Biochemistry of the lysine beta-hydroxybutyrylation pathway

赖氨酸β-羟基丁酰化途径的生物化学

• 批准号: 10210387
• 负责人: PHILIP A COLE
• 金额: $ 53.31万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2022-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10210387
• 关键词: Acetylation; Acetyltransferase; Affinity; Alcoholic liver damage; Area; Binding Proteins; Biochemistry; Biological; Biological Process; Biology; Brain; Cell physiology; Cells; Chemicals; Coenzyme A; Complications of Diabetes Mellitus; Couples; DNA; Data; Data Set; Deacetylase; Diabetes Mellitus; Diabetic Diet; Disease; Energy Metabolism; Enzymatic Biochemistry; Enzymes; Epigenetic Process; Foundations; Functional disorder; Gene Expression; Genes; Goals; Histone Deacetylase; Histones; Hydroxybutyrates; In Vitro; Infrastructure; Insulin-Dependent Diabetes Mellitus; Ketone Bodies; Label; Laboratories; Lead; Libraries; Link; Liver; Lysine; Mass Spectrum Analysis; Mediating; Metabolic Pathway; Metabolism; Methods; Modification; Molecular; Molecular Biology; Morbidity - disease rate; Nutrient; Obesity; Output; Pathologic; Pathway interactions; Patients; Peptide Library; Peptides; Physiological; Plasma; Positioning Attribute; Post-Translational Protein Processing; Proteins; Proteomics; Recombinant Proteins; Recombinants; Regulatory Element; Research; Risk; Serum; Solid; Source; Starvation; Testing; Therapeutic; Tissues; Transfection; Western Blotting; anti-cancer; base; beta-Hydroxybutyrate; cancer clinical trial; experimental study; histone modification; improved; in vitro Assay; in vivo; insight; mortality; mouse model; novel; nutrition; programs; promoter; response

Emerging lines of evidence suggest a close link between obesity, energy metabolism, nutrients and epigenetic mechanism. Epigenetic changes, such as dynamic histone modifications, are associated with cellular metabolism and diabetic complications. Nevertheless, the molecular mechanisms mediating the crosstalk between metabolism and epigenetics remain incompletely understood. We recently discovered and comprehensively validated a new, evolutionarily-conserved lysine modification, lysine beta(β)- hydroxybutyrylation (Kbhb), on core histones. We detected 44 non-redundant Kbhb marks on histones and identified Sirt2 enzyme as the first enzyme to remove histone Kbhb. Levels of Kbhb are very dynamic and are influenced by physiological conditions (e.g., starvation and type I diabetes) and nutrition sources. Increased levels of β-hydroxybutyrate (also called 3-hydroxybutyrate) lead to increased histone Kbhb, presumably via conversion of β-hydroxybutyrate to β-hydroxybutyryl CoA. Interestingly, histone Kbhb is enriched in active gene promoters, and the increased H3K9bhb levels that occur during prolonged starvation are associated with genes up-regulated in starvation-responsive metabolic pathways, thus representing a new epigenetic regulatory mark that couples metabolism to gene expression. β-Hydroxybutyrate is a key component of “ketone bodies” and it has been employed in dozens of anti-cancer clinical trials as a potential therapeutic in combination with other agents. The plasma/cellular concentration of β-hydroxybutyrate can increase up to 20 mM during starvation and in pathological conditions such as diabetes mellitus (DM) and alcoholic liver damage and this can drive histone Kbhb formation. Hyperketonemia and ketoacidosis are known to increase the risk of morbidity and mortality in patients. Thus, molecular characterization of Kbhb pathway will not only improve our understanding of epigenetic mechanism but also characterize functions of β-hydroxybutyrate in physiopathology. We hypothesize that the Kbhb pathway is molecularly distinct from the lysine acetylation pathway. We therefore propose to characterize the Kbhb pathway by defining its key regulatory elements, including its substrates, a unique set of regulatory enzymes and direct binding proteins, thus laying a foundation for studying its biology functions. We will use an integrated strategy in this study involving enzymology, chemical biology, biochemistry and proteomics approaches. Our team, the Zhao laboratory and the Cole laboratory, is well positioned to carry out this project, because of our combined expertise in these areas and the relevant preliminary data that we have already obtained. In this proposal, we will first comprehensively identify and quantify dynamic changes of Kbhb-containing substrates using a quantitative proteomics approach. We will then identify and characterize Kbhb-regulatory enzymes that can add or remove Kbhb. We will finally identify and confirm the direct protein binders of histone Kbhb peptides.

新兴的证据表明，肥胖，能量代谢，营养和表观遗传学之间的紧密联系 机制。表观遗传变化，例如动态组蛋白的修饰，与细胞有关 代谢和糖尿病并发症。然而，介导串扰的分子机制 新陈代谢和表观遗传学之间仍然没有完全理解。我们最近发现了 全面验证了一种新的，进化保存的赖氨酸修饰，赖氨酸β（β） - 羟基丁酰化（KBHB），核心组蛋白。我们在组蛋白上检测到44个非冗余KBHB标记 将SIRT2酶确定为去除组蛋白KBHB的第一种酶。 KBHB的水平非常动态，并且是 受身体状况（例如饥饿和I型糖尿病）和营养来源的影响。增加 β-羟基丁酸的水平（也称为3-羟基丁酸）导致组蛋白KBHB增加，大概是通过 β-羟基丁酸转化为β-羟基丁酰胺COA。有趣的是，组蛋白KBHB富含活性 基因启动子以及长期饥饿期间发生的H3K9BHB水平增加与 在饥饿响应的代谢途径中上调的基因，因此代表了一种新的表观遗传 调节标记将代谢与基因表达伴侣。 β-羟基丁酸是 “酮体”，并且已在数十个抗癌临床试验中被用作潜在的治疗疗法 与其他代理商结合。 β-羟基丁酸的血浆/细胞浓度最多可以增加20 饥饿期间和病理状况（例如糖尿病（DM）和酒精肝损害）的MM 这可以驱动组蛋白KBHB形成。已知高酮血症和酮症酸中毒会增加 患者的发病率和死亡率。这是KBHB途径的分子表征不仅会改善我们的 了解表观遗传机制，但也表征了β-羟基丁酸的功能 生理病理学。我们假设KBHB途径与赖氨酸乙酰化分子不同 路径。因此，我们建议通过定义其关键调节元素来表征KBHB途径 包括其底物，一组独特的调节酶和直接结合蛋白，从而铺设 研究其生物学功能的基础。我们将在涉及的这项研究中使用综合策略 酶学，化学生物学，生物化学和蛋白质组学方法。我们的团队，Zhao实验室和 Cole实验室，由于我们在这些项目中的综合专业知识，因此可以很好地执行该项目 我们已经获得的领域和相关初步数据。在此提案中，我们将首先 全面识别和量化含KBHB的底物的动态变化 蛋白质组学方法。然后，我们将识别并表征可以添加或删除的KBHB调节酶 KBHB。我们最终将识别并确认组蛋白KBHB肽的直接蛋白质结合剂。

项目成果

Class I histone deacetylases (HDAC1-3) are histone lysine delactylases.

• DOI: 10.1126/sciadv.abi6696
• 发表时间: 2022-01-21
• 期刊: Science advances
• 影响因子: 13.6
• 作者: Moreno-Yruela C;Zhang D;Wei W;Bæk M;Liu W;Gao J;Danková D;Nielsen AL;Bolding JE;Yang L;Jameson ST;Wong J;Olsen CA;Zhao Y
• 通讯作者: Zhao Y