野田村病毒RNA的复制机制

野田村病毒科Nodaviradae分为2个属,分别为主要感染昆虫的α野田村病毒属(Alphanodavirus)和主要感染鱼类的β野田村病毒属(Betanodavirus)。野田村病毒的基因组由2条单链正义RNA分子(RNA1和RNA2)所组成,RNA1编码蛋白A,即病毒负责复制病毒两条基因组的依赖RNA的RNA聚合酶催化亚基。RNA2编码衣壳前体蛋白α,此前体蛋白α先组装成原病毒粒子,再经历一次自我催化的成熟切割成2个病毒的衣壳蛋白β和γ,就成了成熟的有感染性的病毒粒子。在RNA复制过程中,从RNA1的3′末端会合成一个不被包装进病毒粒子的亚基因组RNA3。RNA1能在无RNA2的情况下自我复制,并持续地产生亚基因组RNA3,RNA3的合成采取的是提前终止机制。本文还介绍了野田村病毒复制的调节、非结构蛋白的功能和病毒复制在细胞内的定位。     

黄病毒属病毒复制子载体研究进展

RNA复制子是一种能自主复制的RNA载体,保留了病毒非结构蛋白(复制/转录酶)基因,而结构蛋白基因缺失或由外源抗原基因替代,复制/转录酶可控制载体RNA在细胞质中高水平复制以及外源基因的高水平表达。在黄病毒属病毒感染性克隆基础上,其复制子载体得到了成功的构建。黄病毒属病毒复制子为病毒基因组结构功能研究、表达载体构建、假病毒包装及新型疫苗制备等提供了新的技术平台。本文综述黄病毒属病毒复制子的构建原理、方法及应用。     

黄瓜绿斑驳花叶病毒辽宁分离物外壳蛋白基因与3'非编码区的序列分析

黄瓜绿斑驳花叶病毒(Cucumber green mottle mosaic virus, CGMMV) 为烟草花叶病毒属(Tobamovirus)成员,Tobamovirus属病毒基因组至少编码4个蛋白,靠近5'端的126 kDa和183 kDa两个蛋白与病毒的复制有关,其中183 kDa是由126 kDa 蛋白终止子超读产生的;另外两个蛋白分别为约30 kDa的移动蛋白(Movement protein, MP)和约17.5 kDa 外壳蛋白(Coat protein, CP),这两个蛋白分别由不同的亚基因组RNA表达产生;病毒基因组5'和3'端均含有一段非编码区(Noncoding region, NCR),5'端含帽子结构,3'端有一个可接受组氨酸的类似tRNA状结构[1].     

昆津病毒复制子——一种新型病毒载体

病毒复制子 (Replicon) 是指来源于病毒基因组的能够自主复制的RNA分子,保留了病毒非结构蛋白基因,而结构蛋白基因缺失或由外源基因替代。昆津病毒 (Kunjun virus) 为黄病毒科黄病毒属成员,其复制子具有表达效率高、细胞毒性低、遗传稳定等特点,在病毒基因组复制调控机制、外源蛋白表达、新型疫苗和基因治疗等领域得到了广泛应用。以下就昆津病毒复制子系统的构建、特性及应用方面的研究进展作一综述。     

黄病毒基因组非编码区的结构与功能研究进展

黄病毒科黄病毒属是由一组含单股正链RNA基因组的囊膜病毒组成,包括登革病毒、流行性乙型脑炎病毒、寨卡病毒、西尼罗病毒、黄热病病毒等,经由虫媒传播,可引起人类和动物的严重虫媒病毒病。黄病毒基因组由1个开放阅读框、5′非编码区和3′非编码区三部分组成。5′和3′非编码区含有病毒基因组复制所必需的启动元件;高度结构化的3′非编码区负责黄病毒亚基因组RNA的产生,从而有助于病毒逃避宿主免疫反应;此外3′非编码区还可作为疫苗研究的靶标。鉴于非编码区在黄病毒的蛋白翻译、基因组复制和免疫调节中发挥的重要作用,本文就黄病毒基因组非编码区的结构与功能最新研究进展作一简要综述。     

RNA噬菌体病毒样颗粒包装机制及其应用研究进展

RNA噬菌体是一类结构简单的较小病毒,病毒衣壳为T=3的20面体对称结构,由180拷贝的衣壳蛋白亚基组成,其基因组为正义单链RNA,约含有3500个核苷酸,具有mRNA的作用,编码4种蛋白:病毒衣壳蛋白,成熟酶蛋白,复制酶亚基和裂解蛋白.这些噬菌体最初从大肠埃希菌属中分离出,尽管后来在柄杆菌属和假单胞菌属中也被陆续发现,但迄今为止,对大肠埃希菌噬菌体的研究最为广泛和透彻,根据血清学和生化性质的不同,此类噬菌体可被分成4个类群.     

