HCV全长cDNA细胞培养适应性突变体的构建及其体外转录制备感染性RNA的研究

运用重叠延伸PCR方法对HCV全长基因组cDNANS3和NS5A上的E1202G、T1280I和S2197P进行细胞培养适应性突变,构建含有细胞培养适应性突变的HCV全长基因组cDNA,体外转录制备RNA,脂质体法转染人肝癌细胞Huh-7,以RT-PCR检测HCV正、负链RNA,间接免疫荧光法和Western blot检测细胞内HCVNS3蛋白的表达。结果证明,转染后细胞内可间断检测到HCV正、负链RNA及HCVNS3蛋白的表达,且突变体RNA与未突变的HCVRNA相比,明显具有更高的复制效率和蛋白表达。该研究为后续HCV体外培养体系的研究提供了可在细胞内高效自主复制的HCV病毒模板。     

丙型肝炎病毒非结构蛋白NS3/4A的研究进展

丙型肝炎病毒(HCV)非结构蛋白NS3共有631个氨基酸组成,具有丝氨酸蛋白酶、三磷酸核苷酶(NTpase)和螺旋酶(Helicase)的功能,在HCV多聚蛋白的成熟和病毒复制过程中发挥着重要作用.非结构蛋白NS4A,其主要功能就是作为NS3丝氨酸蛋白酶的辅助因子,在HCV多氨酸成熟过程中发挥着不可替代的调节作用.此外,NS3/4A还参与NS5A的超磷酸化修饰过程.     

利用质谱技术鉴定寨卡病毒非结构蛋白NS1的细胞内相互作用蛋白

寨卡病毒(Zika Virus)属于黄病毒科中的黄病毒属,虽然很早就已经被人类所发现,但是一直到2015年在南美巴西的大规模爆发,才引起了广泛的关注.寨卡病毒对人类的感染往往引起包括小头畸形和格林-巴利综合征在内的多种症状.寨卡病毒的基因组为单链正链RNA,其基因组可以编码翻译并剪切加工出3个结构蛋白,分别为膜蛋白,囊膜蛋白和核衣壳蛋白,以及7个非结构蛋白(NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5).相关研究已经证明,NS1蛋白与同属黄病毒属的登革病毒的发病有紧密的联系,而且根据其蛋白结构推测其可能与寨卡病毒穿越血脑屏障有关.因此鉴别NS1与细胞内的相互作用蛋白对于发现寨卡病毒在细胞内的转运,转录,以及装配都有重大的意义.在此,该课题构建并在HEK293细胞中表达包含Flag和Strep两种标签的NS1融合蛋白,通过免疫沉淀的方法将与NS1结合的蛋白利用标签蛋白进行分离,利用高分辨生物质谱技术,对蛋白进行分析鉴定.通过分别带有Flag与Strep标签的相互作用蛋白分析,发现了16个两种标签共同的结合蛋白,其进一步的通路分析证明这些蛋白于与病毒转录、病毒复制和免疫反应多个通路有关,相关的研究结果为今后进一步研究寨卡病毒的复制机制以及开发抗病毒药物提供了重要的参考价值.     

An NS3 protease inhibitor with antiviral effects in humans infected with hepatitis C virus

Hepatitis C virus (HCV) infection is a serious cause of chronic liver disease worldwide with more than 170 million infected individuals at risk of developing significant morbidity and mortality. Current interferon-based therapies are suboptimal especially in patients infected with HCV genotype 1, and they are poorly tolerated, highlighting the unmet medical need for new therapeutics. The HCV-encoded NS3 protease is essential for viral replication and has long been considered an attractive target for therapeutic intervention in HCV-infected patients. Here we identify a class of specific and potent NS3 protease inhibitors and report the evaluation of BILN 2061, a small molecule inhibitor biologically available through oral ingestion and the first of its class in human trials. Administration of BILN 2061 to patients infected with HCV genotype 1 for 2 days resulted in an impressive reduction of HCV RNA plasma levels, and established proof-of-concept in humans for an HCV NS3 protease inhibitor. Our results further illustrate the potential of the viral-enzyme-targeted drug discovery approach for the development of new HCV therapeutics.     

