Ergothioneine Biosynthetic Methyltransferase EgtD Reveals the Structural Basis of Aromatic Amino Acid Betaine Biosynthesis

Ergothioneine is an N‐α‐trimethyl‐2‐thiohistidine derivative that occurs in human, plant, fungal, and bacterial cells. Biosynthesis of this redox‐active betaine starts with trimethylation of the α‐amino group of histidine. The three consecutive methyl transfers are catalyzed by the S‐adenosylmethionine‐dependent methyltransferase EgtD. Three crystal structures of this enzyme in the absence and in the presence of N‐α‐dimethylhistidine and S‐adenosylhomocysteine implicate a preorganized array of hydrophilic interactions as the determinants for substrate specificity and apparent processivity. We identified two active site mutations that change the substrate specificity of EgtD 10⁷‐fold and transform the histidine‐methyltransferase into a proficient tryptophan‐methyltransferase. Finally, a genomic search for EgtD homologues in fungal genomes revealed tyrosine and tryptophan trimethylation activity as a frequent trait in ascomycetous and basidomycetous fungi.     

Mycobacterium tuberculosis Rv1916 is an Acetyl-CoA-Binding Protein

Isocitrate lyase (ICL) isoform 2 is an essential enzyme for some clinical Mycobacterium tuberculosis (Mtb) strains during infection. In the laboratory Mtb strain H37Rv, the icl2 gene encodes two distinct gene products – Rv1915 and Rv1916 – due to a frameshift mutation. This study aims to characterise these two gene products to understand their structure and function. While we were unable to produce Rv1915 recombinantly, soluble Rv1916 was obtained with sufficient yield for characterisation. Kinetic studies using UV-visible spectrophotometry and ¹H-NMR spectroscopy showed that recombinant Rv1916 does not possess isocitrate lyase activity, while waterLOGSY binding experiments demonstrated that it could bind acetyl-CoA. Finally, X-ray crystallography revealed structural similarities between Rv1916 and the C-terminal domain of ICL2. Considering the probable differences between full-length ICL2 and the gene products Rv1915 and Rv1916, care must be taken when using Mtb H37Rv as a model organism to study central carbon metabolism.     

结核分枝杆菌融合蛋白亚单位疫苗对BCG初始免疫的加强效应及保护效力

目的探讨结核分枝杆菌融合蛋白亚单位疫苗对BCG初始免疫的加强效应及保护效力。方法将Ag85B、Ag85B-Mpt64190-198-HspX(AMH)、Ag85B-Mpt64190-198-Mtb8.4(AMM)以及AMH+AMM蛋白分别与佐剂二甲基三十六烷基铵(DDA)和卡介苗多糖核酸(BCG-PSN)混合,制备亚单位疫苗。第0周用BCG皮下免疫C57BL/6小鼠,第8、10周分别用各蛋白疫苗皮下加强免疫,以PBS和BCG(仅免疫1次)作为对照。末次免疫后4周,采血检测血清抗体水平,并分离脾淋巴细胞,检测分泌IFNγ的水平;末次免疫后12周,经尾静脉注射H37Rv株,6周后取肺,进行菌落计数,抗酸及HE染色观察。结果各亚单位疫苗加强组诱导产生的特异性抗Ag85BIgG抗体水平均明显高于BCG组;融合蛋白疫苗加强组免疫小鼠脾细胞经Ag85B和PPD刺激后,产生分泌IFNγ的淋巴细胞数明显多于BCG组;融合蛋白加强组免疫小鼠肺组织结核结节面积与BCG组比较,差异无统计学意义;仅AMM+AMH加强组免疫小鼠肺组织菌落计数明显低于BCG组,其抗酸染色阳性细菌数明显低于PBS、BCG及AMH、Ag85B加强组。结论AMH和AMM疫苗联合加强BCG免疫,能诱导小鼠特异性的细胞免疫和体液免疫应答,具有较强的免疫原性,可增强BCG的保护效力。     

Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation

Se-benzyl selenoimidazolium salts are characterized by remarkable alkyl-transfer potential under physiological conditions. Structure-activity relationship studies show that selective monoalkylation of primary amines depends on supramolecular interactions between the selenoimidazole leaving group and the target nucleophile. We demonstrate that these reagents can be used for site-selective and nearly quantitative modification of the model protein lysozyme on Lys13, bypassing the higher intrinsic reactivities of Lys1 and Lys33. These observations introduce selenoimidazolium salts as novel class of electrophiles for selective N-alkylation of native proteins.     

