Inducible Knockdown of Plasmodium Gene Expression Using the glmS Ribozyme

Conventional reverse genetic approaches for study of Plasmodium malaria parasite gene function are limited, or not applicable. Hence, new inducible systems are needed. Here we describe a method to control P. falciparum gene expression in which target genes bearing a glmS ribozyme in the 3′ untranslated region are efficiently knocked down in transgenic P. falciparum parasites in response to glucosamine inducer. Using reporter genes, we show that the glmS ribozyme cleaves reporter mRNA in vivo leading to reduction in mRNA expression following glucosamine treatment. Glucosamine-induced ribozyme activation led to efficient reduction of reporter protein, which could be rapidly reversed by removing the inducer. The glmS ribozyme was validated as a reverse-genetic tool by integration into the essential gene and antifolate drug target dihydrofolate reductase-thymidylate synthase (PfDHFR-TS). Glucosamine treatment of transgenic parasites led to rapid and efficient knockdown of PfDHFR-TS mRNA and protein. PfDHFR-TS knockdown led to a growth/arrest mutant phenotype and hypersensitivity to pyrimethamine. The glmS ribozyme may thus be a tool for study of essential genes in P. falciparum and other parasite species amenable to transfection.     

针对点突变癌基因转录物的核酶细胞内性质的研究

前文［１］已证实在体外（ｉｎｖｉｔｒｏ）实验接近生理环境的条件下,本室设计、合成并克隆到的核酶能够高效选择性的定点切割Ｔ２４－ｒａｓ活化癌基因转录物。在此基础上,为阐明该核酶在体内（ｉｎｖｉｖｏ）的生理活性,本文又进一步把核酶基因片段克隆在真核表达质粒ｐＳＭＧ上,并将重组质粒以磷酸钙沉淀法转染由Ｔ２４－ｒａｓ基因诱导的转化细胞系。在细胞和分子水平上检测了核酶在真核细胞内的生物学活性：表现为各恶性转化细胞系的形态特征逆转,生长速度减慢,并呈现出重叠生长减弱恢复接触抑制的趋势,细胞凝集行为接近正常、软琼脂集落形成能力下降;同时,引物延伸实验结果也表明：在体内实验条件下,核酶能够特异性切割点突变Ｔ２４－ｒａｓ癌基因转录物,抑制癌变细胞的恶性行为,使其得到一定程度的逆转。     

Ribozyme speed limits

The speed at which RNA molecules decompose is a critical determinant of many biological processes, including those directly involved in the storage and expression of genetic information. One mechanism for RNA cleavage involves internal phosphoester transfer, wherein the 2'-oxygen atom carries out an SN2-like nucleophilic attack on the adjacent phosphorus center (transesterification). In this article, we discuss fundamental principles of RNA transesterification and define a conceptual framework that can be used to assess the catalytic power of enzymes that cleave RNA. We deduce that certain ribozymes and deoxyribozymes, like their protein enzyme counterparts, can bring about enormous rate enhancements.     

A Faster Triphosphorylation Ribozyme

In support of the RNA world hypothesis, previous studies identified trimetaphosphate (Tmp) as a plausible energy source for RNA world organisms. In one of these studies, catalytic RNAs (ribozymes) that catalyze the triphosphorylation of RNA 5''-hydroxyl groups using Tmp were obtained by in vitro selection. One ribozyme (TPR1) was analyzed in more detail. TPR1 catalyzes the triphosphorylation reaction to a rate of 0.013 min^-1 under selection conditions (50 mM Tmp, 100 mM MgCl₂, 22°C). To identify a triphosphorylation ribozyme that catalyzes faster triphosphorylation, and possibly learn about its secondary structure TPR1 was subjected to a doped selection. The resulting ribozyme, TPR1e, contains seven mutations relative to TPR1, displays a previously unidentified duplex that constrains the ribozyme''s structure, and reacts at a 24-fold faster rate than the parent ribozyme. Under optimal conditions (150 mM Tmp, 650 mM MgCl₂, 40°C), the triphosphorylation rate of TRP1e reaches 6.8 min^-1.     

