高等植物中的DNA解旋酶

综述了在离体实验条件下高等植物DNA解旋酶在以下多方面具有重要的生物学功能：包括DNA重组、DNA复制、翻译启始、rDNA转录及在prerRNA加工过程早期阶段,双链断裂修复、端粒长度维持、核苷酸切除修复、花发育中的细胞分裂/增殖、基因组甲基化方式保持、植物细胞周期和细胞基本生命活动的维持。最近玉米基因组中发现的解旋子（helitron)插入说明高等植物DNA解旋酶可能在植物生长与发育中有重要调控作用。因而有着重要的生物技术应用价值。     

赖解旋酶恒温基因扩增技术的原理、应用和展望

赖解旋酶恒温基因扩增方法(HDA法)是新近发明的一种简便、快速、高效的体外恒温基因扩增技术.该法依靠DNA解旋酶解开双链DNA、单链DNA结合蛋白(SSB)维持单链状态、DNA聚合酶催化靶片段的扩增.研究表明,HDA能扩增微生物基因组DNA、病原菌DNA、质粒DNA和cDNA等,从灵敏性、准确性和可操作性几方面看,该方法具有广阔的实用前景.     

Mg2+对Bloom综合症解旋酶与G4DNA结合的影响研究

利用荧光偏振技术检测了Mg2+对G4DNA、BLM-G4DNA复合物和BLM642-1290解旋酶与G4DNA结合的影响.结果表明,G4DNA荧光偏振值随着Mg2+浓度的增加而增加(P＜0.01);BLM-G4DNA复合物的荧光偏振值随着Mg2+浓度的增加出现下降—升高—下降的变化趋势(P＜0.01);G4DNA与BLM642-1290解旋酶结合的荧光偏振值随着Mg2+浓度的增加而逐渐下降(P＜0.01);分析不同Mg2+浓度下两种分子结合的Kd值,发现Mg2+浓度为3.0 mmol/L时,BLM642-1290解旋酶与G4DNA最容易结合,表明适量Mg2+浓度会促进BLM642-1290与G4DNA的结合,但会引起两种分子结合的形状、流动性和电荷等性质的改变.这些结果可为进一步研究BLM解旋酶对G4DNA的作用机理提供相关资料.     

植物AGO蛋白的结构预测分析

AGO蛋白家族(Argonaute protein family)是RNA诱导沉默复合物(RISC)的功能核心,参与小RNA介导的基因沉默.AGO蛋白由N末端、PAZ、MID和PIWI四个结构域组成.它和小RNA在植物中共同参与维持基因组的稳定、调控组织发育、DNA修复、对逆境的适应性应答以及在RNA层面对入侵核酸(转基因和植物病毒)的免疫.植物AGO蛋白在胚胎发育,细胞分化和转座子的沉默中具有重要作用.本文运用生物信息学的方法,结合生物信息学两大门户网站,对植物AGO蛋白的分类、平均疏水性、净电荷、不稳定系数等进行预测.     

人RNA解旋酶基因家族新成员DVH的克隆与初步功能研究

一条长3446bp 的人类新基因cDNA已从胎脑cDNA文库中被克隆,该cDNA克隆包长2583bp的开放读框,推测编码一条长860个氨基酸残基的蛋白质,预测分子质量为96．8ku,通过同源性比较及profile搜索,预测氨基酸序列显示出DExH-BOX RNA解旋酶基因家族特有的7保守基序及已知RNA解旋酶氨基酸序列的较高同源性,进一步通过蛋白质结构模型同已知RNA解旋酶结构的比较,可以认定其为一条人类RNA解旋酶基因家族新成员,通过基因编码的氨基酸序列中基序II D－E－V－H残基将其命名为DVH（DEVHbox Helicase),生物信息学手段结合DVH基因表达谱分析结果可推定DVH可能在胎儿发育过程中起作用,由于解旋基因家族同人类遗传疾病关系密切,以上结果可指导DVH基因的进一步功能研究并提示该,基因作为疾病侯选基因的可能性。     

DDX3的病理生理学作用

DEAD-box RNA解旋酶3(DEAD-box RNA helicase 3,DDX3),亦称DEAD-box RNA解旋酶3 X连锁(DEAD-box RNA helicase 3 X-linked,DDX3X),是一种高度保守并依赖ATP的RNA解旋酶,广泛分布于真核生物中,主要定位在细胞核和细胞质发挥生理作用,与RNA剪接和衰变、mRNA输出、转录、翻译相关,进一步参与细胞周期的进展、先天免疫反应、细胞凋亡、癌症发生与抑制、病毒的复制周期等多种重要的细胞生理过程.长期以来,DDX3的基因表达,调控及其功能以及它与疾病的关系一直被关注,尤其是与病毒和癌症的关系更为热点研究.因此,本文主要探讨、总结DDX3的病理生理学作用.     

