A cis-Acting Viral Protein Is Not Required for the Replication of a Coronavirus Defective-Interfering RNA

AbstractMouse hepatitis virus (MHV), a coronavirus, generates defective-interfering (DI) RNAs of different sizes during passages at high multiplicities of infection. All MHV DI RNAs characterized so far contain an open reading frame (ORF) encoding a fused viral protein; in addition, DI RNAs with a long ORF have a competitive advantage over those with a shorter ORF. These findings suggest that DI RNA replication may require an ORF encoding a cis-acting viral protein. In this study, we used a naturally occurring DI RNA and inserted a 12-nucleotide (nt) amber-mutation linker at various positions to truncate the ORF. Most of the mutants replicated as well as the wild-type DI RNA, irrespective of the presence or absence and the length of the ORF in the RNA. Sequence analysis showed that all of the mutants retained the insertional mutations even after two viral passages in tissue culture, establishing that the mutant DI RNAs replicated. We have further introduced two 3-nucleotide substitutions of the first two AUG codons of the ORF, thus completely closing the ORF. This DI RNA replicated as well as the wild-type DL but, after a single passage, the majority of the mutant RNAs was replaced by recombinant RNAs which contain a restored functional ORF. However, an additional insertion of a 12-nt amber-mutation linker downstream of the AUG substitutions prevented recombination, and the DI RNA still replicated. These data indicate that DI RNA replication does not require a DI-specific ORF encoding cis-acting viral proteins and that a 12-nucleotide insertion could prevent or delay the occurrence of RNA recombination, suggesting the importance of direct or indirect RNA alignment in homologous RNA recombination

Hepatitis C Virus NS5B Protein Is a Membrane-Associated Phosphoprotein with a Predominantly Perinuclear Localization

AbstractHepatitis C virus NS5B protein is an RNA-dependent RNA polymerase. To investigate the properties and function of this protein, we have expressed the NS5B protein in insect and mammalian cells. NS5B was found to be present as fine speckles in the cytoplasm, particularly concentrated in the perinuclear region, suggesting its association with the nuclear membrane, the endoplasmic reticulum, or the Golgi complex. This conclusion was supported by the biochemical demonstration that NS5B was associated with the membranes in the cells. Furthermore, it was shown that NS5B protein is a phosphoprotein. These properties may be related to its function as an RNA polymerase

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Coronavirus Defective-Interfering RNA as an Expression Vector: The Generation of a Pseudorecombinant Mouse Hepatitis Virus Expressing Hemagglutinin-Esterase

AbstractWe have developed an expression vector system using a defective-interfering (DI) RNA of mouse hepatitis virus (MHV), a prototype coronavirus, to deliver and express a foreign gene in MHV-infected cells. This vector contains an MHV intergenic sequence to promote the expression of foreign genes. In this study, we used this vector to introduce a hemagglutininesterase (HE) protein, an optional MHV structural protein, into the MHV-infected cells. The engineered HE protein could be efficiently incorporated into the virion which did not synthesize its own HE protein, thus generating a pseudorecombinant virus that expresses an exogenous HE protein. The engineered HE protein could be made distinguishable from the native protein by attaching an 8-amino-acid peptide tag at the carboxyl-terminus. Both the engineered and native HE proteins from the HE-producing virus train could be incorporated into the virion, thus generating phenotypically mixed virus parficles. We also showed that the HE-expressing DI RNA could be incorporated into viruses, and the engineered HE protein expressed in the infected cells for at least three serial virus passages. Furthermore, we have made two mutants, in which parts of the external domain of the HE protein have been deleted, to study the sequence requirements for the stable expression of HE and its incorporation into MHV virions. Although both of the mutant HE proteins could be expressed in the MHV-infected cells, they failed to be incorporated into virions, suggesting the importance of the extracellular domain of HE protein for its incorporation into virus particles. This vector system enabled the first successful incorporation of a selected coronaviral protein into virions and demonstrates its utility as an expression vector for studying the molecular biology of coronaviruses

Cell-free translation of avian erythroblastosis virus RNA yields two specific and distinct proteins with molecular weights of 75,000 and 40,000

