Mismatch repair, but not heteroduplex rejection, is temporally coupled to DNA replication

In eukaryotes, it is unknown whether mismatch repair (MMR) is temporally coupled to DNA replication and how strand-specific MMR is directed. We fused Saccharomyces cerevisiae MSH6 with cyclins to restrict the availability of the Msh2-Msh6 mismatch recognition complex to either S phase or G2/M phase of the cell cycle. The Msh6-S cyclin fusion was proficient for suppressing mutations at three loci that replicate at mid-S phase, whereas the Msh6-G2/M cyclin fusion was defective. However, the Msh6-G2/M cyclin fusion was functional for MMR at a very late-replicating region of the genome. In contrast, the heteroduplex rejection function of MMR during recombination was partially functional during both S phase and G2/M phase. These results indicate a temporal coupling of MMR, but not heteroduplex rejection, to DNA replication.     

MMS19 links cytoplasmic iron-sulfur cluster assembly to DNA metabolism

The function of many DNA metabolism proteins depends on their ability to coordinate an iron-sulfur (Fe-S) cluster. Biogenesis of Fe-S proteins is a multistep process that takes place in mitochondria and the cytoplasm, but how it is linked to nuclear Fe-S proteins is not known. Here, we demonstrate that MMS19 forms a complex with the cytoplasmic Fe-S assembly (CIA) proteins CIAO1, IOP1, and MIP18. Cytoplasmic MMS19 also binds to multiple nuclear Fe-S proteins involved in DNA metabolism. In the absence of MMS19, a failure to transfer Fe-S clusters to target proteins is associated with Fe-S protein instability and preimplantation death of mice in which Mms19 has been knocked out. We propose that MMS19 functions as a platform to facilitate Fe-S cluster transfer to proteins critical for DNA replication and repair.     

茶树基因组DNA提纯与RAPD反应系统建立

DNA的提取质量是决定RAPD分析成功与否的关键。茶树幼嫩新梢中含有大量的茶多酚等次生物质，采用磨样对添加杭酚氧化褐变的物质，在细胞核裂解之前去除细胞质中的茶多酚和蛋白质，而后再用改进的DNA微量快速提取法-SDS法分别从不同茶树品种新梢中提取和纯化基因组DNA，所得到的DNA样品适宜于RAPD反应，通过对茶树RAPD分析中影响扩增结果的因素的研究。建立了茶树RAPD的最适反应系统，即在25ul反应体系中，含20-50ng模板DNA，1.5mmol/1MgCl2，各0.1mmol/1DNTPs,0.2umol/L引物和1UTaqDNA聚合酶；扩增程序为：95℃预变性300s,94℃变性60s,35℃退火60s，72℃延伸120s，共进行40个循环，最后72℃延伸600s，这样可以取得较好的扩增效果。     

Sequence-dependent pausing of single lambda exonuclease molecules

Lambda exonuclease processively degrades one strand of duplex DNA, moving 5'-to-3' in an ATP-independent fashion. When examined at the single-molecule level, the speeds of digestion were nearly constant at 4 nanometers per second (12 nucleotides per second), interspersed with pauses of variable duration. Long pauses, occurring at stereotypical locations, were strand-specific and sequence-dependent. Pause duration and probability varied widely. The strongest pause, GGCGAT TCT, was identified by gel electrophoresis. Correlating single-molecule dwell positions with sequence independently identified the motif GGCGA. This sequence is found in the left lambda cohesive end, where exonuclease inhibition may contribute to the reduced recombination efficiency at that end.     

Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos

Although global erasure of DNA methylation has been observed in zygotes and primordial germ cells, the responsible enzyme(s) have been elusive. The demonstration that members of the Tet (ten eleven translocation) family of proteins are capable of catalyzing conversion of 5-methylcytosine (5mC) of DNA to 5-hydroxymethylcytosine (5hmC) raises the possibility that Tet proteins may participate in this process. Indeed, recent studies have implicated the involvement of Tet3 in the conversion of 5mC to 5hmC in zygotes. This result, combined with the demonstration that Tet proteins can further oxidize 5hmC to 5-carboxylcytosine followed by excision by thymine-DNA glycosylase, raises the possibility that active demethylation may take place in a process that involves Tet3-mediated oxidation followed by base excision repair. We demonstrated by immunostaining of mitotic chromosome spreads of preimplantation embryos that the 5hmC associated with the paternal genome in zygotes is gradually lost during preimplantation development. Our study suggests that, although the conversion of 5mC to 5hmC in zygotes is an enzyme-catalyzed process, loss of 5hmC during preimplantation appears to be a DNA replication-dependent passive process.     

