Virus with a Multipartite Superhelical DNA Genome from the Ichneumonid Parasitoid Campoletis sonorensis

Virus was isolated from the lumen of the calyx region of ovaries in the parasitoid wasp Campoletis sonorensis (Hymenoptera: Ichneumonidae), and the nature of the viral DNA was analyzed. DNA purified from a homogeneous band of virus contained double-stranded superhelical molecules which were polydisperse in molecular weight. At least 25 different covalently closed circles were present, ranging in molecular weight from 4.0 x 10(6) to 13.6 x 10(6). The virus DNA was analyzed with restriction enzymes, and the nature of the genetic complexity was evaluated by Southern blot hybridization of native superhelical and relaxed circular virus DNA and of SalI- and HindIII-digested DNA. The data suggest that most of the variously sized covalently closed DNAs were composed primarily of nonhomologous sequences. The different size classes of covalently closed viral DNAs did not appear to exist in equimolar concentrations. However, there was no evidence from observation of virus particles in the electron microscope or from virus fractionation experiments that a mixture of viruses was present in the calyx fluid. The results from this study suggest' that the virus isolated from C. sonorensis, like those isolated from other endoparasitic hymenoptera, may belong to a new class of DNA viruses in which the genome is multipartite, with each DNA existing as a superhelical molecule.     

Homologous Terminal Sequences in the Double-Stranded RNA Genome Segments of Cytoplasmic Polyhedrosis Virus of the Silkworm Bombyx mori

The 3′-terminal regions (20 to 32 residues) of the genome double-stranded RNA (dsRNA) segments of cytoplasmic polyhedrosis virus were sequenced. The dsRNAs, which were labeled at their 3′ termini by incubation with [5′-³²P]pCp and T4 RNA ligase, were denatured and resolved into the plus and minus strands by agarose-urea gel electrophoresis. Ten single-stranded RNAs thus obtained from the five dsRNA segments IV, V, VIII, IX, and X were sequenced by postlabeling methods. Common 3′-terminal sequences, -GUUAGCC and -UUACU, were found in the plus and minus strands, respectively, of all five dsRNA segments. However, adjacent sequences diverged and were considerably variable. The homologous sequences found in the 3′ end may be important recognition signals for viral RNA polymerases and for assembly of the genome segments.     

Physical Analysis of the Campoletis sonorensis Virus Multipartite Genome and Identification of a Family of Tandemly Repeated Elements

This report is an analysis of cross-hybridizing sequences found within the 28 superhelical (SH) DNAs of the multipartite genome of the polydnavirus Campoletis sonorensis virus (CsV). A Southern cross-blot hybridization analysis showed that the majority of CsV EcoRI restriction fragments cross-hybridize to multiple EcoRI fragments. These sequence homologies were analyzed by hybridizing recombinant clones of the CsV SH DNAs B, H, M, and O¹ to Southern blots of undigested CsV DNA, using different hybridization stringencies. The results indicated that homologous regions among the SH DNAs include closely related sequences that are detectable under stringent conditions and related but more diverged sequences which are only detectable under reduced stringencies. A sequence that hybridized to the majority of the CsV SH DNAs was identified and subcloned from the SH DNAs O¹, H, and B. Nucleotide sequence data revealed that these homologous regions contained a family of imperfectly conserved repeated elements. These repeat elements were arranged singly or in direct tandem arrays and had an average length of 540 base pairs. Within the sequenced regions that contained the repeated elements six putative open reading frames were identified. These results show that the CsV genome consists of SH DNAs with complex sequence interrelationships that may have arisen due to multiple recombinational events.     

