对HCMV UL54 mRNA 片段特异性切割的M1GS构建

人巨细胞病毒是一种DNA病毒,在人群中一般呈亚临床感染和潜伏感染。为研究病毒基因沉默工具和抗病毒制剂,以人巨细胞病毒UL54基因mRNA序列设计互补的外部引导序列,共价结合到大肠杆菌来源RNaseP催化核心M1RNA上,从而构建成M1GS-T6核酶。通过对DNA聚合酶UL54基因亚克隆片段转录产物体外切割研究,证实该核酶具备对UL54mRNA片段的特异切割能力。     

HCMV UL97 mRNA序列特异性M1GS的构建及其体外切割活性研究

HCMV UL97基因编码一种蛋白激酶,该酶参与调控病毒DNA的复制和衣壳的形成,且序列异常保守,可作为抗HCMV治疗的重要靶位。基于HCMV UL97 mRNA T3位点附近的序列,设计一段与该位点互补的引导序列（Guide Sequence,GS）,并将其与大肠杆菌核酶P催化亚基（M1 RNA）的3’末端共价连接,构建了一种序列特异性的M1GS（M1-T3）。体外实验证实,所构建的M1-T3可与UL97 mRNA的T3位点特异性结合并产生有效的切割作用。进一步研究M1-T3的结构与其对底物片段靶向切割活性的关系,结果发现在M1 RNA与GS之间增加一段88核苷酸桥连序列的M1-T3（即M1-T3’）,其靶向切割活性大大增强。此外,去除M1-T3 3’末端的CCA序列,其靶向切割活性将基本丧失。上述结果表明,这段桥连序列和3’末端的CCA序列是M1-T3重要的结构元件。这不仅有助于阐明M1GS与其底物的相互作用机制,同时也为进一步评价M1-T3在体内对UL97基因表达及病毒复制的抑制活性奠定了基础。     

GS介导RNase P对人巨细胞病毒ul54基因mRNA的切割作用

引导序列(Guide Sequences,GSs)是与mRNA靶序列互补并引导RNase P切割的小RNA片段。设计与人巨细胞病毒HCMV(Human Cytomegalovirus,HCMV)ul54基因D片段mRNA序列互补的GS,将其共价结合到大肠杆菌来源RNase P催化核心M1 RNA,构建成T7-M1GS核酶。通过对ul54基因D片段转录产物体外切割实验和将T7-M1GS构建在含有U6启动子的逆转录病毒载体,与构建在真核载体pEGFP-N1的ul54基因D片段共转染人宫颈癌细胞系HeLa的体内切割实验,证实该核酶具备对ul54基因D片段mRNA的特异切割能力,为利用核酶治疗HCMV感染提供实验基础。     

RNase P核酶对人巨细胞病毒UL54基因mRNA体外切割作用

外部引导序列(EGSs)是mRNA靶序列互补并引导RNaseP切割的小RNA片段。我们设计与人巨细胞病毒HCMV(Human Cytomegalovirus)UL54基因mRNA序列互补的EGSs,将其与大肠杆菌来源RNaseP催化核心M1RNA构建成M1GS核酶。通过对UL54基因亚克降片转录产物体外切割研究,证实该核酶具备对UL54 mRNA片段的特异切割能力,可以发展成为一种抗病毒试剂。     

核酶对人巨细胞病毒mRNA片段的体外切割

引导序列GSs(GuideSequences)是能与mRNA互补,引导核酶RNaseP催化核心M1RNA对互补区域特异切割的小片段游离RNA。针对人巨细胞病毒HCMV(humancytomegalovirus)DNA聚合酶mRNA序列设计GS,共价结合到大肠杆菌来源M1RNA中,构建成M1GST7核酶。通过对巨细胞病毒DNA聚合酶亚克隆片段转录产物体外切割实验,表明该核酶具备对DNA聚合酶mRNA片段的特异切割能力 。     

HCV特异性M1GS核酶的构建及体外切割活性研究

针对HCV基因组中较为保守的区域-5'UTR,设计一段GS引导序列,并与大肠杆菌RNase P的催化亚基-M1RNA的3'末端共价结合,构建序列特异性M1GS核酶-M1GS-HCV/C20。体外实验证实,所构建的人工核酶对HCV 5'UTR具有明显的靶向切割活性,且这种切割发生于靶序列的特定位点。本研究将为进一步阐明该核酶在胞内的活性、乃至动物模型内评价其抗病毒效果提供实验材料,从而为新型抗HCV药物及反义基因治疗的研究奠定基础。     

