Structural evidence for common ancestry of the nuclear pore complex and vesicle coats

Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.     

DNA ligase: structure, mechanism, and function

DNA ligase of E. coli is a polypeptide of molecular weight 75,000. The comparable T4-induced enzyme is somewhat smaller (63,000 to 68,000). Both enzymes catalyze the synthesis of phosphodiester bonds between adjacent 5'-phosphoryl and 3'-hydroxyl groups in nicked duplex DNA, coupled to the cleavage of the pyrophosphate bond of DPN (E. coli) or ATP (T4). Phosphodiester bond synthesis catalyzed by both enzymes occurs in a series of these discrete steps and involves the participation of two covalent intermediates (Fig. 1). A steady state kinetic analysis of the reaction-catalyzed E. coli ligase supports this mechanism, and further demonstrates that enzyme-adenylate and DNA-adenylate are kinetically significant intermediates on the direct path of phosphodiester bond synthesis. A strain of E. coli with a mutation in the structural gene for DNA ligase which results in the synthesis of an abnormally thermolabile enzyme is inviable at 42 degrees C. Although able to grow at 30 degrees C, the mutant is still defective at this temperature in its ability to repair damage to its DNA caused by ultraviolet irradiation and by alkylating agents. At 42 degrees C, all the newly replicated DNA is in the form of short 10S "Okazaki fragments," an indication that the reason for the mutant's failure to survive under these conditions is its inability to sustain the ligation step that is essential for the discontinuous synthesis of the E. coli chromosome. DNA ligase is therefore an essential enzyme required for normal DNA replication and repair in E. coli. Purified DNA ligases have proved to be useful reagents in the construction in vitro of recombinant DNA molecules.     

Nuclear pores form de novo from both sides of the nuclear envelope

Nuclear pore complexes are multiprotein channels that span the double lipid bilayer of the nuclear envelope. How new pores are inserted into the intact nuclear envelope of proliferating and differentiating eukaryotic cells is unknown. We found that the Nup107-160 complex was incorporated into assembly sites in the nuclear envelope from both the nucleoplasmic and the cytoplasmic sides. Nuclear pore insertion required the generation of Ran guanosine triphosphate in the nuclear and cytoplasmic compartments. Newly formed nuclear pore complexes did not contain structural components of preexisting pores, suggesting that they can form de novo.     

Role of ANC-1 in tethering nuclei to the actin cytoskeleton

Mutations in anc-1 (nuclear anchorage defective) disrupt the positioning of nuclei and mitochondria in Caenorhabditis elegans. ANC-1 is shown to consist of mostly coiled regions with a nuclear envelope localization domain (called the KASH domain) and an actin-binding domain; this structure was conserved with the Drosophila protein Msp-300 and the mammalian Syne proteins. Antibodies against ANC-1 localized cytoplasmically and were enriched at the nuclear periphery in an UNC-84-dependent manner. Overexpression of the KASH domain or the actin-binding domain caused a dominant negative anchorage defect. Thus, ANC-1 may connect nuclei to the cytoskeleton by interacting with UNC-84 at the nuclear envelope and with actin in the cytoplasm.     

Xeroderma pigmentosum group E cells lack a nuclear factor that binds to damaged DNA

The disease xeroderma pigmentosum is characterized by deficient repair of damaged DNA. Fusions of cells from different patients have defined nine genetic complementation groups (A through I), implying that DNA repair in humans involves multiple gene products. In this report, an extension of the gel electrophoresis binding assay was used to identify at least one nuclear factor that (i) bound to DNA damaged by ultraviolet radiation or the antitumor drug cisplatin, but (ii) was notably absent in cells from complementation group E. Therefore, the factor appears to participate in a versatile DNA repair pathway at the stage of binding and recognition.     

5'-Deoxyribose phosphate lyase activity of human DNA polymerase iota in vitro

DNA polymerase iota (pol iota) is one of several recently discovered DNA polymerases in mammalian cells whose function is unknown. We report here that human pol iota has an intrinsic 5'-deoxyribose phosphate (dRP) lyase activity. In reactions reconstituted with uracil-DNA glycosylase (UDG), apurinic/apyrimidinic (AP) endonuclease and DNA ligase I, pol iota can use its dRP lyase and polymerase activities to repair G*U and A*U pairs in DNA. These data and three distinct catalytic properties of pol iota implicate it in specialized forms of base excision repair (BER).     

RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites

Mutations affecting the BRCT domains of the breast cancer-associated tumor suppressor BRCA1 disrupt the recruitment of this protein to DNA double-strand breaks (DSBs). The molecular structures at DSBs recognized by BRCA1 are presently unknown. We report the interaction of the BRCA1 BRCT domain with RAP80, a ubiquitin-binding protein. RAP80 targets a complex containing the BRCA1-BARD1 (BRCA1-associated ring domain protein 1) E3 ligase and the deubiquitinating enzyme (DUB) BRCC36 to MDC1-gammaH2AX-dependent lysine(6)- and lysine(63)-linked ubiquitin polymers at DSBs. These events are required for cell cycle checkpoint and repair responses to ionizing radiation, implicating ubiquitin chain recognition and turnover in the BRCA1-mediated repair of DSBs.     

植物DNA双链断裂损伤修复机制研究进展

DNA双链断裂(DSBs)是细胞最严重的损伤形式之一。高等动植物中主要通过非同源末端连接（NHEJ）途径进行DNA双链断裂修复。该途径不依赖DNA同源性,由一些修复因子如：Ku蛋白异二聚体、DNA-PKcs 、XRCC4、ligaseⅣ等,将断裂末端直接连接进行修复。综述了植物DNA双链断裂损伤修复的主要途径及其相关基因研究的进展,探讨了植物DNA损伤修复研究中存在的问题与发展方向。     

GRP1.8融合反义4CL1基因调控烟草木质素生物合成

该研究成功地将从刺槐 (Robiniapseudoacacia)中克隆得到的定位于形成层表达的GRP1 8启动子 ,分别与GUS报告基因及从毛白杨 (Populustomentosa)中克隆的香豆酸连接酶 (4CL1)基因连接构建成GRP1 8 GUS和GRP1 8 anti 4CL1融合基因 ,转基因于烟草植物 .经组织化学检测分析 ,GUS基因成功地由GRP1 8启动子驱动定位于形成层表达 ;融合基因GRP1 8 anti 4CL1的表达明显地改变了转基因烟草植株的木质素和纤维素的含量和比例 .转基因烟草的木质素含量较对照平均降低了 13 7% ,而转基因植株的纤维素含量较对照升高了 15 6 % .     

Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine

In mammalian cells, repair of DNA double-strand breaks (DSBs) by nonhomologous end-joining (NHEJ) is critical for genome stability. Although the end-bridging and ligation steps of NHEJ have been reconstituted in vitro, little is known about the end-processing reactions that occur before ligation. Recently, functionally homologous end-bridging and ligation activities have been identified in prokarya. Consistent with its homology to polymerases and nucleases, we demonstrate that DNA ligase D from Mycobacterium tuberculosis (Mt-Lig) possesses a unique variety of nucleotidyl transferase activities, including gap-filling polymerase, terminal transferase, and primase, and is also a 3' to 5' exonuclease. These enzyme activities allow the Mt-Ku and Mt-Lig proteins to join incompatible DSB ends in vitro, as well as to reconstitute NHEJ in vivo in yeast. These results demonstrate that prokaryotic Ku and ligase form a bona fide NHEJ system that encodes all the recognition, processing, and ligation activities required for DSB repair.     

Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding

The nucleoporins Nup58 and Nup45 are part of the central transport channel of the nuclear pore complex, which is thought to have a flexible diameter. In the crystal structure of an alpha-helical region of mammalian Nup58/45, we identified distinct tetramers, each consisting of two antiparallel hairpin dimers. The intradimeric interface is hydrophobic, whereas dimer-dimer association occurs through large hydrophilic residues. These residues are laterally displaced in various tetramer conformations, which suggests an intermolecular sliding by 11 angstroms. We propose that circumferential sliding plays a role in adjusting the diameter of the central transport channel.     

Activation of the cellular DNA damage response in the absence of DNA lesions

The cellular DNA damage response (DDR) is initiated by the rapid recruitment of repair factors to the site of DNA damage to form a multiprotein repair complex. How the repair complex senses damaged DNA and then activates the DDR is not well understood. We show that prolonged binding of DNA repair factors to chromatin can elicit the DDR in an ATM (ataxia telangiectasia mutated)- and DNAPK (DNA-dependent protein kinase)-dependent manner in the absence of DNA damage. Targeting of single repair factors to chromatin revealed a hierarchy of protein interactions within the repair complex and suggests amplification of the damage signal. We conclude that activation of the DDR does not require DNA damage and stable association of repair factors with chromatin is likely a critical step in triggering, amplifying, and maintaining the DDR signal.     

