极端嗜热古菌———芝田硫化叶菌DNA 连接酶的生化性质

极端嗜热古菌———芝田硫化叶菌 DNA 连接酶 (Ssh 连接酶 ) 的最适辅因子为 ATP ,在 dATP 存在时,该酶也能表现出较弱的连接活性 . ATP 或 dATP 都能够使该酶发生腺苷化,腺苷化的 Ssh 连接酶能够将腺苷基团转移至含切刻的 DNA 上 . 电泳迁移率改变实验表明, Ssh 连接酶能够结合双链 DNA ,且与含切刻及不含切刻的 DNA 结合的亲和力相同,但不结合单链 DNA. 酵母双杂交实验显示,硫磺矿硫化叶菌 ( 与芝田硫化叶菌亲缘关系很近 ) 的 DNA 连接酶,与该菌所含的 3 个增殖细胞核抗原 (PCNA) 同源蛋白中的一个 (PCNA-1) 有相互作用,而与另外 2 个同源蛋白 (PCNA-like 和 PCNA-2) 则无相互作用 . 在古菌中高度保守的 Sac10b 蛋白家族成员 Ssh10b 能够激活 Ssh 连接酶的活性,而硫化叶菌中的主要染色体蛋白——— 7 ku DNA 结合蛋白 (Ssh7) 则对该酶活性没有影响 .     

芝田硫化叶菌ssh7a和ssh7b基因在大肠杆菌中的表达及重组蛋白的性质

极端嗜热古菌——芝田硫化叶菌DNA结合蛋白Ssh7a和Ssh7b的编码基因(ssh7a和ssh7b)在大肠杆菌中得到表达,表达量均达到细胞蛋白总量的10%～15%。重组蛋白通过一个包括热处理步骤的简单纯化程序得到纯化。重组Ssh7a和Ssh7b与松弛及负超螺旋DNA的结合与天然Ssh7蛋白无异,与天然Ssh7相似,Ssh7a在与DNA结合时能够固定负超螺旋,每固定一个负超螺旋约需22个Ssh7a分子。这些结果表明天然Ssh7蛋白中的两个同源多肽与DNA结合时无明显差异。另外,Ssh7的甲基化与否似乎不影响该蛋白对DNA的亲和力及固定DNA超螺旋的能力。     

芝田硫化叶菌Ssh7蛋白的进化保守性及DNA结合特性

嗜酸热古菌——芝田硫化叶菌(Sulfolobus shibatae)合成大量7 kD DNA结合蛋白Ssh7. Southern杂交结果显示, 该菌基因组中含有两个编码Ssh7蛋白的基因, 分别命名为ssh7a和ssh7b. 对这两个基因进行了克隆、序列测定和在大肠杆菌中的表达. 测序结果表明, 两个Ssh7多肽仅在3个氨基酸位置上有差异; 此外, ssh7a和ssh7b的顺式调控序列也十分相似, 提示存在着维持两个基因的序列和表达都不变的选择压力. 杂交结果还显示, 与芝田硫化叶菌一样, 硫磺矿硫化叶菌(Sulfolobus solfataricus)基因组中也含有两个编码7 kD蛋白的基因. 结合其他报道, 这一结果提示编码7 kD蛋白的基因可能在硫化叶菌种间分歧形成之前发生了基因复制. 采用电泳迁移率改变试验(EMSA)分析了天然及重组Ssh7蛋白与双链DNA片段之间的相互作用. 天然和重组蛋白的EMSA行为相似, 说明Ssh7与DNA的相互作用既不受发生在天然蛋白赖氨酸残基上的甲基化的影响, 也不受两种多肽异构体之间在序列上的差异的影响. 在所采用的实验条件下, Ssh7与双链DNA片段结合时的结合位点大约为6.6 bp, 表观解离常数为(0.7~1.0)×10^-7 mol/L. 此外, Ssh7与负超螺旋DNA的结合强于与线性和松弛DNA的结合.     