Ribozyme inhibition of alphavirus replication

A model system to examine the expression and antiviral activity of trans-acting ribozymes in mammalian cells has been developed and evaluated. Hairpin ribozymes were engineered to cleave a specific site, identified by a combinatorial activity-based selection method, within genomic and subgenomic RNA species of Sindbis virus. Transiently transfected cells expressed moderate levels of ribozyme (approximately 50,000 molecules/cell) with predominant nuclear localization and a short half-life (23 min). Stable cell lines expressed ribozymes at modest levels (approximately 2,000 molecules/cell). Ribozyme-mediated RNA cleavage activity was detected in cell extracts. Clonal cell lines were challenged with recombinant Sindbis virus, and viral replication was examined using plaque formation and green fluorescent protein assays. Significant inhibition of viral replication was observed in cells expressing the active antiviral ribozyme, and lower levels of inhibition in control cells expressing inactive or irrelevant ribozymes. These findings are consistent with a model in which inhibition of viral replication occurs via ribozyme cleavage of viral RNAs, suggesting that ribozymes may represent useful antiviral agents.     

核酶的22年

核酶发现至今已22年了。1989年的诺贝尔化学奖授于核酶的发现S.Altman和T.Cech。到2004年2月发表有5000多篇有关核酶的研究论和综述。自然界留存的核酶不多,但已能制造出许许多多人工核酶。从1997年人造出‘肽基转移核酶’到2000年根据一系列证据提出‘核糖体是一种核酶’,在理论上和应用上都具有深远意义。核酶出现早于酶（蛋白质）,后来让位于酶的观点,已为数人所接受。在应用上,人们已经设计和制造出各种样的核酶对付各样的疾病,但目前临床应用的极少或几乎没有。     

Ribozyme catalysis via orbital steering

Orbital steering is invoked to explain how the three-dimensional structure of a small self-cleaving RNA, the hammerhead ribozyme, both prevents and enhances RNA autocatalysis. Within the conserved catalytic core of the ribozyme, the position of the 2' oxygen atom of the G8 ribose is observed to be aligned almost perfectly with the phosphorus atom and the 5' oxygen atom of the adjacent A9 phosphate group for self-cleavage via an in-line attack mechanism. Despite this apparent near-perfect atomic positioning, no cleavage takes place. The explanation proposed is that a network of hydrogen bonds in the ribozyme core orients or steers the orbitals containing the electron lone pairs of the attacking nucleophile (the 2' oxygen atom) away from the A9 phosphorus atom, eliminating overlap with the vacant phosphorus d-orbitals despite the near-perfect in-line positioning of the oxygen atom, thus preventing catalysis. Because of the near-perfect atomic positioning of the 2' oxygen atom relative to the phosphate group, orbital steering effects in this case are fortuitously uncoupled from conformational, distance and orientation effects, allowing an assessment of the catalytic power due purely to orbital steering. In contrast, a conformational change at the cleavage site is required to bring the 2' oxygen atom and the scissile phosphate group into atomic positions amenable to an in-line attack mechanism. In addition, the conformationally changed structure must then steer the lone-pair orbitals of the correctly positioned 2' oxygen atom toward the scissile phosphorus atom in order for cleavage to take place. We estimate that fulfillment of each of these two required changes may contribute separately an approximately 1000-fold rate enhancement, potentially accounting for a significant fraction of the catalytic power of this ribozyme. Orbital steering therefore appears to be a general phenomenon that may help to explain catalysis in both ribozymes and protein enzymes in a unified manner.     

Increased Ribozyme Activity in Crowded Solutions

Noncoding RNAs must function in the crowded environment of the cell. Previous small-angle x-ray scattering experiments showed that molecular crowders stabilize the structure of the Azoarcus group I ribozyme, allowing the ribozyme to fold at low physiological Mg²⁺ concentrations. Here, we used an RNA cleavage assay to show that the PEG and Ficoll crowder molecules increased the biochemical activity of the ribozyme, whereas sucrose did not. Crowding lowered the Mg²⁺ threshold at which activity was detected and increased total RNA cleavage at high Mg²⁺ concentrations sufficient to fold the RNA in crowded or dilute solution. After correcting for solution viscosity, the observed reaction rate was proportional to the fraction of active ribozyme. We conclude that molecular crowders stabilize the native ribozyme and favor the active structure relative to compact inactive folding intermediates.     

