SSB蛋白与ssDNA相互作用的动力学和可视化研究

研究大肠杆菌单链结合蛋白(single-stranded DNA-binding protein,SSB)与单链DNA(single-stranded DNA,ssDNA)的相互作用对于了解其在DNA复制、重组和修复中的作用是非常重要的。通过表面等离子共振技术(surface plasmon resonance,SPR)得到了在有、无镁离子的情况下,SSB与ssDNA两者的平衡解离常数(equilibrium dissociation constant,KD)分别为9.67×10-7M和4.79×10-7M,阐明了镁离子对于两者作用形式的影响。利用原子力显微镜技术分别观察SSB蛋白、ssDNA和SSB-ssDNA复合物的成像,为下一步研究SSB在DNA代谢中作用模式的单分子可视化奠定了基础。     

鼠疫菌H-NS蛋白的表达与纯化及其DNA结合活性

摘要：【目的】利用大肠杆菌BL21λDE3的表达系统,表达出有活性的鼠疫耶尔森氏菌（以下简称鼠疫菌）调控子蛋白H-NS,为进一步研究H-NS的转录调控奠定基础。【方法】 PCR扩增鼠疫菌201株hns基因的编码区,将其直接克隆入pET28a质粒中,再将pET28a-hns重组质粒转入大肠杆菌BL21λDE3菌株中,所得菌株经IPTG诱导后能表达出鼠疫菌His-H-NS蛋白;通过体外的凝胶迁移实验（EMSA）和DNaseⅠ足迹实验对His-H-NS蛋白与DNA的结合活性进行分析。【结果】成功表达出有活性的鼠疫菌His-H-NS蛋白,该蛋白对鼠疫菌pH6抗原基因（psaA、psaE）及rovA基因均有结合活性。【结论】鼠疫菌His-H-NS具有DNA结合活性,说明H-NS能调控鼠疫菌基因的转录。     

苜蓿盲蝽气味分子结合蛋白AlinOBP2结合特性初步分析

昆虫具有灵敏的嗅觉系统,能够特异性地识别性信息素和寄主挥发物来进行寻找配偶、定位寄主植物和产卵位点.气味分子结合蛋白在昆虫嗅觉识别过程中发挥关键作用.本研究表达和纯化了一个新的苜蓿盲蝽气味分子结合蛋白AlinOBP2,采用qRT-PCR方法解析了AlinOBP2基因的表达谱,结果表明AlinOBP2绝大部分在触角中表达,且在雌雄触角中的表达量相当,在头部也有少量的表达.以N-phenyl-1-naphthylamine（1-NPN）为荧光探针,采用荧光竞争结合实验研究了5种性信息素类似物和13种棉花挥发物与AlinOBP2蛋白的结合能力.结果显示,5种性信息素类似物均不能和AlinOBP2有效结合,暗示AlinOBP2在苜蓿盲蝽寻找配偶过程中不发挥作用.在13种棉花挥发物中,庚酸乙酯和AlinOBP2的结合能力最强,结合常数为9.22μmol/L.二甲基萘、3-己酮、乙酸叶醇酯、乙酸壬酯、香芹醇5种化合物和AlinOBP2结合能力一般,结合常数分别为15.49,17.31,21.53,18.86和13.47μmol/L.据此推测,AlinOBP2可能为普通气味结合蛋白,能够选择性地结合某些棉花挥发物并参与苜蓿盲蝽识别普通气味过程.     