极端嗜热古菌——芝田硫化叶菌DNA结合蛋白Ssh12对DNA超螺旋的影响

通过SPSepharose,DNA纤维素和磷酸纤维素等柱层析 ,从极端嗜热古菌———芝田硫化叶菌 (Sulfolobusshibatae)中纯化得到分子量为 11.5ku的DNA结合蛋白Ssh12 .Ssh12约占细胞总蛋白的 4% .该蛋白既能与负超螺旋DNA也能与松弛DNA结合 .利用含单切刻环状DNA进行的切刻闭合分析表明 ,Ssh12在与DNA结合时能够固定负超螺旋 .这种能力在室温 ( 2 2℃ )下很弱 ,而在 3 7℃以上则大大增强 .Ssh12的细胞内含量和固定负超螺旋的能力提示 ,该蛋白对于芝田硫化叶菌染色体DNA的组织以及热稳定性起着重要作用 .     

极端嗜热古菌——芝田硫化叶菌DNA解旋酶的分离纯化和性质研究

采用Qsepharose离子交换层析、磷酸纤维素P1 1吸附层析、肝素琼脂糖吸附层析、Su perdex 2 0 0凝胶过滤和PhenylSuperose疏水层析等步骤 ,从嗜酸热芝田硫化叶菌细胞裂解液中分离纯化了一个DNA解旋酶。该解旋酶具有受DNA激活的ATP酶活性。根据SDS PAGE测定结果 ,该酶的分子质量约为 63kD。芝田硫化叶菌DNA解旋酶可以解开底物上 70bp的双链区 ,其解旋活性依赖于双链区旁的单链分叉。该解旋酶的活性依赖于Mg2 + 和ATP的水解 ,在NaCl浓度超过 2 0 0mmol L时受到抑制。该酶的最适pH为 6 7。该酶在 40℃～ 80℃之间均有活性 ,70℃时活性最高。芝田硫化叶菌DNA解旋酶是从古菌中分离得到的第一个天然DNA解旋酶。     

芝田硫化叶菌ssh7a和ssh7b基因在大肠杆菌中的表达及重组蛋白的性质

极端嗜热古菌－－芝田硫化叶菌ＤＮＡ结合蛋白Ｓｓｈ７ａ和Ｓｓｈ７ｂ的编码基因（ｓｓ７α和ｓｓｈ７ь）在大肠杆菌中得到表达。量均达到细胞蛋白总量的１０％￣１５％。重组蛋白通过一个包括热处理步骤的简单纯化程序得到纯化。重组Ｓｓｈ７ａ和Ｓｓｈ７ｂ与松弛及负超螺旋ＤＮＡ的结合与天然Ｓｓｈ７蛋白无异,与天然Ｓｓｈ７相似,Ｓｓｈ７ａ在与ＤＮＡ结合时能免固定负超螺旋,每固定一个负超螺旋约需２２个Ｓｓｈ７ａ分子。这     

一种基于线性DNA片段同源重组的嗜盐古菌高效基因敲除系统

随着功能基因组学研究的深入发展,基因敲除技术日益成为基因功能研究的重要手段。嗜盐古菌Haloferax volcanii易于培养,是研究古菌基因功能的良好模式菌株。虽然现已开发了多种嗜盐古菌的遗传操作系统,但基因敲除成功率不十分理想。这些遗传操作方法基于pyrE筛选标记,利用携带同源片段的环状质粒与基因组同源片段间的两次同源重组,敲除目的基因。由于基于环状质粒和pyrE筛选标记的经典同源重组敲除方法在二次重组时,普遍存在回复到野生型菌株的可能,导致二次重组子中敲除目的基因的阳性菌株比例较低。为了克服传统同源重组技术的上述缺陷,文章建立了基于线性DNA片段的同源重组技术。该方法通过一次重组在目标基因的下游引入一段上游同源片段和pyrE标记,从而限定二次重组的发生部位只能在两段上游同源片段之间,发生二次重组的重组子理论上都敲除了目标基因。利用该方法,文章成功敲除了嗜盐古菌Haloferax volcanii的xpd2基因,阳性克隆率达65%。这种线性DNA片段重组法为嗜盐古菌的基因敲除提供了一种高效策略,便于嗜盐古菌的基因改造。     

