain proteins, that depends on the inhibitor potency, protein molecular mass, and acylation type. The homeostatic nature of these changes is implied by the stability of physiological parameters after the PDH inhibition.

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Ronan, Jade L., Nadia Kadi, Stephen A. McMahon, James H. Naismith, Lona M. Alkhalaf e Gregory L. Challis. "Desferrioxamine biosynthesis: diverse hydroxamate assembly by substrate-tolerant acyl transferase DesC". Philosophical Transactions of the Royal Society B: Biological Sciences 373, n. 1748 (23 aprile 2018): 20170068. http://dx.doi.org/10.1098/rstb.2017.0068.

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Hydroxamate groups play key roles in the biological function of diverse natural products. Important examples include trichostatin A, which inhibits histone deacetylases via coordination of the active site zinc(II) ion with a hydroxamate group, and the desferrioxamines, which use three hydroxamate groups to chelate ferric iron. Desferrioxamine biosynthesis in Streptomyces species involves the DesD-catalysed condensation of various N -acylated derivatives of N -hydroxycadaverine with two molecules of N -succinyl- N -hydroxycadaverine to form a range of linear and macrocyclic tris-hydroxamates. However, the mechanism for assembly of the various N -acyl- N -hydroxycadaverine substrates of DesD from N -hydroxycadaverine has until now been unclear. Here we show that the desC gene of Streptomyces coelicolor encodes the acyl transferase responsible for this process. DesC catalyses the N -acylation of N -hydroxycadaverine with acetyl, succinyl and myristoyl-CoA, accounting for the diverse array of desferrioxamines produced by S. coelicolor . The X-ray crystal structure of DesE, the ferrioxamine lipoprotein receptor, in complex with ferrioxamine B (which is derived from two units of N -succinyl- N -hydroxycadaverine and one of N -acetyl- N -hydroxycadaverine) was also determined. This showed that the acetyl group of ferrioxamine B is solvent exposed, suggesting that the corresponding acyl group in longer chain congeners can protrude from the binding pocket, providing insights into their likely function. This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology'. This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology’.

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Crespo, Marion, Annelaure Damont, Melina Blanco, Emmanuelle Lastrucci, Sara El Kennani, Côme Ialy-Radio, Laila El Khattabi et al. "Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes". Nucleic Acids Research 48, n. 8 (17 marzo 2020): 4115–38. http://dx.doi.org/10.1093/nar/gkaa163.

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Abstract Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. We investigated the dynamics of lysine acetylation and crotonylation on histones H3 and H4 during mouse spermatogenesis. Lysine crotonylation appeared to be of significant abundance compared to acetylation, particularly on Lys27 of histone H3 (H3K27cr) that accumulates in sperm in a cleaved form of H3. We identified the genomic localization of H3K27cr and studied its effects on transcription compared to the classical active mark H3K27ac at promoters and distal enhancers. The presence of both marks was strongly associated with highest gene expression. Assessment of their co-localization with transcription regulators (SLY, SOX30) and chromatin-binding proteins (BRD4, BRDT, BORIS and CTCF) indicated systematic highest binding when both active marks were present and different selective binding when present alone at chromatin. H3K27cr and H3K27ac finally mark the building of some sperm super-enhancers. This integrated analysis of omics data provides an unprecedented level of understanding of gene expression regulation by H3K27cr in comparison to H3K27ac, and reveals both synergistic and specific actions of each histone modification.

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Zhao, Shuai, Xingrun Zhang e Haitao Li. "Beyond histone acetylation—writing and erasing histone acylations". Current Opinion in Structural Biology 53 (dicembre 2018): 169–77. http://dx.doi.org/10.1016/j.sbi.2018.10.001.

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Sabari, Benjamin R., Di Zhang, C. David Allis e Yingming Zhao. "Metabolic regulation of gene expression through histone acylations". Nature Reviews Molecular Cell Biology 18, n. 2 (7 dicembre 2016): 90–101. http://dx.doi.org/10.1038/nrm.2016.140.