HCV非结构基因NS5分子生物学研究进展

丙型肝炎病毒(HCV)非结构基因5(NSS)区是RNA依赖的RNA聚合酶(RDRP)及一种磷蛋白的编码区,与HCV的复制、致病及抗药性关系密切。就HCV NS5区有关的分子生物学研究进展进行了综述。     

X-ray structure of NS1 from a highly pathogenic H5N1 influenza virus

The recent emergence of highly pathogenic avian (H5N1) influenza viruses, their epizootic and panzootic nature, and their association with lethal human infections have raised significant global health concerns. Several studies have underlined the importance of non-structural protein NS1 in the increased pathogenicity and virulence of these strains. NS1, which consists of two domains-a double-stranded RNA (dsRNA) binding domain and the effector domain, separated through a linker-is an antagonist of antiviral type-I interferon response in the host. Here we report the X-ray structure of the full-length NS1 from an H5N1 strain (A/Vietnam/1203/2004) that was associated with 60% of human deaths in an outbreak in Vietnam. Compared to the individually determined structures of the RNA binding domain and the effector domain from non-H5N1 strains, the RNA binding domain within H5N1 NS1 exhibits modest structural changes, while the H5N1 effector domain shows significant alteration, particularly in the dimeric interface. Although both domains in the full-length NS1 individually participate in dimeric interactions, an unexpected finding is that these interactions result in the formation of a chain of NS1 molecules instead of distinct dimeric units. Three such chains in the crystal interact with one another extensively to form a tubular organization of similar dimensions to that observed in the cryo-electron microscopy images of NS1 in the presence of dsRNA. The tubular oligomeric organization of NS1, in which residues implicated in dsRNA binding face a 20-A-wide central tunnel, provides a plausible mechanism for how NS1 sequesters varying lengths of dsRNA, to counter cellular antiviral dsRNA response pathways, while simultaneously interacting with other cellular ligands during an infection.     

Structure of the catalytic domain of the hepatitis C virus NS2-3 protease

Hepatitis C virus is a major global health problem affecting an estimated 170 million people worldwide. Chronic infection is common and can lead to cirrhosis and liver cancer. There is no vaccine available and current therapies have met with limited success. The viral RNA genome encodes a polyprotein that includes two proteases essential for virus replication. The NS2-3 protease mediates a single cleavage at the NS2/NS3 junction, whereas the NS3-4A protease cleaves at four downstream sites in the polyprotein. NS3-4A is characterized as a serine protease with a chymotrypsin-like fold, but the enzymatic mechanism of the NS2-3 protease remains unresolved. Here we report the crystal structure of the catalytic domain of the NS2-3 protease at 2.3 A resolution. The structure reveals a dimeric cysteine protease with two composite active sites. For each active site, the catalytic histidine and glutamate residues are contributed by one monomer, and the nucleophilic cysteine by the other. The carboxy-terminal residues remain coordinated in the two active sites, predicting an inactive post-cleavage form. Proteolysis through formation of a composite active site occurs in the context of the viral polyprotein expressed in mammalian cells. These features offer unexpected insights into polyprotein processing by hepatitis C virus and new opportunities for antiviral drug design.     

Investigating Genotype 1a HCV Drug Resistance in NS5A Region via Bayesian Inference

Hepatitis C virus(HCV) treatment is on the cutting edge of medicine. Due to the high rate of mutations and low fidelity of HCV replication, resistant strains quickly become dominant in a viral population under the selection pressure of a drug. In this paper, we examined the drug resistance mechanism in the NS5 A region of genotype1 a HCV virus by comparing the sequence data from interferon-ribavirin treated and untreated patients. To find the drug resistance difference, we used innovative Bayesian probability models to detect mutation combinations and inferred detailed interaction structures of these mutations. We aim to provide reference to drug design and mutation mechanism understanding through our work.     

Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease

Most eukaryotic messenger RNA precursors (pre-mRNAs) undergo extensive maturational processing, including cleavage and polyadenylation at the 3'-end. Despite the characterization of many proteins that are required for the cleavage reaction, the identity of the endonuclease is not known. Recent analyses indicated that the 73-kDa subunit of cleavage and polyadenylation specificity factor (CPSF-73) might be the endonuclease for this and related reactions, although no direct data confirmed this. Here we report the crystal structures of human CPSF-73 at 2.1 A resolution, complexed with zinc ions and a sulphate that might mimic the phosphate group of the substrate, and the related yeast protein CPSF-100 (Ydh1) at 2.5 A resolution. Both CPSF-73 and CPSF-100 contain two domains, a metallo-beta-lactamase domain and a novel beta-CASP (named for metallo-beta-lactamase, CPSF, Artemis, Snm1, Pso2) domain. The active site of CPSF-73, with two zinc ions, is located at the interface of the two domains. Purified recombinant CPSF-73 possesses RNA endonuclease activity, and mutations that disrupt zinc binding in the active site abolish this activity. Our studies provide the first direct experimental evidence that CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.     