硫矿硫化叶菌P2分子伴侣基因的克隆表达及其性质

[目的]研究重组表达的硫矿硫化叶菌P2分子伴侣β亚基体外同源聚合体的结构和生化功能.[方法]利用PCR技术从硫矿硫化叶菌P2的基因组DNA中克隆得到分子伴侣β亚基的基因,将该基因克隆到表达载体pET-21a( )上并在大肠杆菌BL21(DE3)中实现了表达.对纯化后的β亚基单体进行体外聚合,利用透射电镜观察β分子伴侣的结构,并对其促蛋白折叠性质进行了研究.[结果]硫矿硫化叶菌P2分子伴侣β亚基基因在大肠杆菌BL21中实现了高效表达,纯化后的分子伴侣β亚基单体在ATP和Mg2 存在的条件下可自组装形成分子伴侣聚合体.透射电镜观察表明:该β分子伴侣具有Ⅱ型分子伴侣典型的双层面包圈结构,每个环由8个亚基构成.该β分子伴侣具有ATPase活性,最适反应温度为80℃;它不仅能够促进变性的绿色荧光蛋白(GFP)重新折叠,而且还能有效的提高木聚糖酶的热稳定性.[结论]本文根据P2基因组序列分析预测的分子伴侣基因设计引物,克隆表达了硫矿硫化叶菌P2分子伴侣的β亚基,纯化后对其进行体外聚合,透射电镜观察表明该聚合体具有Ⅱ型分子伴侣的经典结构,功能分析表明该β分子伴侣能够在体外促进异源蛋白质的折叠、提高其它酶分子的热稳定性.这为进一步深入研究嗜热古菌耐热抗逆的分子机制,奠定了良好的基础.     

嗜热四膜虫SPO11基因缺陷型细胞株的基因表达变化分析

有性生殖的关键过程是通过减数分裂产生生殖细胞,而减数分裂的一个重要环节是进行基于DNA双链断裂的同源染色体重组。在同源染色体重组过程中,SPO11蛋白催化产生DNA双链断裂,从而起始同源染色体的重组。因此,研究SPO11基因缺失在减数分裂过程中所引起的基因表达变化有助于在转录组水平上了解该基因的作用。本研究通过对嗜热四膜虫(Tetrahymena thermophila)野生型和SPO11敲除细胞株在接合生殖时期2 h、3 h、4 h、5 h四个时间点的转录组进行高通量测序。通过差异表达基因分析和功能富集分析,发现SPO11基因敲除之后嗜热四膜虫在接合生殖时期2 h时,与DNA代谢过程和DNA复制相关基因的表达发生变化,推测SPO11基因敲除导致的减数分裂过程异常可能与DNA代谢过程和DNA复制相关。     

古菌RecJ蛋白的研究进展

RecJ蛋白属于aspartate-histidine-histidine (DHH)磷酸酯酶超家族,存在于细菌、真核生物和古菌中。细菌RecJ蛋白是一种5′→3′ssDNA外切酶,参与错配修复、同源重组、碱基切除修复等生物学过程。真核生物cell division cycle 45 (Cdc45)蛋白是细菌RecJ核酸酶的同源物,但不具有核酸酶活性。Cdc45蛋白能够与minichromosomemaintenance(MCM)和Go-Ichi-Ni-San(GINS)形成Cdc45-MCM-GINS (CMG)复合物,是真核生物DNA复制的重要组分。在古菌中,几乎所有基因组已测序的古菌均编码一种或多种RecJ蛋白同源物。与细菌RecJ核酸酶不同,古菌RecJ蛋白具有多样化的核酸酶活性,并且能够与MCM和GINS形成类似于真核生物CMG的复合物。因此,古菌RecJ蛋白是参与古菌DNA复制、修复和重组的重要成分。基于目前古菌RecJ蛋白的研究报道,本文综述了古菌RecJ蛋白的活性、结构与功能方面的研究进展,聚焦于不同古菌RecJ蛋白以及它们与细菌RecJ核酸酶和真核生物RecJ同源物的...     