In vitro selection of an archaeal RNase P RNA mimics natural variation

Archaeal and bacterial RNase P RNAs are similar in sequence and secondary structure, but in the absence of protein, the archaeal RNAs are much less active and require extreme ionic conditions for activity. To assess how readily the activity of the archaeal RNA alone could be improved by small changes in sequence, in vitro selection was used to generate variants of a Methanobacterium formicicum RNase P RNA: Bacillus subtilus pre-tRNA(Asp) self-cleaving conjugate RNA. Functional variants were generated with a spectrum of mutations that were predominately consistent with natural variation in this RNA. Variants generated from the selection had cleavage rates comparable to that of wild type; variants with improved cleavage rates or lower ionic requirements were not obtained. This suggests that the RNase P RNAs of Bacteria and Archaea are globally optimized and the basis for the large biochemical differences between these two types of RNase P RNA is distributed in the molecule.     

改进型外部引导序列抑制人巨细胞病毒UL49 基因的表达

外部引导序列（EGS）技术（The EGS-based technology）是一种新型的基因沉默技术,能诱导内源性的核酶 P（RNase P）对靶mRNA进行有效切割. 以人类巨细胞病毒（HCMV）UL49基因mRNA片段为靶序列,基于前人实验基础上设计出更为精简与高效的改进型EGS (miniEGS),DNA片段长度仅为12 bp. 构建稳定表达HCMV UL49的细胞系,通过应用荧光定量PCR及Western 印迹分别鉴定miniEGS对内源性UL49的抑制效率.结果显示,miniEGS能在HeLa细胞中能达到很高的转染效率（97.9%）,并且在转染稳定表达UL49的HeLa细胞系后,发现UL49基因的mRNA与蛋白表达水平都出现明显下降（50%）.研究表明, 改进型的EGS序列不仅能有效抑制目的基因的表达,同时因其序列设计的精简性与高效性,可更好地应用到以后的抗病毒研究中.     

抗Caspase-3核酶M1RNA的制备与体内外活性鉴定

为评价抗caspase 3核酶在阻抑细胞凋亡发生中的潜在价值 ,以RNaseP催化亚基M1RNA为模板 ,设计合成 3个特异性针对人caspase 3的核酶pM1 GS716、pM1 GS337和pM1 GS2 35 ,并对它们的体内外切割活性进行探讨 .3 2 P标记的caspase 3基因片段体外转录物作为靶RNA ,体外切割实验表明 ,pM1 GS716和pM1 GS337均有切割活性 ,其中pM1 GS716的切割效率可达到 93% .3个核酶转染HeLa细胞 ,评价其在体内的切割活性 .在TNF α作用下 ,转染pM1 GS716的HeLa细胞内caspase 3mRNA下降了 75 % ,蛋白含量下降了 6 9% ,caspase 3蛋白酶活性下降了 5 2 % .Hoechst 332 5 8染色表明 ,细胞凋亡率较对照明显下降 (分别为 2 1 6± 0 7%和 4 9 4± 0 2 % ,P <0 0 1) .提示体外制备的pM1 GS716具有良好的特异催化切割活性 ,有望通过切割caspase 3而抑制细胞凋亡 .     

Suppression of HIV-1 Replication by a Combination of Endonucleolytic Ribozymes (RNase P and tRNase ZL)

We examined the combinatorial action of RNase P and tRNase ZL-mediated specific inhibition of HIV-1 in cultured cells. We designed two short extra guide sequences (sEGS) that specifically recognize the tat and vif regions of HIV-1 mRNA and mediate the subsequent cleavage of hybridized mRNA by the RNase P and tRNase ZL components. We constructed an RNase P and tRNase ZL-associated vif and tat sEGS expression vector, which used the RNA-polymerase III dependent U6 promoter, as an expression cassette for EGS. Together, the RNase P and tRNase ZL-associated sEGS molecules allow more efficient suppression of HIV-1 mRNA production when separately applied. The possibilities offered by the vector to encode sEGS will provide a powerful tool for gene therapy.     