丙型肝炎病毒NS3基因真核质粒的构建及其在人肝细胞中的诱导表达

目的：进行丙型肝炎病毒非结构蛋白3基因真核表达载体的构建,并分析其在体外培养的人肝细胞中的表达。方法：从含有丙肝病毒全长基因的重组质粒pBRTM／HCV1-3011表达载体中PCR扩增出HCVNS3基因片段,将其与表达载体pcDNA3．1（-）重组,得到重组的真核表达载体pcDNA3．1（-）／NS3。然后采用阳离子多聚体将其转染人肝细胞QSG7701,以免疫组织化学SP法及Western Blotting检测HCVNS3蛋白的表达。结果：所得到的NS3片段正确,序列正确,所构建的真核质粒成功转染QSG7701细胞并表达蛋白,表达的NS3蛋白相对分子质量为70000。结论：成功构建了丙型肝炎病毒非结构蛋白3基因的真核表达载体pcDNA3．1（-）／NS3,并且该载体在体外培养的人肝细胞中能有效表达特异性HCVNS3蛋白。     

Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA

Innate immune defences are essential for the control of virus infection and are triggered through host recognition of viral macromolecular motifs known as pathogen-associated molecular patterns (PAMPs). Hepatitis C virus (HCV) is an RNA virus that replicates in the liver, and infects 200 million people worldwide. Infection is regulated by hepatic immune defences triggered by the cellular RIG-I helicase. RIG-I binds PAMP RNA and signals interferon regulatory factor 3 activation to induce the expression of interferon-alpha/beta and antiviral/interferon-stimulated genes (ISGs) that limit infection. Here we identify the polyuridine motif of the HCV genome 3' non-translated region and its replication intermediate as the PAMP substrate of RIG-I, and show that this and similar homopolyuridine or homopolyriboadenine motifs present in the genomes of RNA viruses are the chief feature of RIG-I recognition and immune triggering in human and murine cells. 5' terminal triphosphate on the PAMP RNA was necessary but not sufficient for RIG-I binding, which was primarily dependent on homopolymeric ribonucleotide composition, linear structure and length. The HCV PAMP RNA stimulated RIG-I-dependent signalling to induce a hepatic innate immune response in vivo, and triggered interferon and ISG expression to suppress HCV infection in vitro. These results provide a conceptual advance by defining specific homopolymeric RNA motifs within the genome of HCV and other RNA viruses as the PAMP substrate of RIG-I, and demonstrate immunogenic features of the PAMP-RIG-I interaction that could be used as an immune adjuvant for vaccine and immunotherapy approaches.     

Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase

The NS3 helicase is essential for cytoplasmic RNA replication by the hepatitis C virus, and it is a representative member of helicase superfamily 2 (SF2). NS3 is an important model system for understanding unwinding activities of DExH/D proteins, and it has been the subject of extensive structural and mutational analyses. Despite intense interest in NS3, the molecular and kinetic mechanisms for RNA unwinding by this helicase have remained obscure. We have developed a combinatorial, time-resolved approach for monitoring the microscopic behaviour of a helicase at each nucleotide of a duplex substrate. By applying this analysis to NS3, we have independently established the 'physical' and 'kinetic' step size for unwinding of RNA (18 base pairs, in each case), which we relate to the stoichiometry of the functional, translocating species. Having obtained microscopic unwinding rate constants at each position along the duplex, we demonstrate that NS3 unwinds RNA through a highly coordinated cycle of fast ripping and local pausing that occurs with regular spacing along the duplex substrate, much like the stepping behaviour of cytoskeletal motor proteins.     

丙型肝炎病毒感染与ras,p53基因表达的相关性

为了探讨丙型肝炎病毒（ＨＣＶ）感染与肝细胞癌（ＨＣＣ）的关系以及ＨＣＶ可能的致癌机理，采用免疫组织化学方法及巢式ＰＣＲ法检测了１３６例肝细胞癌等肝病组织中的ＨＣＶＮＳ３抗原、ＨＣＶＲＮＡ及Ｐ２１、Ｐ５３蛋白。结果表明，肝细胞癌及癌周肝组织中有ＨＣＶＮＳ３抗原及ＨＣＶＲＮＡ检出，支持ＨＣＶ与ＨＣＣ的关联。Ｐ２１在ＨＣＣ、肝炎后肝硬化、慢性肝炎、体质性黄疸各组中的检出率随病变的加重而逐渐增高，在ＨＣＣ的癌及癌周组织中Ｐ２１呈致密的过量表达，提示ｒａｓ癌基因的激活在ＨＣＣ的发生过程中起一定作用。Ｐ５３的阳性率较Ｐ２１低，但ｐ５３的突变似乎也是肝癌发生的协同因素之一。组织中Ｐ２１的过量表达与ＨＣＶＮＳ３抗原阳性检出呈正相关，ＨＣＶＮＳ３抗原与Ｐ２１的这种关联提示，ＨＣＶ感染作为ＨＣＣ的密切相关因素之一，可能通过激活某些癌基因或使某些抑癌基因突变而致肝细胞癌变     