Ssh10b2 differs from its paralogue Ssh10b in cellular abundance and the ability to constrain DNA supercoils]

The ssh10b and ssh10b2 genes, a pair of distantly related paralogues in Sulfolobus shibatae, encode members of the Sac10b DNA binding protein family in thermophilic archaea. It has been shown previously that Ssh10b exists in abundance in S. shibatae and is capable of constraining negative DNA supercoils, properties that are consistent with a speculated architectural role for the protein in chromosomal organization. In this study, the ssh10b2 gene was cloned and expressed in Escherichia coli, and the recombinant Ssh10b2 protein was purified to apparent homogeneity. Immunoblotting analysis using a specific anti - Ssh10b2 antibody showed that ssh10b2 was expressed in S. shibatae, but the cellular level of Ssh10b2 was only - 10% of that of Ssh10b. Recombinant Ssh10b2 was capable of interacting with both double-stranded and single-stranded DNA. The affinity of the protein for double-stranded DNA was higher than that reported for Ssh10b. The Ssh10b2 and Ssh10b proteins appeared to generate similar gel shift patterns on duplex DNA fragments. However, unlike Ssh10b, Ssh10b2 was unable to constrain DNA supercoils. These data suggest that Ssh10b2 does not serve as a general architectural factor in DNA compaction and organization in S. shibatae.     

Evolutionary conservation and DNA binding properties of the Ssh7 proteins from Sulfolobus shibatae

The thermoacidophilic archaeon Sulfolobus shibatae synthesizes a large amount of the 7-ku DMA binding proteins known as Ssh7. Our hybridization experiments showed that two Ssh7-encoding genes existed in the genome of S. shibatae. These two genes, designated ssh7a and ssh7b, have been cloned, sequenced and expressed in Escherichia coli. The two Ssh7 proteins differ only at three amino acid positions. In addition, the cis-regulatory sequences of the ssh7a and ssh7b genes are highly conserved. These results suggest the presence of a selective pressure to maintain not only the sequence but also the expression of the two genes. We have also found that there are two genes encoding the 7-ku protein in Sulfolobus solfataricus. Based on this and other studies, we suggest that the gene encoding the 7-ku protein underwent duplication before the separation of Sulfolobus species. Binding of native Ssh7 and recombinant (r)Ssh7 to short duplex DNA fragments was analyzed by electrophoretic mobility shift assays. Both n     

Ssh10b, a conserved thermophilic archaeal protein, binds RNA in vivo

Proteins of the Sac10b family, which is highly conserved among hyperthermophilic archaea, have been regarded as DNA-binding proteins. Based on their in vitro DNA-binding properties, these proteins are thought to be involved in chromosomal organization or DNA repair/recombination. We show that Ssh10b, a member of the Sac10b family from Sulfolobus shibatae, bound with similar affinities to double-stranded DNA, single-stranded DNA and RNA in vitro. However, the protein was exclusively bound to RNA in S. shibatae cells, as revealed by in vivo UV cross-linking and co-immunoprecipitation. Ribosomal RNAs were among the RNA species co-immunoprecipitated with Ssh10b. Consistent with this observation, Ssh10b was co-purified with ribosomes under low salt conditions. Furthermore, we demonstrate by UV-cross-linking hybridization that, when the cells were irradiated with UV, Ssh10b became cross-linked to 16S, 23S rRNAs and mRNAs. Our data indicate that RNA is the physiological binding target of the Sac10b family.     