一个未知的特异结合雌激素效应元件编码链的单链结合蛋白

本文介绍一个不是雌激素受体（ＥＲ）却能专一地结合雌激素效应元件（ＥＲＥ）编码单链的单链结合蛋白,对此蛋白在细胞中的定位、组织中的分布、热稳定性、同二价金属离子的关系作一初步研究。发现其受雌激素负调控。此蛋白在人病理样品２９例乳癌中同ＥＲ的含量似有一定的负相关关系,讨论了上述结果的意义。     

利用序列比较寻找胰岛素基因表达启动区与DNA结合蛋白的结合位点

NDFl、IPFl和HNF4是与胰岛素基因表达有关的DNA结合蛋白,通过比较SWISSPROT蛋白质数据库中人类、小鼠、大鼠这三种核蛋白氨基酸一级序列、模体和结构域,发现其结构十分相似,根据蛋白质结构和功能的关系,推测这些DNA结合蛋白与胰岛素基因结合的核苷酸序列相似;从GenBanl(核酸数据库中获得人类、小鼠、大鼠胰岛素DNA序列,用ClustalW比较三者Promoter区的核苷酸序列,显示有一段核苷酸序列较为相似,同时搜索TRANSFAC基因转录数据库中NDFl、IPFl和NHF4蛋白核苷酸结合位点,发现核酸比对保守的部分序列与TRANSFAC数据库中这三个转录因子的DNA结合位点一致,另外一些核酸保守序列可能为其他未知DNA结合蛋白的结合位点。这种核酸序列比对设计为分子生物学实验寻找和验证胰岛素DNA结合蛋白与核苷酸的结合位点提供了简单而实用的方法。     

噬菌体434单链阻遏蛋白高亲和力DNA配体的筛选和设计

单链阻遏蛋白R R_TRES是噬菌体434阻遏蛋白的衍生物,含有两个DBD(DNA结合结构域),一个是野生型噬菌体434的DBD-R,另一个是突变型DBD-R_TRES,二者用重组接头以头接尾的方式连接起来.R_TRES的α-3-螺旋中-1,1,2,5位DNA结合氨基酸分别为T,R,E,S. 利用核心序列是CATACAAGAAAGNNNNNNTTTATG的随机DNA库, 体外循环筛选R_TRES的DNA结合位点,将筛选到的群体克隆、测序.单链阻遏蛋白RR_TRES的亲和力测定表明,最适操纵区序列含有TTAC或TTCC(上述画线部分)时,K_d值在10^-12~10^-11mol/L的范围.天然噬菌体434阻遏蛋白与其操纵区的亲和力的K_d值在10^-9 mol/L数量级,与之相比,所筛选操纵区的亲和力明显提高.同时发现,亲和力大小还受到最适结合位点两侧碱基的影响,特别是5′位碱基的影响.根据R_TRES的识别特性,设计了共有序列为GTAAGAAARNTTACN或GGAAGAAARNTTCCN (R为A或G)的单链阻遏蛋白R_TRES R_TRE的操纵区序列.结果表明,它们之间有特异性结合,且亲和力也很高.此方法可望用于其他DNA结合蛋白新的结合特异性的筛选.     

人巨细胞病毒IE基因调节子特异DNA结合蛋白cDNA的克隆和鉴定

本文利用人巨细胞病毒(HCMV)IE基因调节子中特异DNA片段作为探针,自人Hela细胞cDNA表达库中筛选并分离出两个编码能与该探针结合的DNA结合蛋白cDNA克隆(DJ-1和EH-2)。其中EH-2编码的蛋白具有明显的DNA结合序列特异性。比较DJ-1和EH-2克隆在HCMV戚染不容性和可容性畸胎瘤细胞中mRNA表达水平,未见明显差异。DJ-1和EH-2克隆可能涉及IE基因表达调控过程。     

桃蛀螟性信息素结合蛋白CpunPBP3的表达模式及性信息素结合特性

[目的]本研究旨在对桃蛀螟Conogethes punctiferalis性信息素结合蛋白CpunPBP3进行鉴定和定性分析,完善对桃蛀螟性信息素感受机制的理解.[方法]扩增、分析桃蛀螟CpunPBP3的cDNA序列,并与其他草螟科昆虫的同源蛋白氨基酸序列进行比较.利用qRT-PCR测定桃蛀螟不同日龄雄成虫触角中Cpu...     