染色体结构维持蛋白Smc5/6复合体的结构与功能

真核生物基因组DNA主要以染色体的形式存在于细胞核中，染色体结构的稳定及其动态变化对于真核生物遗传信息从亲代到子代中的准确传递和维持细胞的正常功能是必不可少的。染色体结构维持蛋白（Structure Maintenance of Chromosome，Smc）在染色体结构维持及DNA损伤修复方面发挥着关键性的作用。Smc蛋白家族包括3类：黏连蛋白（Cohesin）、凝缩蛋白（Condesin）和Smc5/6复合体（Smc5/6 complex）。Smc5/6复合体在真核生物中分布广泛且高度保守，在DNA损伤同源重组修复、DNA复制、端粒长度维持及胚胎发育中发挥重要作用。本文系统介绍了Smc5/6复合体结构特征和生物学功能领域的相关进展，为深入研究Smc5/6复合体提供理论参考。     

TET双加氧酶和TDG糖苷酶介导的DNA主动去甲基化

<正>DNA甲基化是表观遗传修饰的一种重要方式。哺乳动物中DNA甲基化主要发生在Cp G双核苷酸中胞嘧啶的五位碳原子上,可以引起染色质结构和基因活性的改变,在基因印迹、X染色体失活、发育调控以及转座子沉默和基因组稳定性的维持等方面发挥重要作用。有人把基因组甲基化比作细胞的记忆,当分化成生殖细胞和精卵结合产生下一代时就要抹去"前世"的记忆,涅槃重生。这么比喻是由于在哺乳动物中,基因组甲基化水平随着个体发育和繁殖呈现周期性的变化,其     

高等植物的性别表达及其调控——外界因子对植物性别表达的影响

高等植物的性别表达研究是成花生理及发育生理的一个特殊组成部分,是生殖生理学中的最重要问题之一,在理论上、实践上都具有重要意义.由于植物性别表达本身的特点,使高等植物成为研究发育、性别表达及其决定的优良实验系统.     

水生高等植物对湖泊生态系统的影响

从多种角度分析了水生高等植物在湖泊生态系统中的作用以及和其它生物的关系,并从覆盖率、群落结构、植物配比等角度讨论了湖泊水生高等植物的最佳保有生物量。表明水生高等植物在湖泊生态系统中具有重要的环境生态功能和初级生产功能,水生高等植物的消退与过量生长都会导致湖泊生态系统生物多样性下降、生态系统变得脆弱和不稳定;维持湖泊生态系统良性循环,水生植物的生物量至少要大于1000g/m2,水生植物的覆盖度要大于30%,除了控制水生植物在水体中的总体生物量,还应重视挺水植物、浮叶植物、沉水植物和漂浮植物之间生物量的合适比例,并需密切注意水生植被群落结构的变化情况。     

Kinetic study of the DNA annealing properties of RECQ5β helicase

RecQ family helicases are critical for maintaining genomic integrity. Many RecQ family helicases not only unwind duplex, and other more complicated DNA structures, but also possess, interestingly, DNA annealing (strand pairing) activity. Here, we systematically investigated the DNA annealing properties of RECQ5β by measuring DNA annealing kinetics, equilibrium DNA binding, and kinetics of dissociation from ssDNA. RECQ5β catalyzed DNA annealing most efficiently when the enzyme molecules covered approximately 40%-50% of the DNA strand, in the absence or presence of different nucleotide cofactors (AMPPNP, ATPγS, or ADP) under our buffer conditions. A comparative study with RECQ5β1-662 confirmed that the C-terminal region of RECQ5β was essential for its high DNA annealing activity. These results contribute to our understanding of the mechanism of DNA annealing catalyzed by RecQ family helicases.     

RecBCD enzyme is a bipolar DNA helicase

Escherichia coli RecBCD is a heterotrimeric helicase/nuclease that catalyses a complex reaction in which double-strand breaks in DNA are processed for repair by homologous recombination. For some time it has been clear that the RecB subunit possesses a 3' --> 5' DNA helicase activity, which was thought to drive DNA translocation and unwinding in the RecBCD holoenzyme. Here we show that purified RecD protein is also a DNA helicase, but one that possesses a 5' --> 3' polarity. We also show that the RecB and RecD helicases are both active in intact RecBCD, because the enzyme remains capable of processive DNA unwinding when either of these subunits is inactivated by mutation. These findings point to a bipolar translocation model for RecBCD in which the two DNA helicases are complementary, travelling with opposite polarities, but in the same direction, on each strand of the antiparallel DNA duplex. This bipolar motor organization helps to explain various biochemical properties of RecBCD, notably its exceptionally high speed and processivity, and offers a mechanistic insight into aspects of RecBCD function.     

The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase

The transfer of DNA across membranes and between cells is a central biological process; however, its molecular mechanism remains unknown. In prokaryotes, trans-membrane passage by bacterial conjugation, is the main route for horizontal gene transfer. It is the means for rapid acquisition of new genetic information, including antibiotic resistance by pathogens. Trans-kingdom gene transfer from bacteria to plants or fungi and even bacterial sporulation are special cases of conjugation. An integral membrane DNA-binding protein, called TrwB in the Escherichia coli R388 conjugative system, is essential for the conjugation process. This large multimeric protein is responsible for recruiting the relaxosome DNA-protein complex, and participates in the transfer of a single DNA strand during cell mating. Here we report the three-dimensional structure of a soluble variant of TrwB. The molecule consists of two domains: a nucleotide-binding domain of alpha/beta topology, reminiscent of RecA and DNA ring helicases, and an all-alpha domain. Six equivalent protein monomers associate to form an almost spherical quaternary structure that is strikingly similar to F1-ATPase. A central channel, 20 A in width, traverses the hexamer.     