A stabilizing alpha/beta-hydrophobic core greatly contributes to hyperthermostability of archaeal [P62A]Ssh10b

The hyperthermophilic Ssh10b from Sulfolobus shibatae is a member of the Sac10b family, which has been postulated to play a role in chromosomal organization in Archaea. Ssh10b is capable of significantly constraining negative DNA supercoils at elevated temperatures. In this study, the solution structure of the dimeric P62A mutant Ssh10b ([P62A]Ssh10b) was determined by multidimensional NMR spectroscopy. The backbone 15N dynamics, H/D exchange with and without the denaturant GdmSCN, and chemical and thermal denaturation experiments were performed to investigate the molecular basis of high thermostability of [P62A]Ssh10b. Data analysis has revealed an alpha/beta-hydrophobic core consisting of two alpha-helices and one beta-sheet which are stabilized by cooperative hydrophobic and hydrogen-bonding interactions. This stabilizing alpha/beta-hydrophobic core of [P62A]Ssh10b exhibiting highly restricted internal motions is composed of residues having highly protected amide protons which exchange with solvent mostly by means of a global unfolding process. The K40N mutation greatly destabilizes the mutant [P62A]Ssh10b because this mutation disturbs the packing of alpha-helix against the beta-sheet reducing the stability of the alpha/beta-hydrophobic core in the mutant protein. In comparison with homologous mesophilic and thermophilic proteins, it can be presumed that the stabilizing alpha/beta-hydrophobic core in the [P62A]Ssh10b structure greatly contributes to the high thermostability of the protein.     

An abundant DNA binding protein from the hyperthermophilic archaeon Sulfolobus shibatae affects DNA supercoiling in a temperature-dependent fashion

The DNA binding protein Ssh10b, a member of the Sac10b family, has been purified from the hyperthermophilic archaeon Sulfolobus shibatae. Ssh10b constitutes about 4% of the cellular protein. Electrophoretic mobility shift assays showed that Ssh10b first bound a double-stranded DNA fragment with an estimated binding size of approximately approximately 12 bp, forming distinct shifts, until the DNA was coated with the protein. Binding of more Ssh10b resulted in the formation of smears of lower mobilities. The migration pattern of the smearing Ssh10b-DNA complexes was affected by temperature, whereas that of complexes associated with the distinct shifts was not. Interestingly, Ssh10b was capable of constraining negative DNA supercoils in a temperature-dependent fashion. While the ability of the protein to constrain supercoils was weak at 25 degrees C, it was enhanced substantially at 45 degrees C or higher temperatures (up to 80 degrees C). Taken together, our data suggest that archaeal proteins of the Sac10b family may affect the topology of chromosomal DNA in thermophilic archaea at their growth temperatures.     

Effect of DNA binding protein Ssh12 from hyperthermophilic archaeonSulfolobus shibatae on DNA supercoiling

An 11.5-ku DNA binding protein, designated as Ssh12, was purified from the hyperthermophilic archaeonSulfolobus shibatae by column chromatography in SP Sepharose, DNA cellulose and phosphocellulose. Ssh12 accounts for about 4 % of the total cellular protein. The protein is capable of binding to both negatively supercoiled and relaxed DNAs. Nick closure analysis revealed that Ssh12 constrains negative supercoils upon binding to DNA. While the ability of the protein to constrain supercoils is weak at 22°C, it is enhanced substantially at temperatures higher than 37°C. Both the cellular content and supercoil-constraining ability of Ssh12 suggest that the protein may play an important role in the organization and stabilization of the chromosome ofS. shibatae.     