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Dutta, Arnob, Susan M. Abmayr e Jerry L. Workman. "Diverse Activities of Histone Acylations Connect Metabolism to Chromatin Function". Molecular Cell 63, n. 4 (agosto 2016): 547–52. http://dx.doi.org/10.1016/j.molcel.2016.06.038.

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Fernandes, Mariane Font, e Marco Aurélio Ramirez Vinolo. "Histone acylations as a mechanism for regulation of intestinal epithelial cells". Digestive Medicine Research 7 (marzo 2024): 4. http://dx.doi.org/10.21037/dmr-23-3.

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Shi, Jiale, Xuemei Jia, Yujia He, Xinyue Ma, Xiaoyu Qi, Wan Li, Shou-Jiang Gao, Qin Yan e Chun Lu. "Immune evasion strategy involving propionylation by the KSHV interferon regulatory factor 1 (vIRF1)". PLOS Pathogens 19, n. 4 (6 aprile 2023): e1011324. http://dx.doi.org/10.1371/journal.ppat.1011324.

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Post-translational modifications (PTMs) are essential for host antiviral immune response and viral immune evasion. Among a set of novel acylations, lysine propionylation (Kpr) has been detected in both histone and non-histone proteins. However, whether protein propionylation occurs in any viral proteins and whether such modifications regulate viral immune evasion remain elusive. Here, we show that Kaposi’s sarcoma-associated herpesvirus (KSHV)-encoded viral interferon regulatory factor 1 (vIRF1) can be propionylated in lysine residues, which is required for effective inhibition of IFN-β production and antiviral signaling. Mechanistically, vIRF1 promotes its own propionylation by blocking SIRT6’s interaction with ubiquitin-specific peptidase 10 (USP10) leading to its degradation via a ubiquitin-proteasome pathway. Furthermore, vIRF1 propionylation is required for its function to block IRF3-CBP/p300 recruitment and repress the STING DNA sensing pathway. A SIRT6-specific activator, UBCS039, rescues propionylated vIRF1-mediated repression of IFN-β signaling. These results reveal a novel mechanism of viral evasion of innate immunity through propionylation of a viral protein. The findings suggest that enzymes involved in viral propionylation could be potential targets for preventing viral infections.

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Peterson, Francis C., Dawei Chen, Betsy L. Lytle, Marianna N. Rossi, Ivan Ahel, John M. Denu e Brian F. Volkman. "Orphan Macrodomain Protein (Human C6orf130) Is an O-Acyl-ADP-ribose Deacylase". Journal of Biological Chemistry 286, n. 41 (17 agosto 2011): 35955–65. http://dx.doi.org/10.1074/jbc.m111.276238.

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Post-translational modification of proteins/histones by lysine acylation has profound effects on the physiological function of modified proteins. Deacylation by NAD+-dependent sirtuin reactions yields as a product O-acyl-ADP-ribose, which has been implicated as a signaling molecule in modulating cellular processes. Macrodomain-containing proteins are reported to bind NAD+-derived metabolites. Here, we describe the structure and function of an orphan macrodomain protein, human C6orf130. This unique 17-kDa protein is a stand-alone macrodomain protein that occupies a distinct branch in the phylogenic tree. We demonstrate that C6orf130 catalyzes the efficient deacylation of O-acetyl-ADP-ribose, O-propionyl-ADP-ribose, and O-butyryl-ADP-ribose to produce ADP-ribose (ADPr) and acetate, propionate, and butyrate, respectively. Using NMR spectroscopy, we solved the structure of C6orf130 in the presence and absence of ADPr. The structures showed a canonical fold with a deep ligand (ADPr)-binding cleft. Structural comparisons of apo-C6orf130 and the ADPr-C6orf130 complex revealed fluctuations of the β5-α4 loop that covers the bound ADPr, suggesting that the β5-α4 loop functions as a gate to sequester substrate and offer flexibility to accommodate alternative substrates. The ADPr-C6orf130 complex identified amino acid residues involved in substrate binding and suggested residues that function in catalysis. Site-specific mutagenesis and steady-state kinetic analyses revealed two critical catalytic residues, Ser-35 and Asp-125. We propose a catalytic mechanism for deacylation of O-acyl-ADP-ribose by C6orf130 and discuss the biological implications in the context of reversible protein acylation at lysine residues.