结核分枝杆菌早期分泌性蛋白ESAT-6的原核表达及纯化

目的原核表达并纯化结核分枝杆菌早期分泌性蛋白ESAT-6。方法将ESAT-6基因自pET-24b-ESAT-6质粒亚克隆至pGEX-3C载体中,构建重组表达质粒pGEX-ESAT-6,经酶切及测序鉴定正确后,分别转化大肠杆菌JM107和BL21(DE3),以不同浓度IPTG诱导表达,表达产物经GSH-Sepharose4 B亲和层析纯化。结果所构建的重组表达质粒pGEX-ESAT-6经酶切及测序鉴定正确;重组融合蛋白在大肠杆菌JM107中的表达量较高,可达菌体总蛋白的24.2%;最适IPTG诱导浓度为0.1mmol/L;纯化的目的蛋白纯度可达83.9%。结论已成功构建了重组表达质粒pGEX-ESAT-6,并在大肠杆菌JM107中高效表达,为结核分枝杆菌亚单位疫苗及核酸疫苗的研制提供了材料。     

以结核分枝杆菌38kD重组蛋白为抗原的血清学诊断

目的克隆表达结核分枝杆菌38kD抗原基因,并以此蛋白为抗原,进行分枝杆菌的血清学诊断。方法采用PCR自结核分枝杆菌基因组DNA中扩增38kD抗原基因,经测序鉴定正确后,克隆于pGEX-4T-2表达载体,转化大肠杆菌BL21进行诱导表达,利用GSTrapFF蛋白柱纯化表达产物,经ELISA检测其抗原的灵敏度与特异性。结果目的蛋白表达量约占菌体总蛋白量的28%,ELISA检测灵敏度为79.8%,特异性为99.0%。结论重组38kD抗原可用于结核分枝杆菌的诊断。     

结核分枝杆菌RD1区重组11 kD蛋白的克隆表达及效力

目的在大肠杆菌中表达结核分枝杆菌RD1区11kD蛋白,并检测表达产物的效力。方法构建11kD蛋白编码基因原核表达载体,转化大肠杆菌BL21(DE3)IPTG诱导表达,离子层析柱分离纯化重组蛋白。以结核分枝杆菌致敏豚鼠进行皮肤变态反应(DTH)测定。结果结核分枝杆菌11kD蛋白在大肠杆菌中以可溶形式表达,表达蛋白占总菌体蛋白的33%以上,纯化后纯度达95%以上,并可诱导结核分枝杆菌致敏豚鼠产生迟发型超敏反应,5μg/ml11kD蛋白的效力与50IU/ml TB-PPD相当。结论重组11kD蛋白已在大肠杆菌中成功表达,并有望成为结核病皮试鉴别诊断用新试剂。     

Mechanistic Insights into the Allosteric Regulation of the Clr4 Protein Lysine Methyltransferase by Autoinhibition and Automethylation

Clr4 is a histone H3 lysine 9 methyltransferase in Schizosaccharomyces pombe that is essential for heterochromatin formation. Previous biochemical and structural studies have shown that Clr4 is in an autoinhibited state in which an autoregulatory loop (ARL) blocks the active site. Automethylation of lysine residues in the ARL relieves autoinhibition. To investigate the mechanism of Clr4 regulation by autoinhibition and automethylation, we exchanged residues in the ARL by site-directed mutagenesis leading to stimulation or inhibition of automethylation and corresponding changes in Clr4 catalytic activity. Furthermore, we demonstrate that Clr4 prefers monomethylated (H3K9me1) over unmodified (H3K9me0) histone peptide substrates, similar to related human enzymes and, accordingly, H3K9me1 is more efficient in overcoming autoinhibition. Due to enzyme activation by automethylation, we observed a sigmoidal dependence of Clr4 activity on the AdoMet concentration, with stimulation at high AdoMet levels. In contrast, an automethylation-deficient mutant showed a hyperbolic Michaelis–Menten type relationship. These data suggest that automethylation of the ARL could act as a sensor for AdoMet levels in cells and regulate the generation and maintenance of heterochromatin accordingly. This process could connect epigenome modifications with the metabolic state of cells. As other human protein lysine methyltransferases (for example, PRC2) also use automethylation/autoinhibition mechanisms, our results may provide a model to describe their regulation as well.     