甲型流行性感冒病毒NS蛋白研究进展

甲型流行性感冒(流感)病毒基因组由8个分节段的负链RNA组成,共编码10种蛋白,其中在病毒复制的早期即有NP蛋白和NS1蛋白的大量表达,提示这两种蛋白在病毒复制过程中及与细胞蛋白的相互作用中发挥着重要的功能.RNA第8节段编码两种蛋白,即非结构蛋白1(NS1)和2(NS2).     

大麦黄矮病毒GAV基因组全序列测定及其结构分析

测定了在中国分离得到由麦二叉蚜和麦长管蚜传播的大麦黄矮病毒GAV的基因组核苷酸全序列, 该病毒分离物的RNA由5685个核苷酸组成, 内含6个开放阅读框架(ORF)和4个非编码区(UTR), 基因组大小和结构与黄症病毒属(Luteovirus)的大麦黄矮病毒PAV(BYDV-PAV)和MAV(BYDV-MAV)相似. 序列分析表明, 它与BYDV-MAV的PS1分离物基因组序列的同源性最高. 在6个开放阅读框架中, 除ORF6核苷酸序列同源性为72.0%外, 其他ORF的核苷酸序列同源性均大于90%. 两者全基因组的同源性为90.4%. 推导的编码产物氨基酸序列同源性除P6和通读蛋白(RTP)分别为67.4%和87.4%外, 其他均大于90%, 其中外壳蛋白(CP)为95.5%. 根据与BYDV-MAV的相似性, BYDV-GAV应是一种与BYDV-MAV类似的病毒.     

丙型肝炎病毒非结构蛋白5B的研究进展

已知丙型肝炎病毒非结构蛋白(NS5B)具有RNA依赖的RNA聚合酶的功能,负责病毒基因组的复制。通过体外表达及晶体衍射分析,目前对NS5B的三维结构已有了清晰的描述,对顺B催化该病毒基因组复制的分子机制也有了初步了解;对RNA聚合酶抑制物的研究将为人工设计特异性的抗该病毒药物奠定扎实基础。     

登革病毒非结构蛋白NS3研究进展

登革病毒非结构蛋白NS3是一种多功能蛋白,N端具有Ser蛋白酶活性,C端具有RNA解旋酶及NTP磷酸酶、5'RNA-Z磷酸酶等活性,参与病毒前体的加工和病毒RNA的复制及基因组RNA的5’端加帽。NS3具有良好的免疫原性,存在多个登革病毒特异性CD4^ ,CD8^ T细胞表位,且多具有型间交叉免疫特性。登革病毒非结构蛋白NS3已成为有吸引力的抗病毒靶标。     

Similarities in the genomic sequence and coat protein structure of plant virsuses

The genomic sequences of several RNA plant viruses including cucumber mosaic virus, brome mosaic virus, alfalfa mosaic virus and tobacco mosaic virus have become available recently. The former two viruses are icosahedral while the latter two are bullet and rod shaped, respectively in particle morphology. The non-structural 3a proteins of cucumber mosaic virus and brome mosaic virus have an amino acid sequence homology of 35% and hence are evolutionarily related. In contrast, the coat proteins exhibit little homology, although the circular dichroism spectrum of these viruses are similar. The non-coding regions of the genome also exhibit variable but extensive homology. Comparison of the brome mosaic virus and alfalfa mosaic virus sequences reveals that they are probably related although with a much larger evolutionary distance. The polypeptide folds of the coat protein of three biologically distinct isometric plant viruses, tomato Bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been shown to display a striking resemblance. All of them consist of a topologically similar 8-standard β-Barrel. The implications of these studies to the understanding of the evolution of plant viruses will be discussed.     

A snapshot of viral evolution from genome analysis of the tectiviridae family

The origin, evolution and relationships of viruses are all fascinating topics. Current thinking in these areas is strongly influenced by the tailed double-stranded (ds) DNA bacteriophages. These viruses have mosaic genomes produced by genetic exchange and so new natural isolates are quite dissimilar to each other, and to laboratory strains. Consequently, they are not amenable to study by current tools for phylogenetic analysis. Less attention has been paid to the Tectiviridae family, which embraces icosahedral dsDNA bacterial viruses with an internal lipid membrane. It includes viruses, such as PRD1, that infect Gram-negative bacteria, as well as viruses like Bam35 with Gram-positive hosts. Although PRD1 and Bam35 have closely related virion morphology and genome organization, they have no detectable sequence similarity. There is strong evidence that the Bam35 coat protein has the "double-barrel trimer" arrangement of PRD1 that was first observed in adenovirus and is predicted to occur in other viruses with large facets. It is very likely that a single ancestral virus gave rise to this very large group of viruses. The unprecedented degree of conservation recently observed for two Bam35-like tectiviruses made it important to investigate those infecting Gram-negative bacteria. The DNA sequences for six PRD1-like isolates (PRD1, PR3, PR4, PR5, L17, PR772) have now been determined. Remarkably, these bacteriophages, isolated at distinctly different dates and global locations, have almost identical genomes. The discovery of almost invariant genomes for the two main Tectiviridae groups contrasts sharply with the situation in the tailed dsDNA bacteriophages. Notably, it permits a sequence analysis of the isolates revealing that the tectiviral proteins can be dissected into a slowly evolving group descended from the ancestor, the viral self, and a more rapidly changing group reflecting interactions with the host.     