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Olp, Michael D., Nan Zhu e Brian C. Smith. "Metabolically Derived Lysine Acylations and Neighboring Modifications Tune the Binding of the BET Bromodomains to Histone H4". Biochemistry 56, n. 41 (5 ottobre 2017): 5485–95. http://dx.doi.org/10.1021/acs.biochem.7b00595.

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Wang, Bo, Po-Hsien Huang, Ching-Shih Chen e Craig J. Forsyth. "Total Syntheses of the Histone Deacetylase Inhibitors Largazole and 2-epi-Largazole: Application ofN-Heterocyclic Carbene Mediated Acylations in Complex Molecule Synthesis". Journal of Organic Chemistry 76, n. 4 (18 febbraio 2011): 1140–50. http://dx.doi.org/10.1021/jo102478x.

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Nelson, John, Neil V. McFerran, Géraldine Pivato, Emma Chambers, Caroline Doherty, David Steele e David J. Timson. "The 67 kDa laminin receptor: structure, function and role in disease". Bioscience Reports 28, n. 1 (1 febbraio 2008): 33–48. http://dx.doi.org/10.1042/bsr20070004.

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The 67LR (67 kDa laminin receptor) is a cell-surface receptor with high affinity for its primary ligand. Its role as a laminin receptor makes it an important molecule both in cell adhesion to the basement membrane and in signalling transduction following this binding event. The protein also plays critical roles in the metastasis of tumour cells. Isolation of the protein from either normal or cancerous cells results in a product with an approx. molecular mass of 67 kDa. This protein is believed to be derived from a smaller precursor, the 37LRP (37 kDa laminin receptor precursor). However, the precise mechanism by which cytoplasmic 37LRP becomes cell-membrane-embedded 67LR is unclear. The process may involve post-translational fatty acylation of the protein combined with either homo- or hetero-dimerization, possibly with a galectin-3-epitope-containing partner. Furthermore, it has become clear that acting as a receptor for laminin is not the only function of this protein. 67LR also acts as a receptor for viruses, such as Sindbis virus and dengue virus, and is involved with internalization of the prion protein. Interestingly, unmodified 37LRP is a ribosomal component and homologues of this protein are found in all five kingdoms. In addition, it appears to be strongly associated with histones in the eukaryotic cell nucleus, although the precise role of these interactions is not clear. Here we review the current understanding of the structure and function of this molecule, as well as highlighting areas requiring further research.

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LIAU, Y. H., J. ZIELENSKI, S. R. CARTER, A. SLOMIANY e B. L. SLOMIANY. "Enzymatic Acylation of Mucus Glycoprotein in Rat Salivary Glands". Annals of the New York Academy of Sciences 494, n. 1 Third Colloqu (maggio 1987): 345–47. http://dx.doi.org/10.1111/j.1749-6632.1987.tb29568.x.

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RICH, JOSEPH O., e JONATHAN S. DORDICK. "Controlling Regioselectivity in Enzyme-catalyzed Acylation of Polyhydroxyl Compounds". Annals of the New York Academy of Sciences 799, n. 1 Enzyme Engine (ottobre 1996): 226–30. http://dx.doi.org/10.1111/j.1749-6632.1996.tb33205.x.

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Ito, Minami, Yuya Nishida, Tatsuya Iwamoto, Akiko Kanai, Shuhei Aoyama, Kyosei Ueki, Hirotsugu Uzawa, Hitoshi Iida e Hirotaka Watada. "Protein acylations induced by a ketogenic diet demonstrate diverse patterns depending on organs and differ between histones and global proteins". Biochemical and Biophysical Research Communications 712-713 (giugno 2024): 149960. http://dx.doi.org/10.1016/j.bbrc.2024.149960.

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45

Hu, Bin, Han Gong, Chaoying Yang, Ling Nie, Ji Zhang, Long Liang, Mohandas Narla, Yue Sheng e Jing Liu. "Dynamic Changes in Lysine Succinylation As Important Regulators of Erythropoiesis". Blood 142, Supplement 1 (28 novembre 2023): 2448. http://dx.doi.org/10.1182/blood-2023-182646.