结核分枝杆菌PPE68蛋白的原核表达及纯化

目的构建结核分枝杆菌PPE68基因的原核表达质粒,并在大肠杆菌中进行表达和纯化。方法以结核分枝杆菌H37Rv基因组DNA为模板,PCR法扩增PPE68基因,将其克隆至pET-32a(+)载体中,构建重组原核表达质粒pET-32a(+)-PPE68,转化至大肠杆菌BL21(DE3)中,IPTG诱导表达。表达产物经SDS-PAGE及Western blot鉴定后,进行纯化。结果重组表达质粒pET-32a(+)-PPE68经PCR及双酶切鉴定构建正确,测序结果与GenBank中登录的PPE68基因序列一致。表达的Trx-PPE68融合蛋白相对分子质量约为57000,表达量约占菌体总蛋白的41%,可与结核分枝杆菌免疫小鼠血清发生特异性反应。纯化的重组蛋白纯度约为93%。结论已成功构建了结核分枝杆菌PPE68基因重组原核表达质粒pET-32a(+)-PPE68,原核表达并纯化了重组蛋白,为PPE68作为结核病特异性诊断抗原的开发及重组BCG疫苗的研制奠定了基础。     

Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase from Mycobacterium tuberculosis

3‐Dehydroquinase, the third enzyme in the shikimate pathway, is a potential target for drugs against tuberculosis. Whilst a number of potent inhibitors of the Mycobacterium tuberculosis enzyme based on a 3‐dehydroquinate core have been identified, they generally show little or no in vivo activity, and were synthetically complex to prepare. This report describes studies to develop tractable and drug‐like aromatic analogues of the most potent inhibitors. A range of carbon–carbon linked biaryl analogues were prepared to investigate the effect of hydrogen bond acceptor and donor patterns on inhibition. These exhibited inhibitory activity in the high‐micromolar range. The addition of flexible linkers in the compounds led to the identification of more potent 3‐nitrobenzylgallate‐ and 5‐aminoisophthalate‐based analogues.     

结核分枝杆菌与非结核分枝杆菌分泌蛋白指纹图谱的比较

目的比较结核分枝杆菌和非结核分枝杆菌分泌蛋白的指纹图谱,分析分泌蛋白表达的差异,为分枝杆菌的快速鉴别奠定基础。方法选取结核分枝杆菌和非结核分枝杆菌标准菌株,培养后灭活,提取分泌蛋白,用表面增强激光解吸电离飞行时间质谱(SELDI-TOF-MS)检测菌株分泌蛋白的表达,Biomaker Wizard Software分析软件筛选差异蛋白。重复测定20次分枝杆菌分泌蛋白,评价SELDI-TOF-MS检测分枝杆菌分泌蛋白相对分子质量的重复性。结果AU芯片能捕获近30个分枝杆菌分泌蛋白峰,4个蛋白峰为分枝杆菌共有。与非结核分枝杆菌分泌蛋白指纹图谱比较,有1个蛋白峰为结核分枝杆菌所特有。SELDI-TOF-MS重复检测20次分枝杆菌分泌蛋白显示,同一蛋白峰的相对分子质量变异系数≤0.05%。结论结核分枝杆菌和非结核分枝杆菌差异蛋白的发现,可能有助于分枝杆菌的鉴别。     

The Veterinary Anti-Parasitic Selamectin Is a Novel Inhibitor of the Mycobacterium tuberculosis DprE1 Enzyme

Avermectins are macrocyclic lactones with anthelmintic activity. Recently, they were found to be effective against Mycobacterium tuberculosis, which accounts for one third of the worldwide deaths from antimicrobial resistance. However, their anti-mycobacterial mode of action remains to be elucidated. The activity of selamectin was determined against a panel of M. tuberculosis mutants. Two strains carrying mutations in DprE1, the decaprenylphosphoryl-β-D-ribose oxidase involved in the synthesis of mycobacterial arabinogalactan, were more susceptible to selamectin. Biochemical assays against the Mycobacterium smegmatis DprE1 protein confirmed this finding, and docking studies predicted a binding site in a loop that included Leu275. Sequence alignment revealed variants in this position among mycobacterial species, with the size and hydrophobicity of the residue correlating with their MIC values; M. smegmatis DprE1 variants carrying these point mutations validated the docking predictions. However, the correlation was not confirmed when M. smegmatis mutant strains were constructed and MIC phenotypic assays performed. Likewise, metabolic labeling of selamectin-treated M. smegmatis and M. tuberculosis cells with ¹⁴C-labeled acetate did not reveal the expected lipid profile associated with DprE1 inhibition. Together, our results confirm the in vitro interactions of selamectin and DprE1 but suggest that selamectin could be a multi-target anti-mycobacterial compound.     