Genomic organization of GB viruses A and B: two new members of the Flaviviridae associated with GB agent hepatitis.

The genomes of two positive-strand RNA viruses have recently been cloned from the serum of a GB agent-infected tamarin by using representational difference analysis. The two agent, GB viruses A and B (GBV-A and GBV-B, respectively), have genomes of 9,493 and 9,143 nucleotides, respectively, and single large open reading frames that encode potential polyprotein precursors of 2,972 and 2,864 amino acids, respectively. The genomes of these agents are organized much like those of other pestiviruses and flaviviruses, with genes predicted to encode structural and nonstructural proteins located at the 5' and 3' ends, respectively. Amino acid sequence alignments and subsequent phylogenetic analysis of the RNA-dependent RNA polymerases (RdRps) of GBV-A and GBV-B show that they possess conserved sequence motifs associated with supergroup II RNA polymerases of positive-strand RNA viruses. On the basis of similar analyses, the GBV-A- and GBV-B-encoded helicases show significant identity with the supergroup II helicases of positive-strand RNA viruses. Within the supergroup II RNA polymerases and helicases, GBV-A and GBV-B are most closely related to the hepatitis C virus group. Across their entire open reading frames, the GB agents exhibit 27% amino sequence identity to each other, approximately 28% identity to hepatitis C virus type 1, and approximately 20% identity to either bovine viral diarrhea virus or yellow fever virus. The degree of sequence divergence between GBV-A and GBV-B and other Flaviviridae members demonstrates that the GB agents are representatives of two new genera within the Flaviviridae family.     

Variable region of betanodavirus RNA2 is sufficient to determine host specificity

Betanodaviruses, the causative agents of viral nervous necrosis in marine fish, have bipartite positive-sense RNA genomes. The viruses have been classified into 4 distinct types based on nucleotide sequence similarities in the variable region (the so-called T4 region) of the smaller genomic segment RNA2 (1.4 kb). Betanodaviruses have marked host specificity, although the primary structures of the viral RNAs and encoded proteins are similar among the viruses. We have previously demonstrated, using reassortants between striped jack nervous necrosis virus (SJNNV) and redspotted grouper nervous necrosis virus (RGNNV), that RNA2, which encodes the coat protein, strictly controls host specificity. However, because RNA2 is large, we were unable to propose a mechanism underlying this RNA2-based host specificity. To identify the RNA2 region that controls host specificity, we constructed RNA2 chimeric viruses from SJNNV and RGNNV and tested their infectivity in the original host fish, striped jack Pseudocaranx dentex and sevenband grouper Epinephelus septemfasciatus. Among these chimeric viruses, SJNNV mutants containing the variable region of RGNNV RNA2 infected sevenband grouper larvae in a manner similar to RGNNV, while RGNNV mutants containing the variable region of SJNNV RNA2 infected striped jack larvae in a manner similar to SJNNV. Immunofluorescence microscopic studies using anti-SJNNV polyclonal antibodies revealed that these chimeric viruses multiplied in the brains, spinal cords and retinas of the infected fish, as in infections by the parental viruses. These results indicate that the variable region of RNA2 is sufficient to control host specificity in SJNNV and RGNNV.     

The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae

In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article.     

Large conformational changes in the maturation of a simple RNA virus, nudaurelia capensis omega virus (NomegaV)

An assembly intermediate of a small, non-enveloped RNA virus has been discovered that exhibits striking differences from the mature virion. Virus-like particles (VLPs) of Nudaurelia capensis omega virus (NomegaV), a T=4 icosahedral virus infecting Lepidoptera insects, were produced in insect cells using a baculovirus vector expressing the coat protein. A procapsid form was discovered when NomegaV VLPs were purified at neutral pH conditions. These VLPs were fragile and did not undergo the autoproteolytic maturation that occurs in the infectious virus. Electron cryo-microscopy (cryoEM) and image analysis showed that, compared with the native virion, the VLPs were 16% larger in diameter, more rounded, porous, and contained an additional internal domain. Upon lowering the pH to 5.0, the VLP capsids became structurally indistinguishable from the authentic virion and the subunits autoproteolyzed. The NomegaV protein subunit coordinates, which were previously determined crystallographically, were modelled into the 28 A resolution cryoEM map of the procapsid. The resulting pseudo-atomic model of the NomegaV procapsid demonstrated the large rearrangements in quaternary and tertiary structure needed for the maturation of the VLPs and presumably of the virus. Based on this model, we propose that electrostatically driven rearrangements of interior helical regions are responsible for the large conformational change. These results are surprising because large structural rearrangements have not been found in the maturation of any other small RNA viruses. However, similarities of this conformational change to the maturational processes of more complex DNA viruses (e.g. bacteriophages and herpesvirus) and to the swelling of simple plant viruses suggest that structural changes in icosahedral viruses, which are integral to their function, have similar strategies and perhaps mechanisms.     