Novel function of C5 protein as a metabolic stabilizer of M1 RNA

Escherichia coli RNase P is a ribonucleoprotein composed of a large RNA subunit (M1 RNA) and a small protein subunit (C5 protein). We examined if C5 protein plays a role in maintaining metabolic stability of M1 RNA. The sequestration of C5 protein available for M1 RNA binding reduced M1 RNA stability in vivo, and its reduced stability was recovered via overexpression of C5 protein. In addition, M1 RNA was rapidly degraded in a temperature-sensitive C5 protein mutant strain at non-permissive temperatures. Collectively, our results demonstrate that the C5 protein metabolically stabilizes M1 RNA in the cell.     

Binding of C5 Protein to P RNA Enhances the Rate Constant for Catalysis for P RNA Processing of Pre-tRNAs Lacking a Consensus G(+ 1)/C(+ 72) Pair

The RNA subunit of the ribonucleoprotein enzyme ribonuclease P (RNase P (P RNA) contains the active site, but binding of Escherichia coli RNase P protein (C5) to P RNA increases the rate constant for catalysis for certain pre-tRNA substrates up to 1000-fold. Structure-swapping experiments between a substrate that is cleaved slowly by P RNA alone (pre-tRNA^f-met605) and one that is cleaved quickly (pre-tRNA^met608) pinpoint the characteristic C(+ 1)/A(+ 72) base pair of initiator tRNA^f-met as the sole determinant of slow RNA-alone catalysis. Unlike other substrate modifications that slow RNA-alone catalysis, the presence of a C(+ 1)/A(+ 72) base pair reduces the rate constant for processing at both correct and miscleavage sites, indicating an indirect but nonetheless important role in catalysis. Analysis of the Mg²⁺ dependence of apparent catalytic rate constants for pre-tRNA^met608 and a pre-tRNA^met608 (+ 1)C/(+ 72)A mutant provides evidence that C5 promotes rate enhancement primarily by compensating for the decrease in the affinity of metal ions important for catalysis engendered by the presence of the CA pair. Together, these results support and extend current models for RNase P substrate recognition in which contacts involving the conserved (+ 1)G/C(+ 72) pair of tRNA stabilize functional metal ion binding. Additionally, these observations suggest that C5 protein has evolved to compensate for tRNA variation at positions important for binding to P RNA, allowing for tRNA specialization.     

Human DNA Exonuclease TREX1 Is Also an Exoribonuclease That Acts on Single-stranded RNA

3′ repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent K_m of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native tRNA substrates. Previously reported TREX1 crystal structures have revealed that the substrate binding sites are open enough to accommodate the extra hydroxyl group in RNA, further supporting our conclusion that TREX1 acts on RNA. These findings indicate that its RNase activity needs to be taken into account when evaluating the physiological role of TREX1.     

Novel application of Phi29 DNA polymerase: RNA detection and analysis in vitro and in situ by target RNA-primed RCA

We present a novel Phi29 DNA polymerase application in RCA-based target RNA detection and analysis. The 3′→5′ RNase activity of Phi29 DNA polymerase converts target RNA into a primer and the polymerase uses this newly generated primer for RCA initiation. Therefore, using target RNA-primed RCA, padlock probes may be targeted to inner RNA sequences and their peculiarities can be analyzed directly. We demonstrate that the exoribonucleolytic activity of Phi29 DNA polymerase can be successfully applied in vitro and in situ. These findings expand the potential for detection and analysis of RNA sequences distanced from 3′-end.     

Identification of Nucleotide Residues Essential for RNase P Activity from the Hyperthermophilic Archaeon Pyrococcus horikoshii OT3

Ribonuclease P (RNase P) is involved in the processing of the 5′ leader sequence of precursor tRNA (pre-tRNA). We have found that RNase P RNA (PhopRNA) and five proteins (PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38) reconstitute RNase P activity with enzymatic properties similar to those of the authentic ribozyme from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. We report here that nucleotides A40, A41, and U44 at helix P4, and G269 and G270 located at L15/16 in PhopRNA, are, like the corresponding residues in Esherichia coli RNase P RNA (M1RNA), involved in hydrolysis by coordinating catalytic Mg²⁺ ions, and in the recognition of the acceptor end (CCA) of pre-tRNA by base-pairing, respectively. The information reported here strongly suggests that PhopRNA catalyzes the hydrolysis of pre-tRNA in approximately the same manner as eubacterial RNase P RNAs, even though it has no enzymatic activity in the absence of the proteins.     