DNA拓扑异构酶基因PagTOP2b对银腺杨‘84K’生长发育的影响

  目的  DNA拓扑异构酶基因是一类能够改变DNA拓扑结构的酶，在基础生命活动如DNA复制、转录、有丝分裂等过程中发挥重要作用。研究DNA拓扑异构酶基因对杨树Populus生长发育的影响，能够进一步了解DNA拓扑异构酶基因在木本植物中的作用机制，评估其是否可作为林木分子育种的靶标。  方法  从银腺杨‘84K’ Populus alba × P. glandulosa ‘84K’ (84K杨)中克隆得到DNA拓扑异构酶基因PagTOP2b，利用生物信息学方法对其进行序列分析、蛋白理化性质及结构分析。实时荧光定量PCR分析PagTOP2b在杨树不同组织中的表达水平。利用农杆菌Agrobacterium tumefaciens介导的叶盘转化法转化84K杨，得到PagTOP2b过表达转基因植株。通过表型及茎段切片分析过表达PagTOP2b基因对84K杨植株生长的影响。  结果  以84K杨cDNA为模板，克隆得到PagTOP2b基因全长序列，该基因蛋白质编码区(CDS)长度为4 449 bp，编码1 482个氨基酸，根据蛋白结构域分析属于ⅡA型DNA拓扑异构酶。PagTOP2b主要在杨树幼嫩组织中有较高的表达量。过量表达PagTOP2b基因会导致转基因植株高度、基部节间直径和木质部宽度显著增加。  结论  DNA拓扑异构酶作为一类参与基础生命活动的重要功能酶，在杨树中过量表达ⅡA型DNA拓扑异构酶基因PagTOP2b可促进植株的纵向及径向生长，增加植株生物量。图4表1参28     

RanGTPase激活蛋白RanGAP1的研究现状

RanGTPase的活性蛋白RanGAP1位于细胞质中,是RanGTP/GDP循环的一个关键调节器,对细胞的核质运输和有丝分裂都有重要作用。RanGAP1是第一个为人们所证实的可被SUMO-1的蛋白质,SUMO化的RanGAP1位于核孔,与核孔蛋白RanBP2/Nup358及其相关因子相结合,对细胞周期起到调控作用。     

番茄DDB2蛋白的生物信息学分析、亚细胞定位及在E3复合体中的相互作用关系

紫外(UV)辐射诱导的DNA损伤可导致农作物减产。DDB2蛋白参与由紫外辐射造成的DNA损伤的修复过程已经在人类、水稻和拟南芥中得到证实。DDB2与DDB1、CUL4相互作用形成E3泛素连接酶复合体,该复合体对植物根茎生长、花期调控和光形态建成等多种植物发育过程起调控作用。成功克隆了番茄DDB2基因,构建了DDB2-黄色荧光蛋白融合表达载体。通过对野生型番茄UV辐射后DDB2基因表达水平的半定量分析,证明番茄DDB2基因受UV诱导表达;运用生物信息学分析对DDB2蛋白序列与模式生物进行同源比对,发现2个WD-40重复和一个DWD盒保守结构域;通过对DDB2融合黄色荧光蛋白转基因番茄根尖的荧光显微观察,证实番茄DDB2定位于细胞核。利用酵母双杂交实验证明了番茄DDB2与DDB1和CUL4之间的相互作用关系,推测DDB1蛋白作为DDB2与CUL4蛋白的桥梁形成CUL4-DDB1-DDB2复合体。     