结核分枝杆菌H_(37)Rv株Rv0341编码基因iniB的克隆与表达

目的克隆并表达编码结核分枝杆菌H37Rv株Rv0341蛋白的iniB基因。方法利用PCR从结核分枝杆菌H37Rv株中扩增iniB基因,克隆于pET-22b(+)原核表达载体,转化大肠杆菌BL21(DE3),经IPTG诱导表达,镍离子亲和层析柱纯化后,通过SDS-PAGE和Western-blot鉴定目的蛋白的表达及反应原性。结果克隆并表达了iniB基因,表达的蛋白相对分子质量约43000,诱导2h表达量较高,约为25%。目的蛋白主要以包涵体形式存在于超声沉淀中,纯化后蛋白纯度可达98%以上。经Western blot检测,纯化蛋白与依赖利福平结核分枝杆菌(依R菌)肺结核患者血清呈现强阳性反应,而与非依R菌肺结核患者血清不反应。结论已成功克隆并表达了编码结核分枝杆菌H37Rv株Rv0341蛋白的iniB基因,表达的重组蛋白具有反应原性及特异性,为依R菌结核病临床血清学快速诊断方法的建立及试剂盒的研发奠定了基础。     

Discovery of an Acyclic Nucleoside Phosphonate that Inhibits Mycobacterium tuberculosis ThyX Based on the Binding Mode of a 5‐Alkynyl Substrate Analogue

The urgent need for new antibiotics poses a challenge to target un(der)exploited vital cellular processes. Thymidylate biosynthesis is one such process due to its crucial role in DNA replication and repair. Thymidylate synthases (TS) catalyze a crucial step in the biosynthesis of thymidine 5‐triphosphate (TTP), an elementary building block required for DNA synthesis and repair. To date, TS inhibitors have only been successfully applied in anticancer therapy due to their lack of specificity for antimicrobial versus human enzymes. However, the discovery of a new family of TS enzymes (ThyX) in a range of pathogenic bacteria that is structurally and biochemically different from the “classic” TS (ThyA) has opened the possibility to develop selective ThyX inhibitors as potent antimicrobial drugs. Here, the interaction of the known inhibitor 5‐(3‐octanamidoprop‐1yn‐1yl)‐2′‐deoxyuridine‐5′‐monophosphate ( 1 ) with Mycobacterium tuberculosis ThyX enzyme is explored using molecular modeling starting from published crystal structures, with further confirmation through NMR experiments. While the deoxyuridylate (dUMP) moiety of compound 1 occupies the cavity of the natural substrate in ThyX, the rest of the ligand (the “5‐alkynyl tail”) extends to the outside of the enzyme between two of its four subunits. The hydrophobic pocket that accommodates the alkyl part of the tail is formed by displacement of Tyr 44.C, Tyr 108.A and Lys 165.A. Changes to the resonance of the Lys 165 NH₃ group upon ligand binding were monitored in a titration experiment by 2D HISQC NMR. Guided by the results of the modeling and NMR studies, and inspired by the success of acyclic antiviral nucleosides, compounds where a 5‐alkynyl uracyl moiety is coupled to an acyclic nucleoside phosphonate (ANP) were synthesized and evaluated. Of the compounds evaluated, sodium (6‐(5‐(3‐octanamidoprop‐1‐yn‐1‐yl)‐2,4‐dioxo‐3,4‐dihydropyrimidin‐1(2H)‐yl)hexyl)phosphonate ( 3 e ) exhibited 43 % of inhibitory effect on ThyX at 50 μM . While only modest activity was achieved, this is the first example of an ANP inhibiting ThyX, and these results can be used to further guide structural modifications to this class to develop more potent compounds with potential application as antibacterial agents acting through a novel mechanism of action.     