Avian erythroblastosis virus (AEV) 28 S virion RNA was translated in vitro in cell-free reticulocyte lysates. Two AEV-specific proteins, one of 75,000 (p75) the other of 40,000 (p40) molecular weight, were detected. p75 is a fusion protein containing gag-specific and AEV-specific peptides. It appears to be translated from the 5′-end of the 28 S AEV RNA and is indistinguishable from the p75 detected in AEV-transformed cells (Hayman et al., 1979). p40 does not share sequences with any viral structural protein. It also contains peptides distinct from those of p75, but one of the five identifiable p40 peptides comigrates with one of the p75 peptides. p40 is translated from a 20 S RNA which contains the 3′-half of the AEV-specific sequences of the genome. These two proteins account for all of the coding capacity of the AEV-specific gene sequences in the 28 S AEV RNA and are candidates for leukemia-specific transforming proteins

Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus

Heterogeneous nuclear ribonucleoprotein (hnRNP A1) is involved in pre-mRNA splicing in the nucleus and translational regulation in the cytoplasm. In the present study, we demonstrate that hnRNP A1 also participates in the transcription and replication of a cytoplasmic RNA virus, mouse hepatitis virus (MHV). Overexpression of hnRNP A1 accelerated the kinetics of viral RNA synthesis, whereas the expression in the cytoplasm of a dominant-negative hnRNP A1 mutant that lacks the nuclear transport domain significantly delayed it. The hnRNP A1 mutant caused a global inhibition of viral mRNA transcription and genomic replication, and also a preferential inhibition of the replication of defective-interfering RNAs. Similar to the wild-type hnRNP A1, the hnRNP A1 mutant complexed with an MHV polymerase gene product, the nucleocapsid protein and the viral RNA. However, in contrast to the wild-type hnRNP A1, the mutant protein failed to bind a 250 kDa cellular protein, suggesting that the recruitment of cellular proteins by hnRNP A1 is important for MHV RNA synthesis. Our findings establish the importance of cellular factors in viral RNA-dependent RNA synthesis

Is avian influenza A (H7N9) virus staggering its way to humans?

Human infections by a new avian influenza A (H7N9) virus have been reported. As of April 23, 2013, there were 108 confirmed cases including 22 deaths in China. Methods: Influenza protein sequences were downloaded from the Influenza Virus Resource and GISAID EpiFlu databases. Pairwise nucleotide identities were computed for assessing the evolutionary distance of H7N9 to other known avian and human viruses, and multiple sequence alignments with their position-specific entropy values were used in discussing how mutations on species-associated signature positions were introduced in the new H7N9 which may steer its way to human infection. Results: This report analyzed the genomic characteristics of this new H7N9 virus. Nucleotide sequence analysis clearly reveals its origin from avian viruses. In this article, we particularly focus on its internal genes that are found to derive from H9N2—another subtype of avian influenza A virus which has been circulating in birds for years. Amino acid sequences at species-specific genomic positions were examined. Although the new virus contains mostly avian-like residues at these signature positions, it does contain several human-like signatures. For instance, at the position 627 of PB2, the new virus has human-characteristic K instead of avian-characteristic E; in addition, PB2-627K, PA-100A, PA-356R, and PA-409N are also human-like signatures in the new H7N9 virus. Conclusion: The new H7N9 is an avian influenza A virus; however, it does harbor several human virus-like signatures, which raises great concern that it may have a higher probability to cross species barriers and infect humans

Zika virus cleaves GSDMD to disseminate prognosticable and controllable oncolysis in a human glioblastoma cell model

Glioblastoma (GBM) is the most common aggressive malignant brain cancer and is chemo- and radioresistant, with poor therapeutic outcomes. The “double-edged sword” of virus-induced cell death could be a potential solution if the oncolytic virus specifically kills cancer cells but spares normal ones. Zika virus (ZIKV) has been defined as a prospective oncolytic virus by selectively targeting GBM cells, but unclear understanding of how ZIKV kills GBM and the consequences hinders its application. Here, we found that the cellular gasdermin D (GSDMD) is required for the efficient death of a human GBM cell line caused by ZIKV infection. The ZIKV protease specifically cleaves human GSDMD to activate caspase-independent pyroptosis, harming both viral protease-harboring and naive neighboring cells. Analyzing human GSDMD variants showed that most people were susceptible to ZIKV-induced cytotoxicity, except for those with variants that resisted ZIKV cleavage or were defective in oligomerizing the N terminus GSDMD cleavage product. Consistently, ZIKV-induced secretion of the pro-inflammatory cytokine interleukin-1β and cytolytic activity were both stopped by a small-molecule inhibitor targeting GSDMD oligomerization. Thus, potential ZIKV oncolytic therapy for GBM would depend on the patient’s GSDMD genetic background and could be abolished by GSDMD inhibitors if required