Identification of a Plant Viral RNA Genome in the Nucleus

Viruses contain either DNA or RNA as genomes. DNA viruses replicate within nucleus, while most RNA viruses, especially (+)-sense single-stranded RNA, replicate and are present within cytoplasm. We proposed a new thought that is contrary to the common notion that (+)-sense single-stranded RNA viruses are present only in the cytoplasm. In this study, we question whether the genome of a plant RNA virus (non-retroviral) is present in the nucleus of infected cells? Hibiscus chlorotic ringspot virus (HCRSV) RNA was detected in the nucleus of infected cells, as shown by fluorescent in situ hybridization. Western blot using anti-histone 3 and anti-phosphoenolpyruvate carboxylase showed that nuclei were highly purified from mock and HCRSV-infected kenaf (Hibiscus cannabilis L.) leaves, respectively. The p23 and HCRSV coat protein (CP) coding regions were both amplified from total RNA extracted from isolated nuclei. Viral RNA in the nucleus may be used to generate viral microRNAs (vir-miRNAs), as five putative vir-miRNAs were predicted from HCRSV using the vir-miRNAs prediction database. The vir-miRNA (hcrsv-miR-H1-5p) was detected using TaqMan® stem-loop real-time PCR, and by northern blot using DIG-end labeled probe in HCRSV-infected kenaf leaves. Finally, a novel nuclear localization signal (NLS) was discovered in p23 of HCRSV. The NLS interacts with importin α and facilitates viral RNA genome to enter nucleus. We demonstrate the presence of a (+)-sense single-stranded viral RNA within nucleus.     

Hormone-activated Expression of the C-type RNA Tumour Virus Genome

THE concept of vertical transmission of specific viral information, particularly that possibly associated with the induction of malignancy in mice has been postulated. Moreover, it has been hypothesized that this genetic information may be expressed either in the form of whole virus in certain selected laboratory animal strains or as the operon involved in regulating cellular replication (oncogene)¹. To detect this proposed genetically transmitted message, one uses a group specific antisera against the C-type RNA tumour viruses having as one of its components, gs-3, first described by Gerring et al.². A similar group specific antigen has subsequently been reported by Schafer³, Gilden⁴ and Sarma et al.⁵ and designated “interspec”, meaning that the antigen is common to the internal components of the C-type RNA virion of several mammalian species.     

Expression and Processing of a Small Nucleolar RNA from the Epstein-Barr Virus Genome

Small nucleolar RNAs (snoRNAs) are localized within the nucleolus, a sub-nuclear compartment, in which they guide ribosomal or spliceosomal RNA modifications, respectively. Up until now, snoRNAs have only been identified in eukaryal and archaeal genomes, but are notably absent in bacteria. By screening B lymphocytes for expression of non-coding RNAs (ncRNAs) induced by the Epstein-Barr virus (EBV), we here report, for the first time, the identification of a snoRNA gene within a viral genome, designated as v-snoRNA1. This genetic element displays all hallmark sequence motifs of a canonical C/D box snoRNA, namely C/C′- as well as D/D′-boxes. The nucleolar localization of v-snoRNA1 was verified by in situ hybridisation of EBV-infected cells. We also confirmed binding of the three canonical snoRNA proteins, fibrillarin, Nop56 and Nop58, to v-snoRNA1. The C-box motif of v-snoRNA1 was shown to be crucial for the stability of the viral snoRNA; its selective deletion in the viral genome led to a complete down-regulation of v-snoRNA1 expression levels within EBV-infected B cells. We further provide evidence that v-snoRNA1 might serve as a miRNA-like precursor, which is processed into 24 nt sized RNA species, designated as v-snoRNA1^24pp. A potential target site of v-snoRNA1^24pp was identified within the 3′-UTR of BALF5 mRNA which encodes the viral DNA polymerase. V-snoRNA1 was found to be expressed in all investigated EBV-positive cell lines, including lymphoblastoid cell lines (LCL). Interestingly, induction of the lytic cycle markedly up-regulated expression levels of v-snoRNA1 up to 30-fold. By a computational approach, we identified a v-snoRNA1 homolog in the rhesus lymphocryptovirus genome. This evolutionary conservation suggests an important role of v-snoRNA1 during γ-herpesvirus infection.     

