In-depth Profiling and Quantification of the Lysine Acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide with limited therapeutic options. Comprehensive investigation of protein posttranslational modifications in HCC is still limited. Lysine acetylation is one of the most common types of posttranslational modification involved in many cellular processes and plays crucial roles in the regulation of cancer. In this study, we analyzed the proteome and K-acetylome in eight pairs of HCC tumors and normal adjacent tissues using a timsTOF Pro instrument. As a result, we identified 9219 K-acetylation sites in 2625 proteins, of which 1003 sites exhibited differential acetylation levels between tumors and normal adjacent tissues. Interestingly, many novel tumor-specific K-acetylation sites were characterized, for example, filamin A (K865), filamin B (K697), and cofilin (K19), suggesting altered activities of these cytoskeleton-modulating molecules, which may contribute to tumor metastasis. In addition, we observed an overall suppression of protein K-acetylation in HCC tumors, especially for enzymes from various metabolic pathways, for example, glycolysis, tricarboxylic acid cycle, and fatty acid metabolism. Moreover, the expression of deacetylase sirtuin 2 (SIRT2) was upregulated in HCC tumors, and its role of deacetylation in HCC cells was further explored by examining the impact of SIRT2 overexpression on the proteome and K-acetylome in Huh7 HCC cells. SIRT2 overexpression reduced K-acetylation of proteins involved in a wide range of cellular processes, including energy metabolism. Furthermore, cellular assays showed that overexpression of SIRT2 in HCC cells inhibited both glycolysis and oxidative phosphorylation. Taken together, our findings provide valuable information to better understand the roles of K-acetylation in HCC and to treat this disease by correcting the aberrant acetylation patterns.     

绿色木霉组蛋白去乙酰化酶编码基因TvRpd3在木霉生物防治作用中的功能分析

【目的】本文借助基因编辑技术在具有生物防治潜力的绿色木霉(Trichoderma viride)中敲除组蛋白去乙酰化酶编码基因TvRpd3,来研究TvRpd3基因及其编码蛋白在提高木霉病原菌拮抗能力中的作用。【方法】利用融合PCR和同源重组策略构建了TvRpd3基因缺失的突变菌株,通过对峙培养、表型观察、免疫组化检测、代谢组学分析等系统比较TvRpd3基因敲除前后菌株的组蛋白乙酰化修饰水平、次级代谢产物合成、病原菌拮抗能力以及田间防治效果等。【结果】与野生型菌株相比,缺失TvRpd3基因的木霉工程菌(?TvRpd3)对多种病原菌表现出了更强的对峙抑制效果,其所产的发酵液对小麦白粉病、烟草黑胫病和番茄枯萎病的防治效果分别提高了62.27%、57.45%和70.71%。同时,敲除TvRpd3基因也显著改变了木霉工程菌所产次级代谢产物的种类和产量,抗生性物质的产量大幅提高。【结论】绿色木霉TvRpd3基因及其介导的组蛋白乙酰化修饰在提高绿色木霉生物防治中起着重要作用。     

Novel (E)-3-(3-Oxo-4-substituted-3,4-dihydro-2H-benzo[b][1,4]oxazin-6-yl)-N-hydroxypropenamides as Histone Deacetylase Inhibitors: Design,Synthesis and Bioevaluation

Herein, we report the design, synthesis and evaluation of novel (E)-3-(3-oxo-4-substituted-3,4-dihydro-2H-benzo[b][1,4]oxazin-6-yl)-N-hydroxypropenamides ( 4 a – i , 7 a – g ) targeting histone deacetylases. Three human cancer cell lines were used to test the cytotoxicity of the synthesized compounds (SW620, colon; PC-3, prostate; NCI−H23, lung cancer); inhibitory activity towards HDAC; anticancer activity; as well as their impact on the cell cycle and apoptosis. As a result, compounds 4 a – i bearing the alkyl substituents seemed to be less potent than the benzyl-containing compounds 7 a – g in all biological assays. Compounds 7 e – f were found to be the most active HDAC inhibitors with IC₅₀ of 1.498±0.020 μM and 1.794±0.159 μM, respectively. In terms of cytotoxicity and anticancer assay, 7 e and 7 f also showed good activity with IC₅₀ values in the micromolar range. In addition, the cell cycle and apoptosis of SW620 were affected by compound 7 f in almost a similar manner to that of reference compound SAHA. Docking assays were carried out for analysis the binding mode and selectivity of this compound toward 8 HDAC isoforms. Overall, our data confirmed that the inhibition of HDAC plays a pivotal role in their anticancer activity.     

X‐ray crystallographic structure of BshB,the zinc‐dependent deacetylase involved in bacillithiol biosynthesis

Many gram‐positive bacteria produce bacillithiol to aid in the maintenance of redox homeostasis and degradation of toxic compounds, including the antibiotic fosfomycin. Bacillithiol is produced via a three‐enzyme pathway that includes the action of the zinc‐dependent deacetylase BshB. Previous studies identified conserved aspartate and histidine residues within the active site that are involved in metal binding and catalysis, but the enzymatic mechanism is not fully understood. Here we report two X‐ray crystallographic structures of BshB from Bacillus subtilis that provide insight into the BshB catalytic mechanism.     