禾谷镰孢核孔蛋白基因FgNup42的功能分析

【目的】核孔蛋白Nup42在真核生物基因表达调控以及mRNA加工运输等生物学过程中发挥着重要作用,本研究旨在分析禾谷镰孢（Fusarium graminearum）中核孔蛋白基因FgNup42在病原菌生长发育、逆境胁迫、致病和产毒等生物学过程中的功能。【方法】通过融合PCR（double-joint PCR）和酵母空隙修复（gap repair）技术分别构建FgNup42基因敲除和回补载体,再利用PEG介导的原生质体转化的方法获得基因敲除突变体ΔFgNup42和回补体ΔFgNup42-C。观察测定基因敲除突变体ΔFgNup42在营养生长、无性繁殖和有性生殖过程中的变化,同时测定突变体ΔFgNup42对渗透、杀菌剂以及细胞壁胁迫因子的敏感性。将突变体ΔFgNup42进行田间麦穗和室内玉米花丝接种试验明确其致病力情况。通过液相色谱-串联质谱（LC-MS/MS）检测ΔFgNup42的产毒能力,同时利用qRT-PCR比较分析参与单端孢霉烯族毒素生物合成的7个TRI在野生型PH-1和基因敲除突变体ΔFgNup42中的相对表达量。【结果】表型测定发现,基因敲除突变体ΔFgNup42的生长速率只有野生型PH-1的50%,菌落边缘菌丝分枝变多且致密。显微观察分生孢子形成情况,发现敲除突变体ΔFgNup42相较野生型PH-1分生孢子产量降低了85.45%,并且隔膜数在0—2的分生孢子比例明显增多。有性生殖诱导结果显示ΔFgNup42的有性生殖能力增强,较野生型产生了更多的子囊壳。突变体ΔFgNup42对渗透胁迫因子NaCl和KCl,细胞壁胁迫因子刚果红,以及杀菌剂戊唑醇和氰烯菌酯的敏感性减弱。致病力分析发现敲除基因FgNup42后菌体在麦穗和玉米花丝上的致病力严重降低。此外,与野生型相比,ΔFgNup42中毒素DON、3ADON和15ADON的合成量明显减少。【结论】核孔蛋白基因FgNup42在禾谷镰孢生长发育、抵御逆境以及致病和产毒过程中发挥着重要作用。     

Identification of a DNA nonhomologous end-joining complex in bacteria

In eukaryotic cells, double-strand breaks (DSBs) in DNA are generally repaired by the pathway of homologous recombination or by DNA nonhomologous end joining (NHEJ). Both pathways have been highly conserved throughout eukaryotic evolution, but no equivalent NHEJ system has been identified in prokaryotes. The NHEJ pathway requires a DNA end-binding component called Ku. We have identified bacterial Ku homologs and show that these proteins retain the biochemical characteristics of the eukaryotic Ku heterodimer. Furthermore, we show that bacterial Ku specifically recruits DNA ligase to DNA ends and stimulates DNA ligation. Loss of these proteins leads to hypersensitivity to ionizing radiation in Bacillus subtilis. These data provide evidence that many bacteria possess a DNA DSB repair apparatus that shares many features with the NHEJ system of eukarya and suggest that this DNA repair pathway arose before the prokaryotic and eukaryotic lineages diverged.     

用CRISPR-Cas9在绵羊成纤维细胞ACTG1导入荧光标记基因

【目的】在绵羊成纤维细胞中,针对ACTG1基因羧基端,定点导入荧光蛋白标记基因,将外源基因定点导入绵羊基因组中,建立有效的方法。【方法】CRISPR-Cas9系统在绵羊成纤维细胞基因组特定区域引起DNA双链断裂,从而诱导细胞修复断裂的的基因组。通过NHEJ修复途径,在特定位点导入外源基因,改善定点导入效率。【结果】采用CRISPaint通用供体模板,结合CRISPR-Cas9系统,在绵羊成纤维细胞ACTG1基因导入荧光标记效率达1.4%,获得了外源基因定点导入的单克隆细胞株。【结论】CRISPR-Cas9系统结合NHEJ,能够有效的将大的外源DNA序列导入绵羊成纤维细胞的预定基因组位点。     

Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase

Cells respond to DNA double-strand breaks by recruiting factors such as the DNA-damage mediator protein MDC1, the p53-binding protein 1 (53BP1), and the breast cancer susceptibility protein BRCA1 to sites of damaged DNA. Here, we reveal that the ubiquitin ligase RNF8 mediates ubiquitin conjugation and 53BP1 and BRCA1 focal accumulation at sites of DNA lesions. Moreover, we establish that MDC1 recruits RNF8 through phosphodependent interactions between the RNF8 forkhead-associated domain and motifs in MDC1 that are phosphorylated by the DNA-damage activated protein kinase ataxia telangiectasia mutated (ATM). We also show that depletion of the E2 enzyme UBC13 impairs 53BP1 recruitment to sites of damage, which suggests that it cooperates with RNF8. Finally, we reveal that RNF8 promotes the G2/M DNA damage checkpoint and resistance to ionizing radiation. These results demonstrate how the DNA-damage response is orchestrated by ATM-dependent phosphorylation of MDC1 and RNF8-mediated ubiquitination.