结核分枝杆菌杂交信号放大检测方法的建立

目的建立结核分枝杆菌杂交信号放大检测方法。方法构建纳米颗粒信号放大载体,建立杂交信号放大方法,检测标本中结核分枝杆菌特异性的插入序列IS6110。应用该方法检测124份临床结核患者标本,并与细菌培养和生化鉴定法的检测结果进行比较,确定该方法的灵敏度和特异性。结果杂交信号放大方法检测临床标本的灵敏度为87.7%,特异性为92.2%,假阳性率为7.8%,假阴性率为12.3%。结论已建立具有较高灵敏度和特异性的杂交信号放大检测方法,该方法操作简便、快速,可作为结核分枝杆菌临床标本的检测方法。     

Development of Tyrphostin Analogues to Study Inhibition of the Mycobacterium tuberculosis Pup Proteasome System**

Tuberculosis is a global health problem caused by infection with the Mycobacterium tuberculosis (Mtb) bacteria. Although antibiotic treatment has dramatically reduced the impact of tuberculosis on the population, the existence and spreading of drug resistant strains urgently demands the development of new drugs that target Mtb in a different manner than currently used antibiotics. The prokaryotic ubiquitin-like protein (Pup) proteasome system is an attractive target for new drug development as it is unique to Mtb and related bacterial genera. Using a Pup-based fluorogenic substrate, we screened for inhibitors of Dop, the Mtb depupylating protease, and identified I-OMe-Tyrphostin AG538 ( 1 ) and Tyrphostin AG538 ( 2 ). The hits were validated and determined to be fast-reversible, non-ATP competitive inhibitors. We synthesized >25 analogs of 1 and 2 and show that several of the synthesized compounds also inhibit the depupylation actions of Dop on native substrate, FabD-Pup. Importantly, the pupylation activity of PafA, the sole Pup ligase in Mtb, was also inhibited by some of these compounds.     

结核分枝杆菌分泌蛋白抗原免疫电化学检测方法的建立

目的建立一种新型、快速的结核分枝杆菌(Mycobacterium tuberculosis,MTB)分泌蛋白抗原85B(Ag85B)免疫电化学检测方法。方法先在玻碳电极(Glassy carbon electrode,GCE)表面电沉积一层纳米金,通过静电吸附固定普鲁士蓝壳聚糖(Chitosan-prussian blue,CS-PB)纳米复合物,利用壳聚糖的氨基功能团固定微米金磁微粒(Au-Fe3O4),再吸附兔抗Ag85B多克隆抗体,制得电流型免疫传感器。测定电极制备过程的电化学特征,通过原子力显微镜对免疫传感器进行表征,确定免疫传感器的最佳pH值、反应时间、检测线性响应范围及检测下限,验证该方法的特异性和重复性,并与ELISA检测结果进行比较。结果原子力显微镜结果表明,Au-Fe3O4与兔抗Ag85B多克隆抗体可连接到电极表面。在最佳pH值(pH7.5)和反应时间(12min)的条件下,该传感器响应的峰电流值与Ag85B浓度在10～500ng/ml的范围内呈良好的线性关系,检测下限可达10ng/ml,且具有良好的特异性和重复性。免疫传感器与ELISA检测结果的吻合性较好。结论已成功制备了检测Ag85B的免疫传感器,该传感器制备简单,操作便捷,灵敏度高。     

Elucidation of Mycobacterium tuberculosis type II dehydroquinase inhibitors using a fragment elaboration strategy

A library of novel Mycobacterium tuberculosis type II dehydroquinase (DHQase) inhibitors were discovered through the use of a fragment elaboration approach. Putative active site binding fragments were initially assessed in silico which led to the selection of two small aromatic fragments for further investigation. Synthetic elaboration of the fragments provided a library of 34 inhibitors that exhibited low-micromolar inhibition of type II DHQase. A number of these inhibitors also showed antibacterial activity in the low-micromolar range in screens against M. tuberculosis in vitro; these now serve as lead compounds for further development of therapeutics for the treatment of tuberculosis.     

结核分枝杆菌复活促进因子E的原核表达及纯化

目的构建结核分枝杆菌复活促进因子E(RpfE)的原核表达质粒,在大肠杆菌中表达并纯化。方法采用PCR方法从结核分枝杆菌H37Rv基因组DNA中扩增出RpfE基因,双内切酶消化后,与同样酶消化的pET32a(+)载体连接,转化大肠杆菌Top10。阳性克隆经酶切和DNA测序鉴定正确后,将重组质粒转化至大肠杆菌BL21中,经IPTG诱导,由T7启动子调控表达RpfE蛋白,并对表达蛋白进行鉴定和纯化。结果双酶切鉴定所切下的片段大小与预期相符,测序结果与文献报道一致。经SDS-PAGE分析和Western blot鉴定,在相对分子质量41000处均可见特异性蛋白条带。经Ni2+-NTA金属螯合层析后,重组蛋白纯度可达90%以上。结论已成功地克隆并构建了RpfE基因的重组表达质粒pET32a(+)-RpfEv,并获得了高纯度的重组蛋白,为以后的深入研究奠定了基础。