表观遗传的化学干预对金龟子绿僵菌次生代谢产物影响的研究

[背景] 表观遗传酶类化学抑制剂对真菌的影响研究主要集中在新次生代谢产物挖掘方面,而对大量已知次生代谢物含量的变化却关注较少。金龟子绿僵菌是一种常用杀虫真菌,能代谢出多种已知生物活性物质,其含量可能会影响到该菌与环境间关系及利用潜力。[目的] 评估组蛋白去乙酰化酶和DNA甲基转移酶的化学抑制剂对金龟子绿僵菌代谢物安全性和可利用性的影响。[方法] 在金龟子绿僵菌培养基中添加表观遗传酶类化学抑制剂,培养一定时间后用高分辨液质联用及标准品对照方法分析次生代谢产物变化。根据差异代谢物的生物活性评估化学抑制剂的影响。[结果] 高分辨液质联用分析结果表明当抑制剂浓度达500μmol/L时,金龟子绿僵菌有16种主要次生代谢产物出现明显量的变化,包括destruxin A、A1、A2、B、B1、B2、E、E2、Ed、didesmethyldestruxin C、dihydrodestruxin A、desmethyldestruxin B、12-hydroxyovalicin、subglutinol C、fungerin和ustilagic Acid C。其中,丁酸钠处理可使15种主要代谢物含量升高。苯甲酰胺可使12种主要代谢物含量升高。伏立诺他虽然仅能使10种主要代谢物含量升高,但部分代谢物的升高幅度明显高于前两者。2种DNA甲基转移酶抑制剂可使金龟子绿僵菌代谢物中绿僵菌素类代谢物含量普遍下降。[结论] 组蛋白去乙酰化酶抑制剂可引起金龟子绿僵菌主要代谢物含量普遍升高,而DNA甲基转移酶抑制剂使金龟子绿僵菌的绿僵菌素含量普遍下降。由于变化的代谢物都具有显著的杀虫、免疫抑制或抗菌抗癌等生物活性,因此上述化学抑制剂可增强或降低金龟子绿僵菌对环境中昆虫毒性,同时也增加或降低其代谢物利用潜力。另外,subglutinol C、fungerin和ustilagic Acid C是首次在金龟子绿僵菌中被发现。     

龙眼组蛋白去乙酰化酶基因DlHDT1的克隆与特性分析

组蛋白去乙酰化是植物表观遗传调控的重要组成部分,对染色体结构修饰和基因表达调控发挥着重要的作用。为深入探究组蛋白去乙酰化酶基因(histone deacetylase 1,HDT1)在龙眼体胚发生过程中的功能,该研究结合龙眼基因组数据,采用RT-PCR方法克隆得到龙眼组蛋白去乙酰化酶基因(DlHDT1),对其进行生物信息学分析及亚细胞定位观察,同时结合转录组数据分析DlHDT1在体胚发生过程中的FPKM值,并利用qRT-PCR技术检测PEG6000和NaCl处理下DlHDT1的表达模式。结果表明:(1)DlHDT1基因CDS序列全长918 bp,编码305个氨基酸,该蛋白为不稳定亲水性蛋白,不含信号肽和跨膜结构,共含43个磷酸化位点,相对分子量为32 585.54 Da,等电点为4.65;进化树分析显示龙眼DlHDT1与漾濞槭亲缘关系最近(78.76%)。(2)亚细胞定位显示,DlHDT1蛋白定位于细胞核中;顺式作用元件分析发现DlHDT1基因含有大量光响应元件和脱落酸、茉莉酸甲酯等激素及逆境胁迫响应元件;转录组数据显示,DlHDT1在龙眼体胚发生不同时期均有表达,在胚性愈伤组织(EC)阶段表达最低,在球形胚(GE)阶段表达最高。(3)qRT-PCR显示,在PEG6000和NaCl处理下DlHDT1基因,呈下调表达趋势,推测DlHDT1可能参与调控龙眼对干旱及盐胁迫的响应,并存在负调控关系。研究认为,DlHDT1为核定位基因,可能参与龙眼体胚形态建成并在龙眼响应非生物逆境胁迫过程中发挥重要作用。     

细胞自噬中关键蛋白乙酰化修饰与相关疾病诊治的研究进展

自噬是一种在进化上保守的溶酶体依赖的降解途径。近十多年来,自噬过程的分子机制研究得到了长足的发展。自噬过程中关键蛋白复合物的乙酰化修饰发挥了十分重要的作用。为此,该文阐述了细胞自噬过程中主要蛋白复合物的乙酰化修饰作用进展,并对蛋白质乙酰化修饰与肿瘤、神经退行性疾病等的关系作一总结。总之,自噬过程中蛋白乙酰化修饰已经成为自噬研究的热点之一,随着相关研究的不断深入,其必将为相关疾病的治疗提供重要的理论基础。