RNA内切酶CPSF3受E3D泛素连接酶UBE3D调控

泛素化是泛素分子在系列特殊酶作用下,对靶蛋白进行特异性修饰的过程,该过程参与细胞周期、基因表达、信号传递等几乎一切生命活动的调控,近年来成为开发新药物的新靶点.泛素化研究中,确定E3泛素连接酶和其特异性底物之间的作用是研究的重点和难点,探索底物蛋白翻译后修饰命运,对于研究E3泛素酶的修饰类型具有指示性的作用.E3D泛素...     

去泛素化酶及其与人类疾病相关性的研究进展

去泛素化酶(Deubiquitinating enzymes, DUBs)通过与泛素化靶蛋白的相互作用,切割或去除靶蛋白的泛素链,进而逆转靶蛋白的降解,参与泛素相关的信号转导及人类许多疾病的发生和发展。研究DUBs系统及其与人类疾病的相关性,挖掘出DUBs中新药的靶点对人类健康有重要作用。近年来,针对DUBs的种类、结构以及相关生理作用取得了新进展。本文通过对DUBs的分类、结构以及在肿瘤、免疫和神经系统疾病中的关系和靶向DUBs的先导化合物的研究进展进行综述,以期为DUBs相关的深入研究提供参考。     

λ噬菌体切除酶基因Xis在大肠杆菌中的可溶性融合表达

λ噬菌体切除酶Xis(excisionase)是调控λ噬菌体溶源裂解转换过程中的一种重要蛋白质.通过密码子优化及两步法将来自λ噬菌体切除酶基因Xis在体外合成,然后克隆到带有类泛素蛋白SUMO标签的定向原核表达载体SUMO-p ETG上,测序正确后,然后转化至E.coli BL21(DE3)细胞可溶性表达.经SDS-PAGE及质谱检测证实表达蛋白确实为目的蛋白.该研究通过融合表达λ噬菌体切除酶Xis不仅解除了Xis对E.coli宿主细胞的毒害作用,而且实现在E.coli中的高水平可溶性表达.因此,Xis的大量制备,将会促进Gateway克隆技术的广泛应用.     

泛素-蛋白酶体途径的组成及其生物功能

泛素-蛋白酶体途径(UPP)是20世纪70年代末期新发现的一种细胞内蛋白降解途径,在多种蛋白质降解中发挥重要作用,具有高度特异性。UPP介导的细胞蛋白降解是一个复杂、缜密的调控过程。UPP可识别、标记、进而降解那些被泛素化的蛋白质。它在抗原提呈、细胞周期、NF-kB代谢等方面发挥重要调控作用,而且UPP的异常与许多疾病如肿瘤、脓毒症、骨骼肌损伤等的致病机制有关。就UPP的组成、作用机制及其功能进行综述。     

小麦TaUBC基因泛素结合酶活性分析

已报道的RNA水平研究表明TaUBC可能是小麦产量相关基因,生物信息学分析显示该基因属于泛素结合酶家族.荧光定量PCR显示TaUBC在小麦根茎叶中均有表达.为了验证TaUBC蛋白是否具有泛素结合酶活性,本文利用原核系统表达野生型TaUBC及三种点突变TaUBC~(C21S)、TaUBC~(C85S)、TaUBC~(C107S)蛋白,并对这些蛋白进行体外泛素化活性分析.结果证实TaUBC是一个有活性的泛素结合酶.另外,点突变C85S使得TaUBC丧失E2活性,C21S和C107S则对活性没有影响,证明其UBC结构域中第85位Cys是结合泛素的关键作用位点.     

人MRP4蛋白结构与功能预测

多药耐药相关蛋白4(multidrug resistance-associated protein 4,MRP4)是一种能够利用ATP水解产生的能量转运多种物质的六重跨膜蛋白。本研究应用Expasy、Jpred4、UniProtKB、NCBI等公共数据库和在线软件分析其理化性质、蛋白结构、结构域、亚细胞定位、互作蛋白以及功能等信息,为其在多种生理病理过程中的作用与机制研究奠定基础。MRP4蛋白含有1325个氨基酸,相对分子质量约为149526.77,理论等电点为8.41。以α-螺旋为主,占比58.42%。含有2个跨膜结构域和2个ATP结合盒以及8个保守结构域。表观遗传学修饰位点56个,其中磷酸化位点27个,泛素化位点27个,乙酰化位点2个。MRP4蛋白分布于质膜上,具有ATP酶和跨膜转运蛋白活性,参与内外源性物质运输、前列腺素分泌、纤毛组装、信号转导运输等生命过程。本研究系统性梳理并整合了MRP4蛋白结构及功能等信息,为深入研究其在机体生命活动及疾病发生中的作用与机制奠定理论依据。     