鉴定免疫细胞中DNA疫苗结合蛋白

为研究DNA疫苗从细胞质到细胞核的过程,对免疫细胞中DNA疫苗的结合蛋白进行初步鉴定。 提取小鼠脾脏免疫细胞的细胞质蛋白,将细胞质蛋白分别与 DNA 疫苗 pVAX-OVA 和空载体 pVAX 共孵育,孵育后首先由琼脂糖凝胶电泳分离与DNA结合的蛋白,然后通过SDS-PAGE进行分离和纯化,最后应用质谱技术分析其蛋白组分。质谱结果初步鉴定了免疫细胞中pVAX-OVA 结合的蛋白有IQ motif containing F4 等。免疫细胞中与 pVAX 结合的蛋白有Foxl2,SUV420H2 和 gamma actin 等。Foxl2具有核定位序列,DNA结合区域和与核转运蛋白相互作用的特点,可能对DNA疫苗的进入具有促进作用。这些蛋白质是否可以影响DNA疫苗有效进入细胞核进行基因表达需要进一步研究。     

Characterization of a mitochondrially targeted single-stranded DNA-binding protein in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

A gene encoding a predicted mitochondrially targeted single-stranded DNA binding protein (mtSSB) was identified in the Arabidopsis thaliana genome sequence. This gene (At4g11060) codes for a protein of 201 amino acids, including a 28-residue putative mitochondrial targeting transit peptide. Protein sequence alignment shows high similarity between the mtSSB protein and single-stranded DNA binding proteins (SSB) from bacteria, including residues conserved for SSB function. Phylogenetic analysis indicates a close relationship between this protein and other mitochondrially targeted SSB proteins. The predicted targeting sequence was fused with the GFP coding region, and the organellar localization of the expressed fusion protein was determined. Specific targeting to mitochondria was observed in in-vitro import experiments and by transient expression of a GFP fusion construct in Arabidopsis leaves after microprojectile bombardment. The mature mtSSB coding region was overexpressed in Escherichia coli and the protein was purified for biochemical characterization. The purified protein binds single-stranded, but not double-stranded, DNA. MtSSB stimulates the homologous strand-exchange activity of E. coli RecA. These results indicate that mtSSB is a functional homologue of the E. coli SSB, and that it may play a role in mitochondrial DNA recombination.     

A Single Residue Determines the Cooperative Binding Property of a Primosomal DNA Replication Protein,PriB, to Single-Stranded DNA

PriB is a primosomal protein required for re-initiation of replication in bacteria. We characterized and compared the DNA-binding properties of PriB from Salmonella enterica serovar Typhimurium LT2 (StPriB) and Escherichia coli (EcPriB). Only one residue of EcPriB, V6, was different in StPriB (replaced by A6). Previous structural information revealed that this residue is located on the putative dimer-dimer interface of PriB and is not involved in single-stranded DNA (ssDNA) binding. The cooperative binding mechanism of StPriB to DNA is, however, very different from that of EcPriB. Unlike EcPriB, which forms a single complex with ssDNAs of various lengths, StPriB forms two or more distinct complexes. Based on these results, as well as information on structure, binding modes for forming a stable complex of PriB with ssDNA of 25 nucleotides (nt), (EcPriB)₂₅, and (StPriB)₂₅ are proposed.     

Inhibition of RecBCD enzyme by antineoplastic DNA alkylating agents

To understand how bulky adducts might perturb DNA helicase function, three distinct DNA-binding agents were used to determine the effects of DNA alkylation on a DNA helicase. Adozelesin, ecteinascidin 743 (Et743) and hedamycin each possess unique structures and sequence selectivity. They bind to double-stranded DNA and alkylate one strand of the duplex in cis, adding adducts that alter the structure of DNA significantly. The results show that Et743 was the most potent inhibitor of DNA unwinding, followed by adozelesin and hedamycin. Et743 significantly inhibited unwinding, enhanced degradation of DNA, and completely eliminated the ability of the translocating RecBCD enzyme to recognize and respond to the recombination hotspot chi. Unwinding of adozelesin-modified DNA was accompanied by the appearance of unwinding intermediates, consistent with enzyme entrapment or stalling. Further, adozelesin also induced "apparent" chi fragment formation. The combination of enzyme sequestering and pseudo-chi modification of RecBCD, results in biphasic time-courses of DNA unwinding. Hedamycin also reduced RecBCD activity, albeit at increased concentrations of drug relative to either adozelesin or Et743. Remarkably, the hedamycin modification resulted in constitutive activation of the bottom-strand nuclease activity of the enzyme, while leaving the ability of the translocating enzyme to recognize and respond to chi largely intact. Finally, the results show that DNA alkylation does not significantly perturb the allosteric interaction that activates the enzyme for ATP hydrolysis, as the efficiency of ATP utilization for DNA unwinding is affected only marginally. These results taken together present a unique response of RecBCD enzyme to bulky DNA adducts. We correlate these effects with the recently determined crystal structure of the RecBCD holoenzyme bound to DNA.     