Mutually-induced Conformational Switching of RNA and Coat Protein Underpins Efficient Assembly of a Viral Capsid

Single-stranded RNA viruses package their genomes into capsids enclosing fixed volumes. We assayed the ability of bacteriophage MS2 coat protein to package large, defined fragments of its genomic, single-stranded RNA. We show that the efficiency of packaging into a T = 3 capsid in vitro is inversely proportional to RNA length, implying that there is a free-energy barrier to be overcome during assembly. All the RNAs examined have greater solution persistence lengths than the internal diameter of the capsid into which they become packaged, suggesting that protein-mediated RNA compaction must occur during assembly. Binding ethidium bromide to one of these RNA fragments, which would be expected to reduce its flexibility, severely inhibited packaging, consistent with this idea. Cryo-EM structures of the capsids assembled in these experiments with the sub-genomic RNAs show a layer of RNA density beneath the coat protein shell but lack density for the inner RNA shell seen in the wild-type virion. The inner layer is restored when full-length virion RNA is used in the assembly reaction, implying that it becomes ordered only when the capsid is filled, presumably because of the effects of steric and/or electrostatic repulsions. The cryo-EM results explain the length dependence of packaging. In addition, they show that for the sub-genomic fragments the strongest ordered RNA density occurs below the coat protein dimers forming the icosahedral 5-fold axes of the capsid. There is little such density beneath the proteins at the 2-fold axes, consistent with our model in which coat protein dimers binding to RNA stem-loops located at sites throughout the genome leads to switching of their preferred conformations, thus regulating the placement of the quasi-conformers needed to build the T = 3 capsid. The data are consistent with mutual chaperoning of both RNA and coat protein conformations, partially explaining the ability of such viruses to assemble so rapidly and accurately.     

Nodavirus-induced membrane rearrangement in replication complex assembly requires replicase protein a, RNA templates, and polymerase activity

Positive-strand RNA [(+)RNA] viruses invariably replicate their RNA genomes on modified intracellular membranes. In infected Drosophila cells, Flock House nodavirus (FHV) RNA replication complexes form on outer mitochondrial membranes inside ～50-nm, virus-induced spherular invaginations similar to RNA replication-linked spherules induced by many (+)RNA viruses at various membranes. To better understand replication complex assembly, we studied the mechanisms of FHV spherule formation. FHV has two genomic RNAs; RNA1 encodes multifunctional RNA replication protein A and RNA interference suppressor protein B2, while RNA2 encodes the capsid proteins. Expressing genomic RNA1 without RNA2 induced mitochondrial spherules indistinguishable from those in FHV infection. RNA1 mutation showed that protein B2 was dispensable and that protein A was the only FHV protein required for spherule formation. However, expressing protein A alone only "zippered" together the surfaces of adjacent mitochondria, without inducing spherules. Thus, protein A is necessary but not sufficient for spherule formation. Coexpressing protein A plus a replication-competent FHV RNA template induced RNA replication in trans and membrane spherules. Moreover, spherules were not formed when replicatable FHV RNA templates were expressed with protein A bearing a single, polymerase-inactivating amino acid change or when wild-type protein A was expressed with a nonreplicatable FHV RNA template. Thus, unlike many (+)RNA viruses, the membrane-bounded compartments in which FHV RNA replication occurs are not induced solely by viral protein(s) but require viral RNA synthesis. In addition to replication complex assembly, the results have implications for nodavirus interaction with cell RNA silencing pathways and other aspects of virus control.     

Differential translation of turnip yellow mosaic virus mRNAs in vitro

Total TYMV RNA was incubated in a reticulocyte lysate, and the initiation peptides of the main proteins synthesized $\text{in vitro}$ (195 K, 150 K and 20 K daltons) analyzed after tryptic digestion. The 195 K and the 150 K dalton proteins present analogous patterns, different from the one obtained with the 20 K dalton protein (coat protein), suggesting that only one initiation site exists on the genomic RNA for the synthesis of the two high molecular proteins. The results of competition experiments between genomic and coat protein mRNA indicate that the ribosomes have a much greater affinity for the coat protein mRNA. This may represent a regulatory mechanism for the preferential amplification of coat protein synthesis in the infected cells.