Evolutionary conservation and DNA binding properties of the Ssh7 proteins fromSulfolobus shibatae

The thermoacidophilic archaeonSulfolobus shibatae synthesizes a large amount of the 7-ku DNA binding proteins known as Ssh7. Our hybridization experiments showed that two Ssh7-encoding genes existed in the genome of S.shibatae. These two genes, designatedssh7a andssh7b, have been cloned, sequenced and expressed inEscherichia coli. The two Ssh7 proteins differ only at three amino acid positions. In addition, thecis-regulatory sequences of thessh7a andssh7b genes are highly conserved. These results suggest the presence of a selective pressure to maintain not only the sequence but also the expression of the two genes. We have also found that there are two genes encoding the 7-ku protein inSulfolobus solfataricus. Based on this and other studies, we suggest that the gene encoding the 7-ku protein underwent duplication before the separation ofSulfolobus species. Binding of native Ssh7 and recombinant (r)Ssh7 to short duplex DNA fragments was analyzed by electrophoretic mobility shift assays. Both native and recombinant forms of the protein behaved in a similar fashion in the assays, suggesting that the interaction of Ssh7 with DNA is not affected either by specific lysine methylation found in the native Ssh7 proteins or by the difference between the two Ssh7 isomers in amino acid sequence. Our data show that Ssh7 binds duplex DNA fragments with a binding size of ∼ 6.6 base pairs and an apparent dissociation constant of (0.7–1.0) × 10^-7 mol/L under the assay conditions employed in the present study. In addition, Ssh7 binds more tightly to negatively supercoiled DNA than to linear or relaxed DNA.     

Two conformations of archaeal Ssh10b. The origin of its temperature-dependent interaction with DNA

The DNA-binding protein Ssh10b from the hyperthermophilic archaeon Sulfolobus shibatae is a member of the Sac10b family, which has been speculated to be involved in the organization of the chromosomal DNA in Archaea. Ssh10b affects the DNA topology in a temperature dependent fashion that has not been reported for any other DNA-binding proteins. Heteronuclear NMR and site-directed mutagenesis were used to analyze the structural basis of the temperature-dependent Ssh10b-DNA interaction. The data analysis indicates that two forms of Ssh10b homodimers co-exist in solution, and the slow cis-trans isomerization of the Leu61-Pro62 peptide bond is the key factor responsible for the conformational heterogeneity of the Ssh10b homodimer. The T-form dimer, with the Leu61-Pro62 bond in the trans conformation, dominates at higher temperature, whereas population of the C-form dimer, with the bond in the cis conformation, increases on decreasing the temperature. The two forms of the Ssh10b dimer show the same DNA binding site but have different conformational features that are responsible for the temperature-dependent nature of the Ssh10b-DNA interaction.     

Evolutionary conservation and DNA binding properties of the Ssh7 proteins fromSulfolobus shibatae

The thermoacidophilic archaeon Sulfolobus shibatae synthesizes a large amount of the 7-ku DNA binding proteins known as Ssh7. Our hybridization experiments showed that two Ssh7-encoding genes existed in the genome of S. shibatae. These two genes, designated ssh7a and ssh7b, have been cloned, sequenced and expressed in Escherichia coli. The two Ssh7 proteins differ only at three amino acid positions. In addition, the cis-regulatory sequences of the ssh7a and ssh7b genes are highly conserved. These results suggest the presence of a selective pressure to maintain not only the sequence but also the expression of the two genes. We have also found that there are two genes encoding the 7-ku protein in Sulfolobus solfataricus. Based on this and other studies, we suggest that the gene encoding the 7-ku protein underwent duplication before the separation of Sulfolobus species. Binding of native Ssh7 and recombinant (r)Ssh7 to short duplex DNA fragments was analyzed by electrophoretic mobility shift assays. Both native and recombinant forms of the protein behaved in a similar fashion in the assays, suggesting that the interaction of Ssh7 with DNA is not affected either by specific lysine methylation found in the native Ssh7 proteins or by the difference between the two Ssh7 isomers in amino acid sequence. Our data show that Ssh7 binds duplex DNA fragments with a binding size of ~ 6.6 base pairs and an apparent dissociation constant of (0.7—1.0)×10^-7 mol/L under the assay conditions employed in the present study. In addition, Ssh7 binds more tightly to negatively supercoiled DNA than to linear or relaxed DNA. :