Dynamics of ATP-dependent chromatin assembly by ACF

The assembly of DNA into chromatin is a critical step in the replication and repair of the eukaryotic genome. It has been known for nearly 20 years that chromatin assembly is an ATP-dependent process. ATP-dependent chromatin-assembly factor (ACF) uses the energy of ATP hydrolysis for the deposition of histones into periodic nucleosome arrays, and the ISWI subunit of ACF is an ATPase that is related to helicases. Here we show that ACF becomes committed to the DNA template upon initiation of chromatin assembly. We also observed that ACF assembles nucleosomes in localized arrays, rather than randomly distributing them. By using a purified ACF-dependent system for chromatin assembly, we found that ACF hydrolyses about 2#150;4 molecules of ATP per base pair in the assembly of nucleosomes. This level of ATP hydrolysis is similar to that used by DNA helicases for the unwinding of DNA. These results suggest that a tracking mechanism exists in which ACF assembles chromatin as an ATP-driven DNA-translocating motor. Moreover, this proposed mechanism for ACF may be relevant to the function of other chromatin-remodelling factors that contain ISWI subunits.     

Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase

Helicases are motor proteins that couple conformational changes induced by ATP binding and hydrolysis with unwinding of duplex nucleic acid, and are involved in several human diseases. Some function as hexameric rings, but the functional form of non-hexameric helicases has been debated. Here we use a combination of a surface immobilization scheme and single-molecule fluorescence assays--which do not interfere with biological activity--to probe DNA unwinding by the Escherichia coli Rep helicase. Our studies indicate that a Rep monomer uses ATP hydrolysis to move toward the junction between single-stranded and double-stranded DNA but then displays conformational fluctuations that do not lead to DNA unwinding. DNA unwinding initiates only if a functional helicase is formed via additional protein binding. Partial dissociation of the functional complex during unwinding results in interruptions ('stalls') that lead either to duplex rewinding upon complete dissociation of the complex, or to re-initiation of unwinding upon re-formation of the functional helicase. These results suggest that the low unwinding processivity observed in vitro for Rep is due to the relative instability of the functional complex. We expect that these techniques will be useful for dynamic studies of other helicases and protein-DNA interactions.     

Translocation step size and mechanism of the RecBC DNA helicase

DNA helicases are ubiquitous enzymes that unwind double-stranded DNA. They are a diverse group of proteins that move in a linear fashion along a one-dimensional polymer lattice--DNA--by using a mechanism that couples nucleoside triphosphate hydrolysis to both translocation and double-stranded DNA unwinding to produce separate strands of DNA. The RecBC enzyme is a processive DNA helicase that functions in homologous recombination in Escherichia coli; it unwinds up to 6,250 base pairs per binding event and hydrolyses slightly more than one ATP molecule per base pair unwound. Here we show, by using a series of gapped oligonucleotide substrates, that this enzyme translocates along only one strand of duplex DNA in the 3'-->5' direction. The translocating enzyme will traverse, or 'step' across, single-stranded DNA gaps in defined steps that are 23 (+/-2) nucleotides in length. This step is much larger than the amount of double-stranded DNA that can be unwound using the free energy derived from hydrolysis of one molecule of ATP, implying that translocation and DNA unwinding are separate events. We propose that the RecBC enzyme both translocates and unwinds by a quantized, two-step, inchworm-like mechanism that may have parallels for translocation by other linear motor proteins.     

Repetitive shuttling of a motor protein on DNA

Many helicases modulate recombination, an essential process that needs to be tightly controlled. Mutations in some human disease helicases cause increased recombination, genome instability and cancer. To elucidate the potential mode of action of these enzymes, here we developed a single-molecule fluorescence assay that can visualize DNA binding and translocation of Escherichia coli Rep, a superfamily 1 DNA helicase homologous to Saccharomyces cerevisiae Srs2. Individual Rep monomers were observed to move on single-stranded (ss)DNA in the 3' to 5' direction using ATP hydrolysis. Strikingly, on hitting a blockade, such as duplex DNA or streptavidin, the protein abruptly snapped back close to its initial position, followed by further cycles of translocation and snapback. This repetitive shuttling is likely to be caused by a blockade-induced protein conformational change that enhances DNA affinity for the protein's secondary DNA binding site, thereby resulting in a transient DNA loop. Repetitive shuttling was also observed on ssDNA bounded by a stalled replication fork and an Okazaki fragment analogue, and the presence of Rep delayed formation of a filament of recombination protein RecA on ssDNA. Thus, the binding of a single Rep monomer to a stalled replication fork can lead to repetitive shuttling along the single-stranded region, possibly keeping the DNA clear of toxic recombination intermediates.