神经退行性疾病相关蛋白的翻译后修饰

特定靶蛋白的翻译后修饰对其执行细胞功能有重要作用,是细胞对生长、分化和应激等信号刺激所产生的调节功能的一种反应.翻译后修饰包括磷酸化修饰、乙酰化、甲基化、泛素化、类泛素化等不同的修饰.在神经退行性疾病的研究中,翻译后修饰对疾病的发生和病理影响日益受到人们的重视,我们对磷酸化、泛素化和类泛素化(SUMO化)修饰与神经退行疾病的关系及本实验室的工作进行介绍.     

油菜中—未知BnRCH蛋白的E3连接酶活性分析

利用本实验室前期以ATP6为诱饵蛋白,通过酵母双杂交系统筛选到的一个N端含有RINGv结构(RING-variant)的蛋白,暂命名为BnRCH,构建GTK-BnRCH表达载体在原核细胞E.coli BL21(DE3)中高效表达GST-BnRCH融合蛋白,并将纯化的融合蛋白加入体外泛素反应体系,发现BnRCH在ATP、泛素、E1、E2存在的条件下,能催化多聚泛素化形成,具有E3连接酶活性.     

油菜中一未知BnRCH蛋白的E3连接酶活性分析

利用本实验室前期以ATP6为诱饵蛋白,通过酵母双杂交系统筛选到的一个N端含有RINGv结构(RINGvariant)的蛋白,暂命名为BnRCH,构建GTKBnRCH表达载体在原核细胞E.coli BL21(DE3)中高效表达GSTBnRCH融合蛋白,并将纯化的融合蛋白加入体外泛素反应体系,发现BnRCH在ATP、泛素、E1、E2存在的条件下,能催化多聚泛素化形成,具有E3连接酶活性.     

Insights into the ubiquitin transfer cascade from the structure of the activating enzyme for NEDD8

Post-translational modification by ubiquitin-like proteins (Ublps) is an essential cellular regulatory mechanism. The Ublp NEDD8 regulates cell division, signalling and embryogenesis. Ublps are conjugated to their targets by the sequential action of E1, E2 and often E3 enzymes. Each Ublp has a dedicated E1, or activating enzyme, that initiates its conjugation cascade. First, E1 associates with the Ublp and catalyses adenylation of the carboxy terminus of the Ublp. Second, E1 forms a thioester between its catalytic cysteine and the Ublp. Next, E1 is loaded with a second Ublp molecule, adenylating the C terminus of this second Ublp while still carrying the first thioester-bound Ublp. Last, E1 binds E2 and promotes Ublp transfer to the catalytic cysteine of E2. We report here the structure and mutational analysis of human APPBP1-UBA3, the heterodimeric E1 enzyme for NEDD8 (ref. 11). Each E1 activity is specified by a domain: an adenylation domain resembling bacterial adenylating enzymes, an E1-specific domain organized around the catalytic cysteine, and a domain involved in E2 recognition resembling ubiquitin. The domains are arranged around two clefts that coordinate protein and nucleotide binding so that each of E1's reactions drives the next, in an assembly-line fashion.     

The conserved protein DCN-1/Dcn1p is required for cullin neddylation in C. elegans and S. cerevisiae

SCF-type E3 ubiquitin ligases are multi-protein complexes required for polyubiquitination and subsequent degradation of target proteins by the 26S proteasome. Cullins, together with the RING-finger protein Rbx1, form the catalytic core of the ligase, and recruit the substrate-recognition module. Cycles of covalent modification of cullins by the ubiquitin-like molecule Nedd8 (neddylation) and removal of Nedd8 by the COP9 signalosome (deneddylation) positively regulate E3 ligase activity. Here we report the identification and analysis of a widely conserved protein that is required for cullin neddylation in the nematode Caenorhabditis elegans and the yeast Saccharomyces cerevisiae. C. elegans DCN-1 and S. cerevisiae Dcn1p (defective in cullin neddylation) are characterized by a novel UBA-like ubiquitin-binding domain and a DUF298 domain of unknown function. Consistent with their requirements for neddylation, DCN-1 and Dcn1p directly bind Nedd8 and physically associate with cullins in both species. Moreover, overexpression of Dcn1p in yeast results in the accumulation of Nedd8-modified cullin Cdc53p. Both in vivo and in vitro experiments indicate that Dcn1p does not inhibit deneddylation of Cdc53p by the COP9 signalosome, but greatly increases the kinetics of the neddylation reaction.     