Expression and purification of the SsbB protein from Streptococcus pneumoniae

The Gram positive bacterium, Streptococcus pneumoniae, has two genes, designated ssbA and ssbB, which are predicted to encode single-stranded DNA binding proteins (SSB proteins). We have shown previously that the SsbA protein is similar in size and in biochemical properties to the well-characterized SSB protein from Escherichia coli. The SsbB protein, in contrast, is a smaller protein and has no counterpart in E. coli. This report describes the development of an expression system and purification procedure for the SsbB protein. The ssbB gene was amplified from genomic S. pneumoniae DNA and cloned into the E. coli expression vector, pET21a. Although, we had shown previously that the SsbA protein is strongly expressed from pET21a in the E. coli strain BL21(DE3)pLysS, no expression of the SsbB protein was detected in these cells. However, the SsbB protein was strongly expressed from pET21a in the Rosetta(DE3)pLysS strain, a derivative of BL21(DE3)pLysS which supplies the tRNAs for six codons that are used infrequently in E. coli. The differential expression of the two SSB proteins in the parent BL21(DE3)pLysS strain was apparently due to the presence of two rare codons in the ssbB gene sequence that are not present in the ssbA sequence. Using the Rosetta(DE3)pLysS/pETssbB expression system, a protocol was developed in which the SsbB protein was purified to apparent homogeneity. DNA binding assays confirmed that the purified SsbB protein had single-stranded DNA binding activity. The expression and purification procedures reported here will facilitate further investigations into the biological role of the SsbB protein.     

Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site

PriB is not only an essential protein necessary for the replication restart on the collapsed and disintegrated replication fork, but also an important protein for assembling of primosome onto PhiX174 genomic DNA during replication initiation. Here we report a 2.0-A-resolution X-ray structure of a biologically functional form of PriB from Escherichia coli. The crystal structure revealed that despite a low level of primary sequence identity, the PriB monomer, as well as the dimeric form, are structurally identical to the N-terminal DNA-binding domain of the single-stranded DNA-binding protein (SSB) from Escherichia coli, which possesses an oligonucleotides-binding-fold. The oligonucleotide-PriB complex model based on the oligonucleotides-SSB complex structure suggested that PriB had a DNA-binding pocket conserved in SSB from Escherichia coli and might bind to single-stranded DNA in the manner of SSB. Furthermore, surface plasmon resonance analysis and fluorescence measurements demonstrated that PriB binds single-stranded DNA with high affinity, by involving tryptophan residue. The significance of these results with respect to the functional role of PriB in the assembly of primosome is discussed.     