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Lysine succinylation has emerged as a recently discovered protein modification that significantly impacts the chemical environment and exhibits diverse functions in various biological processes. However, the specific role of lysine succinylation in erythropoiesis has not been fully elucidated. In this study, we investigated the levels of six common acylations (acetylation, crotonylation, succinylation, propionylation, butyrylation, and malonylation) in human erythroid cells. Interestingly, we observed a prominent accumulation of lysine succinylation during human erythroid differentiation, suggesting its potential importance in this process. To explore the functional significance of succinylation, we inhibited succinylation in human erythroid progenitor cell line by disrupting the expression of the key succinyltransferases and desuccinylases. The results revealed that succinylation inhibition led to suppressed cell proliferation, increased apoptosis, and disrupted differentiation, indicating the essential role of succinylation in erythropoiesis. Furthermore, integrative proteome and succinylome analysis identifies 939 quantifiable proteins with 2,871 Ksu sites. Notably, we observed inconsistencies between alterations in protein levels and succinylation levels, suggesting that the role of succinylation in proteins' function regulation. These succinylated proteins are widely distributed in various cellular compartments and involved in multiple cell processes, indicating that succinylation is a prevalent modification in erythropoiesis. Mechanically, we identified CYCS as a key target of succinylation during erythropoiesis, emphasizing its essential role in this process. Specially, we implicated KAT2A-mediated histone succinylation in chromatin remodeling, further highlighting the regulatory significance of lysine succinylation in erythropoiesis at the epigenetic level. Collectively, our comprehensive investigation of the succinylation landscape during erythropoiesis provides valuable insights into its regulatory role and offer potential implications for erythroid-related diseases and therapeutic strategies.

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DACQUET, CATHERINE, CHRISTELLE MACIA e MICHAEL SPEDDING. "Acylation Differentiates Two Forms of Agonist Binding to Rat 5-HT1AReceptors." Annals of the New York Academy of Sciences 812, n. 1 Receptor Clas (maggio 1997): 178. http://dx.doi.org/10.1111/j.1749-6632.1997.tb48165.x.

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DUUREN, BENJAMIN L. "Direct-Acting Alkylating and Acylating Agents." Annals of the New York Academy of Sciences 534, n. 1 Living in a C (giugno 1988): 620–34. http://dx.doi.org/10.1111/j.1749-6632.1988.tb30153.x.

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KODELIA, G., e F. N. KOLISIS. "Studies on the Reaction Catalyzed by Protease for the Acylation of Flavonoids in Organic Solvents". Annals of the New York Academy of Sciences 672, n. 1 Enzyme Engine (novembre 1992): 451–57. http://dx.doi.org/10.1111/j.1749-6632.1992.tb32712.x.

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ZHUANG, YING-PING, JIAN-HE XU e SI-LIANG ZHANG. "Effects of Organic Solvent and Acylating Agent on Lipase-Catalyzed Esterification of a Chiral Chlorohydrin in Nonaqueous Mediaa". Annals of the New York Academy of Sciences 864, n. 1 ENZYME ENGINE (dicembre 1998): 656–59. http://dx.doi.org/10.1111/j.1749-6632.1998.tb10399.x.

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Bhattacharya, Saikat, e Benjamin P. Tu. "Histone acylation at a glance". Journal of Cell Science 137, n. 11 (1 giugno 2024). http://dx.doi.org/10.1242/jcs.261250.

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ABSTRACT An important mechanism of gene expression regulation is the epigenetic modification of histones. The cofactors and substrates for these modifications are often intermediary metabolites, and it is becoming increasingly clear that the metabolic and nutritional state of cells can influence these marks. These connections between the balance of metabolites, histone modifications and downstream transcriptional changes comprise a metabolic signaling program that can enable cells to adapt to changes in nutrient availability. Beyond acetylation, there is evidence now that histones can be modified by other acyl groups. In this Cell Science at a Glance article and the accompanying poster, we focus on these histone acylation modifications and provide an overview of the players that govern these acylations and their connections with metabolism.

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