逆转录病毒载体介导胸苷磷酸化酶在胰腺癌细胞表达

人胸腺嘧啶核苷磷酸化酶（ＴＰ）在一些肿瘤组织中活性增高,但其功能目前了解尚少。构建了表达ＴＰ的重组逆转录病毒载体,直接导入人胰腺癌ＰＣ－２细胞,ｍＰＣＲ扩增、Ｓｏｕｔｈｅｒｎ及Ｎｏｒｔｈｅｒｎ印迹和原位杂交证实转染细胞有外源ＴＰ的整合及表达,酶活性检测发现含外源ＴＰ细胞ＴＰ活性比ＰＣ－２细胞的内源性ＴＰ活性高ＴＰ活性高４０－７０倍,生长曲线和＾３Ｈ－ＴｄＲ参入率检测未发现含外源ＴＰ细胞生物学行为的     

抗水稻矮缩病毒的反义核酶及复制酶部分序列的合成、克隆及其水稻表达载体的构建

采用反转录－聚合酶链式反应方法（ＲＴＰ－ＣＲ）,在人工合成的引物引导下,扩增出水稻矮缩病毒基因组第一片段（Ｓ１）全长序列及第五片段的部分序列（ＳＳⅢ）．将扩增的片段分别克隆到克隆载体ｐＧＥＭ７Ｚｆ（＋）及ｐＵＣ１９的ｓｍａｌ位点上,并进行了序列测定。在此基础上,利用ｐＣＲ引入的方法将核酶序列引入到Ｓ５Ⅲ片段反义链上以构成反义核酶基因Ｓ５ⅢＲ,将Ｓ１片段５＇端部分序列（Ｓ１－１）及Ｓ５ⅢＲ基因克隆到植物表达载体ｐＲＯＫⅡ上,构建成水稻转化载体ｐＲＯＫ－Ｓ１－１＇及ｐＲＯＫ－Ｓ５ⅢＲ。     

Postnatal Development and Possible Ligand Function of the CNS-Specific Membrane Glycoprotein CNSgp 130

CNSgp 130 is a CNS-specific membrane glycoprotein present in large amounts in the adult mammalian CNS. Using immunohistological techniques, we demonstrated that CNSgp130 is not detectable in the rat cerebellum at birth, and does not appear in the cerebellum until the tenth day of postnatal life. It is expressed first in the white matter of the cerebellar folia, and subsequently (by day 14) it is expressed also in the molecular layer. Expression in the granular layer is not seen until the 18th day of postnatal life, by which time the adult pattern of expression is established. CNSgp130 is also not detectable in the cerebrum at birth. However, it is expressed weakly but diffusely in the cerebrum by the fourth day of life. By the 10th day, there is strong expression in the cerebrum, in marked contrast to its virtual absence from the cerebellum at this stage. By quantitative absorption analysis, CNSgp 130 was undetectable on the day of birth, and increased steadily to 80% of adult values by the 22nd day of postnatal life. Binding studies with pure CNSgp130 demonstrated a Pronase-sensitive ligand in adult chicken brain. This ligand was absent from neonatal rat brain and non-CNS tissues.     

Adenovirus-Mediated Expression of a Ribozyme to c-myb mRNA Inhibits Smooth Muscle Cell Proliferation and Neointima Formation In Vivo

Smooth muscle cell (SMC) proliferation is an important component of restenosis in response to injury after balloon angioplasty. Inhibition of proliferation in vivo can limit neointima hyperplasia in animal models of restenosis. Ribozymes against c-myb mRNA have been shown to be effective inhibitors of SMC proliferation in vitro. The effectiveness of adenovirus as a gene therapy vector in animal models of restenosis is well documented. In order to test the utility of ribozymes to inhibit SMC proliferation by a gene therapy approach, recombinant adenovirus expressing ribozymes against c-myb mRNA was generated and tested both in vitro and in vivo. This adenovirus ribozyme vector is shown to inhibit SMC proliferation in culture and neointima formation in a rat carotid artery balloon injury model of restenosis.     