HCV非结构区NS3-5B蛋白的真核表达载体构建及其在BHK-21细胞中的表达

通过PCR方法扩增出HCV NS3-5b全长基因序列,克隆入真核表达载体pIRES2-EGFP中,构建重组质粒pIRES2-EGFP-NS3-5b。利用脂质体将该质粒转染至BHK-21细胞,通过荧光成像和Western Blot检测NS3-5b基因的表达。结果显示成功构建了真核表达质粒pIRES2-EGFP-NS3-5b,并且NS3/4A蛋白和NS5B蛋白得到特异性表达,为下一步建立HCV RdRp活性的细胞评价系统和动物模型评价系统奠定了实验和理论基础。     

Domain of E. coli DNA polymerase I showing sequence homology to T7 DNA polymerase

Escherichia coli contains three DNA polymerases that differ in their size, ability to interact with accessory proteins and biological function. Monomeric DNA polymerase I (Pol I) has a relative molecular mass (Mr) of 103,000 (103K) and is involved primarily in the repair of damaged DNA and the processing of Okazaki fragments; polymerase II is of Mr 120K, and polymerase III has a Mr of 140K, is responsible for the replication of the DNA chromosome and is just one of several proteins that are required for replication. DNA polymerases from bacteriophage as well as those of eukaryotic viral and cellular origin also differ with respect to their size and the number of associated proteins that are required for them to function in replication. However, the template-directed copying of DNA is identical in all cases. The crystal structure of the large proteolytic fragment of Pol I shows that it consists of two domains, the larger of which contains a deep crevice whose dimensions are such that it can bind duplex DNA. The T7 polymerase consists of two subunits, the 80K gene 5 protein and the host-encoded 12K thioredoxin of E. coli. We show here that there is an amino acid sequence homology between at least eight polypeptide segments that form the large cleft in the Klenow fragment and polypeptides in T7 DNA polymerase gene 5 protein, suggesting that this domain evolved from a common precursor. The parts of the Pol I and T7 DNA polymerase molecules that bind the DNA substrate appear to share common structural features, and these features may be shared by all of these varied DNA polymerases.     

Structure of the SRP19 RNA complex and implications for signal recognition particle assembly

The signal recognition particle (SRP) is a phylogenetically conserved ribonucleoprotein. It associates with ribosomes to mediate co-translational targeting of membrane and secretory proteins to biological membranes. In mammalian cells, the SRP consists of a 7S RNA and six protein components. The S domain of SRP comprises the 7S.S part of RNA bound to SRP19, SRP54 and the SRP68/72 heterodimer; SRP54 has the main role in recognizing signal sequences of nascent polypeptide chains and docking SRP to its receptor. During assembly of the SRP, binding of SRP19 precedes and promotes the association of SRP54 (refs 4, 5). Here we report the crystal structure at 2.3 A resolution of the complex formed between 7S.S RNA and SRP19 in the archaeon Methanococcus jannaschii. SRP19 bridges the tips of helices 6 and 8 of 7S.S RNA by forming an extensive network of direct protein RNA interactions. Helices 6 and 8 pack side by side; tertiary RNA interactions, which also involve the strictly conserved tetraloop bases, stabilize helix 8 in a conformation competent for SRP54 binding. The structure explains the role of SRP19 and provides a molecular framework for SRP54 binding and SRP assembly in Eukarya and Archaea.     

The location of the polio genome protein in viral RNAs and its implication for RNA synthesis.

Evidence is presented that a small protein (VPg) is covalently attached to the 5'-terminal oligonucleotide VPg-pU-U-A-A-A-A-C-A-Gp of the polio genome, to nascent strands of the polio replicative intermediate and to poly(U) of minus strands. A model of polio RNA replication is proposed implicating VPg in initiation of RNA symthesis, possibly as primer.