人NEDD8 原核表达及兔高免血清制备

摘要: 本研究根据基因比对,将合成的nedd8 基因( HN8) 酶切克隆入pCold-TF 原核表达载体中,命名为pCold-HN8,转化到感受态宿主菌BL21( DE3) 中,加入不同浓度异丙基硫代半乳糖苷( IPTG) 于16℃中诱导表达24 h,超声波裂解,通过His-bind 纯化试剂盒纯化,分别进行SDS-PAGE 检测,结果HN8 蛋白获得可溶性表达,融合蛋白大小为64 kDa。用纯化的蛋白免疫新西兰兔,制备多克隆抗体,经Western Blot 和间接免疫荧光试验证实,兔抗HN8 蛋白的血清能够特异性识别HN8 蛋白。这为进一步研究HN8 蛋白在Neddylation 通路中的修饰作用奠定了基础。     

Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity

Ubiquitin-like proteins (UBLs) are conjugated by dynamic E1-E2-E3 enzyme cascades. E1 enzymes activate UBLs by catalysing UBL carboxy-terminal adenylation, forming a covalent E1 throught UBL thioester intermediate, and generating a thioester-linked E2 throught UBL product, which must be released for subsequent reactions. Here we report the structural analysis of a trapped UBL activation complex for the human NEDD8 pathway, containing NEDD8's heterodimeric E1 (APPBP1-UBA3), two NEDD8s (one thioester-linked to E1, one noncovalently associated for adenylation), a catalytically inactive E2 (Ubc12), and MgATP. The results suggest that a thioester switch toggles E1-E2 affinities. Two E2 binding sites depend on NEDD8 being thioester-linked to E1. One is unmasked by a striking E1 conformational change. The other comes directly from the thioester-bound NEDD8. After NEDD8 transfer to E2, reversion to an alternate E1 conformation would facilitate release of the E2 throught NEDD8 thioester product. Thus, transferring the UBL's thioester linkage between successive conjugation enzymes can induce conformational changes and alter interaction networks to drive consecutive steps in UBL cascades.     

A ubiquitin-like system mediates protein lipidation

Autophagy is a dynamic membrane phenomenon for bulk protein degradation in the lysosome/vacuole. Apg8/Aut7 is an essential factor for autophagy in yeast. We previously found that the carboxy-terminal arginine of nascent Apg8 is removed by Apg4/Aut2 protease, leaving a glycine residue at the C terminus. Apg8 is then converted to a form (Apg8-X) that is tightly bound to the membrane. Here we report a new mode of protein lipidation. Apg8 is covalently conjugated to phosphatidylethanolamine through an amide bond between the C-terminal glycine and the amino group of phosphatidylethanolamine. This lipidation is mediated by a ubiquitination-like system. Apg8 is a ubiquitin-like protein that is activated by an E1 protein, Apg7 (refs 7, 8), and is transferred subsequently to the E2 enzymes Apg3/Aut1 (ref. 9). Apg7 activates two different ubiquitin-like proteins, Apg12 (ref. 10) and Apg8, and assigns them to specific E2 enzymes, Apg10 (ref. 11) and Apg3, respectively. These reactions are necessary for the formation of Apg8-phosphatidylethanolamine. This lipidation has an essential role in membrane dynamics during autophagy.     

Dual E1 activation systems for ubiquitin differentially regulate E2 enzyme charging

Modification of proteins with ubiquitin or ubiquitin-like proteins (UBLs) by means of an E1-E2-E3 cascade controls many signalling networks. Ubiquitin conjugation involves adenylation and thioesterification of the carboxy-terminal carboxylate of ubiquitin by the E1-activating enzyme Ube1 (Uba1 in yeast), followed by ubiquitin transfer to an E2-conjugating enzyme through a transthiolation reaction. Charged E2s function with E3s to ubiquitinate substrates. It is currently thought that Ube1/Uba1 is the sole E1 for charging of E2s with ubiquitin in animals and fungi. Here we identify a divergent E1 in vertebrates and sea urchin, Uba6, which specifically activates ubiquitin but not other UBLs in vitro and in vivo. Human Uba6 and Ube1 have distinct preferences for E2 charging in vitro, and their specificity depends in part on their C-terminal ubiquitin-fold domains, which recruit E2s. In tissue culture cells, Uba6 is required for charging a previously uncharacterized Uba6-specific E2 (Use1), whereas Ube1 is required for charging the cell-cycle E2s Cdc34A and Cdc34B. Our data reveal unexpected complexity in the pathways that control the conjugation of ubiquitin, in which dual E1s orchestrate the charging of distinct cohorts of E2s.     

Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing

Alternative splicing of pre-messenger RNAs diversifies gene products in eukaryotes and is guided by factors that enable spliceosomes to recognize particular splice sites. Here we report that alternative splicing of Saccharomyces cerevisiae SRC1 pre-mRNA is promoted by the conserved ubiquitin-like protein Hub1. Structural and biochemical data show that Hub1 binds non-covalently to a conserved element termed HIND, which is present in the spliceosomal protein Snu66 in yeast and mammals, and Prp38 in plants. Hub1 binding mildly alters spliceosomal protein interactions and barely affects general splicing in S. cerevisiae. However, spliceosomes that lack Hub1, or are defective in Hub1-HIND interaction, cannot use certain non-canonical 5' splice sites and are defective in alternative SRC1 splicing. Hub1 confers alternative splicing not only when bound to HIND, but also when experimentally fused to Snu66, Prp38, or even the core splicing factor Prp8. Our study indicates a novel mechanism for splice site utilization that is guided by non-covalent modification of the spliceosome by an unconventional ubiquitin-like modifier.     

A new protease required for cell-cycle progression in yeast

In eukaryotes, protein function can be modulated by ligation to ubiquitin or to ubiquitin-like proteins (Ubl proteins). The vertebrate Ubl protein SUMO-1 is only 18% identical to ubiquitin but is 48% identical to the yeast protein Smt3. Both SUMO-1 and Smt3 are ligated to cellular proteins, and protein conjugation to SUMO-1/Smt3 is involved in many physiological processes. It remained unknown, however, whether deconjugation of SUMO-1/Smt3 from proteins is also essential. Here we describe a yeast Ubl-specific protease, Ulp1, which cleaves proteins from Smt3 and SUMO-1 but not from ubiquitin. Ulp1 is unrelated to any known deubiquitinating enzyme but shows distant similarity to certain viral proteases, indicating the existence of a widely conserved protease fold. Proteins related to Ulp1 are present in many organisms, including several human pathogens. The pattern of Smt3-coupled proteins in yeast changes markedly throughout the cell cycle, and specific conjugates accumulate in ulp1 mutants. Ulp1 has several functions, including an essential role in the G2/M phase of the cell cycle.     

Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex

SUMO-1 (for small ubiquitin-related modifier) belongs to the ubiquitin (Ub) and ubiquitin-like (Ubl) protein family. SUMO conjugation occurs on specific lysine residues within protein targets, regulating pathways involved in differentiation, apoptosis, the cell cycle and responses to stress by altering protein function through changes in activity or cellular localization or by protecting substrates from ubiquitination. Ub/Ubl conjugation occurs in sequential steps and requires the concerted action of E2 conjugating proteins and E3 ligases. In addition to being a SUMO E3, the nucleoporin Nup358/RanBP2 localizes SUMO-conjugated RanGAP1 to the cytoplasmic face of the nuclear pore complex by means of interactions in a complex that also includes Ubc9, the SUMO E2 conjugating protein. Here we describe the 3.0-A crystal structure of a four-protein complex of Ubc9, a Nup358/RanBP2 E3 ligase domain (IR1-M) and SUMO-1 conjugated to the carboxy-terminal domain of RanGAP1. Structural insights, combined with biochemical and kinetic data obtained with additional substrates, support a model in which Nup358/RanBP2 acts as an E3 by binding both SUMO and Ubc9 to position the SUMO-E2-thioester in an optimal orientation to enhance conjugation.     

拟南芥 AtTR1 在盐胁迫应答中的功能初探

本研究主要探索油菜中E3泛素连接酶BnTR1在拟南芥中的同源基因AtTR1(At3g47550)的功能.通过体外泛素化实验证明AtTR1具有E3连接酶活性.基因表达分析显示该基因受200mmol/L NaCl显著诱导,说明该基因可能在响应盐胁迫中发挥一定的功能.为了更深入的探究该基因在植物耐盐中的作用,构建了植物表达载体pZH01-AtTR1转化突变体.在含有潮霉素的培养基上筛选阳性苗,并利用荧光定量PCR检测表明AtTR1基因已经成功转入突变体中.