外源基因高效转移与整合策略:人工引导转化系统

外源基因的引导转化是相对直接转化而言 ,包括两类蛋白分子对转移DNA的的共价结合和包被 ,涉及转移DNA复合物的形成、转移和在受体细胞核基因中的整合。认为引导转化将提高外源基因转移和整合的频率。在此认识的基础上 ,提出一个人工引导转化系统的技术方案     

Cloning of Thymidine Kinase Gene of Duck Plague Virus Using Degenerate PCR

The DNA of duck plague virus （DPV） thymidine kinase （TK） gene was cloned and sequenced from a vaccine virus in the study. Degenerate oligonucleotide primers for the consensus site of herpesvirus UL24, TK, and glycoprotein H（gH） gene were used in the polymerase chain reaction （PCR） to amplify DNA product with 3 741-base-pairs （bp） in size. DNA sequence analysis revealed a 1 077-base-pairs （bp） open reading frame （ORF） encoding a 358 amino acid polypeptide homologous to herpesvirus TK proteins. The predicted TK protein shared 31.2, 41.3, 35.7, 37.4, and 28.4% identity with herpes simplex virus typel, equine herpesvirus type 4, Marek＇s disease virus 2, herpesvirus turkey, and infectious laryngotracheitis virus, respectively. Comparison of the amino acid sequences of other herpesvirus TK proteins showed that these proteins were not conserved on the whole, otherwise the portion of the TK proteins corresponding to the nucleotide binding domain and the nucleoside binding site were highly conserved among herpesvirus. Comparison with the amino acid sequences of the conserved nucleotide and nucleoside binding domains of other eleven herpesvirus TK proteins to the predicted DPV peptide confirmed its identity as the DPV TK protein.     

The S1-sensitive form of d(C-T)n.d(A-G)n: chemical evidence for a three-stranded structure in plasmids

Homopurine-homopyrimidine sequences that flank certain actively transcribed genes are hypersensitive to single strand-specific nucleases such as S1. This has raised the possibility that an unusual structure exists in these regions that might be involved in recognition or regulation. Several of these sequences, including d(C-T)n.d(A-G)n, are known to undergo a transition in plasmids to an underwound state that is hypersensitive to single strand-specific nucleases; this transition occurs under conditions of moderately acid pH and negative supercoiling. Chemical probes were used to examine the reactivity of a restriction fragment from a human U1 gene containing the sequence d(C-T)18.d(A-G)18 as a function of supercoiling and pH, and thus analyze the structure in this region. Hyperreactivity was seen in the center and at one end of the (C-T)n tract, and continuously from the center to the same end of the (A-G)n tract, in the presence of supercoiling and pH less than or equal to 6.0. These results provide strong support for a triple-helical model recently proposed for these sequences and are inconsistent with other proposed structures.     

细菌单杂交方法在筛选甲基营养菌甲醇脱氢酶启动子结合蛋白中的应用

为了构建甲基营养菌转录因子亚文库及筛选与甲醇脱氢酶启动子DNA相互作用的蛋白质,对甲基营养菌MP688的基因组和转录组数据进行分析,使用关键词对全基因注释信息和转录组结果进行搜索,找到相关基因的核苷酸序列,通过PCR获得目的片段并构建一系列转录因子亚文库,利用细菌单杂交系统筛选转录因子亚文库找到与甲醇脱氢酶启动子具有相互作用的调控因子。成功构建完成含有32个转录因子的亚文库,建立了甲基营养菌中细菌单杂交筛选方法,通过该方法筛选出2个与甲醇脱氢酶启动子具有强相互作用的转录因子基因。对于基因组已测序的细菌来说,构建转录因子亚文库筛选效率要优于构建基因组文库和cDNA文库,细菌单杂交系统能成功用于甲基营养菌,并能快速高效地筛选与启动子具有相互作用的转录因子。这一方法的建立,为阐明甲醇脱氢酶在甲基菌生长和代谢产物合成中的调控机制奠定了基础。     

The Hin invertasome: protein-mediated joining of distant recombination sites at the enhancer

The Hin protein binds to two cis-acting recombination sites and catalyzes a site-specific DNA inversion reaction that regulates the expression of flagellin genes in Salmonella. In addition to the Hin protein and the two recombination sites that flank the invertible segment, a third cis-acting recombinational enhancer sequence and the Fis protein, which binds to two sites within the enhancer, are required for efficient recombination. Intermediates of this reaction were trapped during DNA strand cleavage and analyzed by gel electrophoresis and electron microscopy in order to determine their structure and composition. The analyses demonstrate that the recombination sites are assembled at the enhancer into a complex nucleo-protein structure (termed the invertasome) with the looping of the three segments of intervening DNA. Antibody studies indicated that Fis physically interacts with Hin and that both proteins are intimately associated with the invertasome. In order to achieve this protein-protein interaction and assemble the invertasome, the substrate DNA must be supercoiled.     