Both Genome Segments Contribute to the Pathogenicity of Very Virulent Infectious Bursal Disease Virus

Infectious bursal disease virus (IBDV) causes an economically significant disease of chickens worldwide. Very virulent IBDV (vvIBDV) strains have emerged and induce as much as 60% mortality. The molecular basis for vvIBDV pathogenicity is not understood, and the relative contributions of the two genome segments, A and B, to this phenomenon are not known. Isolate 94432 has been shown previously to be genetically related to vvIBDVs but exhibits atypical antigenicity and does not cause mortality. Here the full-length genome of 94432 was determined, and a reverse genetics system was established. The molecular clone was rescued and exhibited the same antigenicity and reduced pathogenicity as isolate 94432. Genetically modified viruses derived from 94432, whose vvIBDV consensus nucleotide sequence was restored in segment A and/or B, were produced, and their pathogenicity was assessed in specific-pathogen-free chickens. We found that a valine (position 321) that modifies the most exposed part of the capsid protein VP2 critically modified the antigenicity and partially reduced the pathogenicity of 94432. However, a threonine (position 276) located in the finger domain of the virus polymerase (VP1) contributed even more significantly to attenuation. This threonine is partially exposed in a hydrophobic groove on the VP1 surface, suggesting possible interactions between VP1 and another, as yet unidentified molecule at this amino acid position. The restored vvIBDV-like pathogenicity was associated with increased replication and lesions in the thymus and spleen. These results demonstrate that both genome segments influence vvIBDV pathogenicity and may provide new targets for the attenuation of vvIBDVs.     

Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity

Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3’untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3’ UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3’UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3’UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3’ UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs suggests this that interaction is a bona fide target for the design of compounds with antiviral activity.     

植物系统性RNAi的研究进展

RNAi作为反向遗传学手段,以其序列特异性、高效性等特点,在植物基因功能验证、抗病和品种改良等方面发挥了积极作用,RNAi的系统性也同时受到研究者的广泛关注.系统性RNAi(systemic RNA in-terference)传统定义是指沉默信号从一个细胞或一种组织,传递到另外的细胞或同一个体的另外组织中去的现象.本文主要综述植物基因工程研究中应用系统性RNAi技术的研究现状,总结了植物系统性RNAi的特征及沉默效应的抑制.对植物系统性RNAi的研究方法与应用,特别是在植物抗性研究和遗传改良等方面作了重点介绍,并分析了技术存在的限制因素.     

Differing Effects of Herpes Simplex Virus 1 and Pseudorabies Virus Infections on Centrosomal Function

Efficient intracellular transport of the capsid of alphaherpesviruses, such as herpes simplex virus 1 (HSV-1), is known to be dependent upon the microtubule (MT) network. Typically, the MT network radiates from an MT-organizing center (MTOC), which is, in most cases, the centrosome. During herpesvirus egress, it has been assumed that capsids travel first from the nucleus to the centrosome and then from the centrosome to the site of envelopment. Here we report that the centrosome is no longer a primary MTOC in HSV-1-infected cells, but it retains this function in cells infected by another alphaherpesvirus, pseudorabies virus (PrV). As a result, MTs formed at late times after infection with PrV grow from a major, centralized MTOC, while those formed after HSV-1 infection arise from dispersed locations in the cytoplasm, indicating the presence of alternative and minor MTOCs. Thus, loss of the principal MT nucleating center in cells following HSV-1 infection raises questions about the mechanism of HSV-1 capsid egress. It is possible that, rather than passing via the centrosome, capsids may travel directly to the site of envelopment after exiting the nucleus. We suggest that, in HSV-1-infected cells, the disruption of centrosomal functions triggers reorganization of the MT network to favor noncentrosomal MTs and promote efficient viral spread.     

登革热病毒基因组末端cDNA的克隆及序列分析

采用磁性分离技术从登革热病毒(D2-04株)感染的C6/36细胞中分离了D2-04病毒RNA.以该RNA为模板进行RT-PCR,分别扩增了D2-04 RNA 5′和3′端cDNA片段,该cDNA片段分别克隆到pGEM-3Z质粒多聚接头的HincⅡ位点得到含有5′端284 bp及3′端525 bp cDNA的重组质粒.通过荧光标记引物及双脱氧核苷酸PCR方法测定了上述cDNA插入片段的序列.同源性比较结果证明D2-04株与其他不同株间的同源性较高,可达93%～98%;不同型间的同源性较差, 仅80%左右; 属间的同源性更低.