Revisiting the action of bovine ribonuclease A and pancreatic-type ribonucleases on double-stranded RNA

Single-strand-preferring ribonucleases of the pancreatic type, structurally and/or catalytically similar to bovine RNase A but endowed with a higher protein basicity, are able to degrade double-stranded RNA (dsRNA) or DNA: RNA hybrids under standard assay conditions (0.15 M NaCl, 0.015 M sodium citrate, pH 7), where RNase A is inactive. This enzyme too, however, becomes quite active if assay conditions are slightly modified or its basicity is increased (polyspermine-RNase). In the attempt to review these facts, we have analyzed and discussed the role that in the process have the secondary structure of dsRNA as well as other variables whose influence has come to light in addition to that of the basicity of the enzyme protein, i.e., the ionic strength, the presence of carbohydrates on the RNase molecule, and the structure (monomeric or dimeric) of the enzyme. A possible mechanism by which dsRNAs are attacked by pancreatic-type RNases has been proposed.Abbreviations RNase Ribonuclease - dsRNA Double-stranded RNA - ssRNA Single-stranded RNA - poly(A) poly(U), poly(I) : poly(C) Double-stranded Homopolymers formed between Polyadenylate and Polyurydilate, and Polyinosinate and Polycytidylate, respectively - poly(dA): poly (rU) Double-stranded complex formed between Polydeoxyriboadenylate and Polyribouridylate - poly(A), poly(C) Polyadenylate and Polycytidylate, respectively - poly[d(A-T)] Double-stranded Homopolymers formed between Polydeoxyriboadenilate and Polydeoxyribothymidylate - poly(dA-dT) : poly (dA-dT) Double-stranded alternating copolymers - SSC 0.15 M Sodium Chloride, 0.015 M Sodium Citrate pH 7     

Sequence organisation in nuclear DNA from Physarum polycephalum: Genomic organisation of DNA segments containing foldback sequences

DNA clones containing foldback sequences, derived from Physarum polycephalum nuclear DNA, can be classified according to their pattern of hydridisation to Southern blots of genomic DNA. One group of DNA clones map to unique DNA loci when used as a probe to restriction digests of Physarum nuclear DNA. These cloned segments appear to contain dispersed repetitive sequence elements located at many hundreds of sites in the genome. Similar patterns of hybridisation are generated when these cloned DNA probes are annealed to DNA restriction fragments of genomic DNA obtained from a number of different Physarum strains, indicating that no detectable alteration has occurred at these genomic loci subsequent to the divergence of the strains as a result of the introduction or deletion of mobile genetic elements. However, deletion of segments of some cloned DNA fragments occurs following their propagation in Escherichia coli. A second, distinct group of clones are shown to be derived from highly methylated segments of Physarum DNA which contain very abundant repetitive sequences with regular, though complex, arrangements of restriction sites at their various genomic locations. It is suggested that these DNA segments contain clustered repetitive sequence elements. The results lead to the conclusion that foldback elements in Physarum DNA are located in segments of the genome which display markedly different patterns of sequence organisation and degree of DNA methylation.     

Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences

The cellular pool of ribonucleotide triphosphates (rNTPs) is higher than that of deoxyribonucleotide triphosphates. To ensure genome stability, DNA polymerases must discriminate against rNTPs and incorporated ribonucleotides must be removed by ribonucleotide excision repair (RER). We investigated DNA polymerase β (POL β) capacity to incorporate ribonucleotides into trinucleotide repeated DNA sequences and the efficiency of base excision repair (BER) and RER enzymes (OGG1, MUTYH, and RNase H2) when presented with an incorrect sugar and an oxidized base. POL β incorporated rAMP and rCMP opposite 7,8-dihydro-8-oxoguanine (8-oxodG) and extended both mispairs. In addition, POL β was able to insert and elongate an oxidized rGMP when paired with dA. We show that RNase H2 always preserves the capacity to remove a single ribonucleotide when paired to an oxidized base or to incise an oxidized ribonucleotide in a DNA duplex. In contrast, BER activity is affected by the presence of a ribonucleotide opposite an 8-oxodG. In particular, MUTYH activity on 8-oxodG:rA mispairs is fully inhibited, although its binding capacity is retained. This results in the reduction of RNase H2 incision capability of this substrate. Thus complex mispairs formed by an oxidized base and a ribonucleotide can compromise BER and RER in repeated sequences.