提取地衣真菌总DNA的简便方法

利用液氮破碎地衣体的上下表皮层及藻层，再用氯化苄在弱碱条件下破坏真菌细胞壁，从而获得地衣真菌总ＤＮＡ．此方法简便、省时、价廉，获得的总ＤＮＡ蛋白质污染少，产量高，可进一步进行ＰＣＲ扩增．     

A role for DNA-PK in retroviral DNA integration

Retroviral DNA integration is catalyzed by the viral protein integrase. Here, it is shown that DNA-dependent protein kinase (DNA-PK), a host cell protein, also participates in the reaction. DNA-PK-deficient murine scid cells infected with three different retroviruses showed a substantial reduction in retroviral DNA integration and died by apoptosis. Scid cell killing was not observed after infection with an integrase-defective virus, suggesting that abortive integration is the trigger for death in these DNA repair-deficient cells. These results suggest that the initial events in retroviral integration are detected as DNA damage by the host cell and that completion of the integration process requires the DNA-PK-mediated repair pathway.     

水稻白叶枯病菌gacA基因的克隆、测序及敲除研究

根据黄单胞菌gacA基因的同源性设计简并引物，采用PCR方法从水稻白叶枯病菌（Xanthomonas oryzae pvoryzae，Xoo）中克隆了gacA同源基因，命名为gacAxoo。序列比较显示，该基因在黄单胞菌中是相对保守的。蛋白质保守结构域搜索表明，GacAxoo属于LuxR家庭的一员，具有与其他GacA蛋白相似的结构。通过同源重组的方法，构建了gacAxoo的插入突变体，为下一步研究gacAxoo的功能奠定了良好的基础。     

Genetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I

Site-directed mutagenesis of the large fragment of DNA polymerase I (Klenow fragment) yielded two mutant proteins lacking 3',5'-exonuclease activity but having normal polymerase activity. Crystallographic analysis of the mutant proteins showed that neither had any alteration in protein structure other than the expected changes at the mutation sites. These results confirmed the presumed location of the exonuclease active site on the small domain of Klenow fragment and its physical separation from the polymerase active site. An anomalous scattering difference Fourier of a complex of the wild-type enzyme with divalent manganese ion and deoxythymidine monophosphate showed that the exonuclease active site has binding sites for two divalent metal ions. The properties of the mutant proteins suggest that one metal ion plays a role in substrate binding while the other is involved in catalysis of the exonuclease reaction.     

Three-dimensional structure of the Tn5 synaptic complex transposition intermediate

Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.     

牛乳中金黄色葡萄球菌山东分离株（zfb）β-溶血素(hlb)的克隆、表达及溶血活性分析

 【目的】实现牛乳中金黄色葡萄球菌β-溶血素在大肠杆菌中的高效表达,并分析重组β-溶血素的溶血活性。【方法】PCR扩增牛乳中金黄色葡萄球菌山东分离株β-溶血素基因,构建原核表达载体pET32a+/hlb,并在大肠杆菌BL21（DE3）中诱导表达,用96孔血凝板测定重组蛋白的溶血效价,以血琼脂平板法检测重组蛋白的CAMP反应。【结果】测序结果表明,扩增片段含有993 bp的ORF,可编码含330个氨基酸的成熟蛋白;SDS-PAGE分析重组蛋白表达水平,IPTG诱导后表达的融合蛋白分子量为57 kD,表达量占菌体总蛋白的23.9%;溶血效价分析,金葡菌β-溶血素对绵羊红细胞的溶血效价为278 HU?mg-1,对奶牛红细胞的溶血效价为9×103 HU?mg-1;重组蛋白在血琼脂平板上和无乳链球菌能发生明显的CAMP反应。【结论】成功表达了牛乳中金黄色葡萄球菌β-溶血素,该毒素对奶牛红细胞的溶血活性明显大于绵羊红细胞,显示出牛源金黄色葡萄球菌β-溶血素的特性明显不同于人源金黄色葡萄球菌β-溶血素,为进一步研究其致病与免疫机理、疫苗设计提供了理论基础。此外,重组蛋白还可用来特异性诊断、鉴别无乳链球菌,为兽医临床诊断提供新的方法。     

油松种子萌发过程中核酸和蛋白质的变化

随油松种子萌发的进程,种子内核酸总量、DNA,RNA和蛋白质含量发生不同程度的消长,胚蛋白组分的变化尤为明显,其中低等电点(pH4.3～5.2)区域的酸性蛋白质不断增加和累积;与此相反,高等电点(pH6.5～8.0)低分子量(4.3×10~4D以下)区域的碱性蛋白质逐渐降解、消失,用PAS反应证明它们是一组分子量各异的糖蛋白。种胚内的这些在不同时期出现和消失的蛋白质都具有萌发时期的特征性,它们可能对调节胚的生长和幼苗的形态建成有重要作用。