桔小实蝇气味结合蛋白BdorOBP2的cDNA克隆、组织表达及配基结合特性

为了研究桔小实蝇Bactrocera dorsalis气味结合蛋白(odorant-binding proteins, OBPs)参与其嗅觉识别过程中的功能及其与植物气味的结合特性, 本研究克隆了桔小实蝇的一个气味结合蛋白基因, 命名为BdorOBP2（GenBank登录号为KC773766）, 并对该基因进行了原核表达。BdorOBP2开放阅读框长447 bp, 编码148 个氨基酸, 具有典型的6个半胱氨酸位点。定量PCR结果显示, 桔小实蝇BdorOBP2在不同组织中均有表达, 其中头部中的表达量最高, 翅中表达量最低（为头部表达量的63%±6%）。构建了BdorOBP2原核表达载体, 诱导并获得了重组BdorOBP2并进行了亲和层析纯化。最后以N-苯基-1-萘胺（N-phenyl-1-naphthylamine, 1-NPN）为荧光探针, 利用荧光竞争结合实验测定了重组BdorOBP2与7种主要寄主水果气味物质的结合能力, 发现其对多数酯类和醛类化合物亲合力较强, 亲合力最强的气味物质为反-2-己烯醛和β-紫罗兰酮, 结合常数KD分别为9.96和15.37 μmol/L。本研究结果可为高效地开发和设计桔小实蝇的嗅觉引诱剂配方提供一定的理论依据和参考。     

桃蛀螟性信息素结合蛋白Cpun-PBP1的cDNA克隆、表达谱及其与配体化合物的结合特性分析

【目的】为了更好地了解性信息素结合蛋白（pheromone binding proteins, PBPs）在桃蛀螟Conogethes punctiferalis （Guenée）嗅觉识别过程中的作用,明确其与配体化合物的结合特性。【方法】本研究利用RT-PCR结合RACE方法克隆了桃蛀螟一个性信息素结合蛋白基因;采用Real-time PCR方法分析了该蛋白在桃蛀螟不同发育阶段及雌雄蛾间的表达差异;利用荧光竞争结合实验对Cpun-PBP1蛋白与16种配基化合物的结合特性进行了分析。【结果】克隆了一个桃蛀螟性信息素结合蛋白基因,命名为Cpun-PBP 1（GenBank登录号：KP027486）。Cpun-PBP 1开放阅读框全长510 bp,编码 169个氨基酸,预测分子量为19.12 kDa,等电点为5.09,N-末端包括由起始位置开始的30个氨基酸组成的信号肽。蛋白特征分析显示,该氨基酸序列具有昆虫气味结合蛋白的典型特征,即含有6个保守的半胱氨酸残基。Cpun-PBP 1在桃蛀螟成虫阶段表达量最高,且几乎全部在触角中表达,卵期微量表达,幼虫期和蛹期均不表达。通过构建Cpun-PBP 1原核表达载体,诱导并获得Cpun-PBP 1重组蛋白。荧光竞争结合实验对2种性信息素组分和14种寄主植物挥发物的结合力发现,Cpun-PBP1不但能有效地与桃蛀螟性信息素组分（顺-10-十六碳烯醛和十六醛）结合,结合常数分别为7.32和9.39 μmol/L;还能与8种寄主植物挥发物有效结合;其中,与莰烯的结合能力最强,结合常数为3.76 μmol/L。【结论】根据这些结果,我们推测Cpun-PBP1在桃蛀螟感受性信息素和寄主植物挥发物的过程中发挥着双重作用。     

GGNBP1抗体制备及小鼠组织表达谱分析

体外实验研究表明配子生成素结合蛋白1(GGNBP1)可能与GGN1相互作用形成睾丸特异性复合物,在精子生成过程中发挥作用.从小鼠睾丸总RNA中反转录扩增Ggnbpl全长cDNA,构建表达质粒,在大肠杆菌中表达GGNBP1,经聚丙烯酰胺凝胶纯化后免疫新西兰白兔,制备兔多抗血清.镍离子金属螯合柱纯化表达的GGNBP1蛋白,与NHS活化基团交联,制备GGNBP1抗体亲和层析柱,纯化GGNBP1多抗.在293FT细胞中瞬时表达Myc-GGNBP1融合蛋白,用于Mvc单抗验证GGNBP1抗体特异性,结果证明获得了特异性的GGNBP1抗体.分别制备小鼠脑、心、肺、肝、脾、肾、肌肉、卵巢、睾丸和子宫组织匀浆,用GGNBP1抗体进行Western印迹分析,结果仅在睾丸组织匀浆中检测到GGNBP1特异性条带,证明GGNBP1是睾丸特异性表达蛋白.