发夹核酶的研究与应用

核酶 (ｒｉｂｏｚｙｍｅ)是既能特异识别又能特异切割小分子ＲＮＡ的核酸内切酶 ,其本身也是ＲＮＡ ,主要包括发夹核酶、锤头核酶、丁肝病毒、链孢霉属ＶＳ和铅依赖性ＲＮＡ ,共同特点是可逆地切割底物ＲＮＡ的磷酸二酯键 ,生成 5′ ＯＨ和 2′ ,3′ 环磷酸末端。虽然催化产物相似 ,但它们的结构和催化机制却是很不相同的。发夹核酶 (ｈａｉｒｐｉｎｒｉｂｏｚｙｍｅ)发现于三种不同植物ＲＮＡ病毒 ,即烟草环点病毒 (ｔｏｂａｃ ｃｏｒｉｎｇｓｐｏｔｖｉｒｕｓ) ,菊苣黄色斑点病毒型 (ｃｈｉｃｏ ｒｙｙｅｌｌｏｗｍｏｔｔｌｅｖｉｒｕｓｔ…     

Ribozyme pharmacokinetic screening for predicting pharmacodynamic dosing regimens

A significant amount of research has been devoted to the chemical stabilization of synthetic ribozymes, in part, so that applications to systemic disease can be explored. A nuclease-stabilized synthetic hammerhead ribozyme, ANGIOZYME, has been developed which targets the mRNA encoding a vascular endothelial growth factor receptor, Flt-1. Because the stimulation of this receptor may contribute to tumor neovascularization and subsequent tumor growth and metastasis, we have explored the systemic use of ANGIOZYME to down regulate this receptor in a syngeneic model of metastatic cancer. We describe here the application of pharmacokinetic analysis to the selection of a dosing regimen for pharmacodynamic screening in this murine cancer model. These studies demonstrate that the appropriate application of pharmacokinetic analysis is necessary for the optimization of systemic pharmacodynamic studies using synthetic ribozymes.     

Folding Pathways of the Tetrahymena Ribozyme

Like many structured RNAs, the Tetrahymena group I intron ribozyme folds through multiple pathways and intermediates. Under standard conditions in vitro, a small fraction reaches the native state (N) with k_obs ≈ 0.6 min^− 1, while the remainder forms a long-lived misfolded conformation (M) thought to differ in topology. These alternative outcomes reflect a pathway that branches late in folding, after disruption of a trapped intermediate (I_trap). Here we use catalytic activity to probe the folding transitions from I_trap to the native and misfolded states. We show that mutations predicted to weaken the core helix P3 do not increase the rate of folding from I_trap but they increase the fraction that reaches the native state rather than forming the misfolded state. Thus, P3 is disrupted during folding to the native state but not to the misfolded state, and P3 disruption occurs after the rate-limiting step. Interestingly, P3-strengthening mutants also increase native folding. Additional experiments show that these mutants are rapidly committed to folding to the native state, although they reach the native state with approximately the same rate constant as the wild-type ribozyme (~ 1 min^− 1). Thus, the P3-strengthening mutants populate a distinct pathway that includes at least one intermediate but avoids the M state, most likely because P3 and the correct topology are formed early. Our results highlight multiple pathways in RNA folding and illustrate how kinetic competitions between rapid events can have long-lasting effects because the “choice” is enforced by energy barriers that grow larger as folding progresses.     

Ribozyme mediated destruction of RNA in vivo.

Previous studies have demonstrated that high ribozyme to substrate ratios are required for ribozyme inhibitory function in nuclear extracts. To obtain high intracellular levels of ribozymes, tRNA genes, known to be highly expressed in most tissues, have been modified for use as ribozyme expression cassettes. Ribozyme coding sequences were placed between the A and the B box, internal promoter sequences of a Xenopus tRNAMet gene. When injected into the nucleus of frog oocytes, the ribozyme tRNA gene (ribtDNA) produces 'hammerhead' ribozymes which cleave the 5' sequences of U7snRNA, its target substrate, with high efficiency in vitro. Oocytes were coinjected with ribtDNA, U7snRNA and control substrate RNA devoid of a cleavage sequence. It was found that the ribtRNA remained localized mainly in the nucleus, whereas the substrate and the control RNA exited rapidly into the cytoplasm. However, sufficient ribtRNA migrated into the cytoplasm to cleave, and destroy, the U7snRNA. Thus, the action of targeted 'hammerhead' ribozymes in vivo is demonstrated.