Comparative structural studies of bovine viral diarrhea virus IRES RNA

DDX3 Regulates the Cap-Independent Translation of the Japanese Encephalitis Virus via Its Interactions with PABP1 and the Untranslated Regions of the Viral Genome

The translation of global cellular proteins is almost completely repressed in cells with flavivirus infection, while viral translation remains efficient. The mechanisms of flaviviruses evade host translational shutoff are largely unknown. Here, it is found that Japanese encephalitis virus (JEV) can adopt cap-independent (CI) translation to escape the host translational shutoff. Furthermore, the elements DB2 and sHP-SL within 3'UTR are involved in the regulation of CI translation, which is conserved in the genus Orthoflavivirus. By RNA affinity purification and mass spectrometry analysis, cellular DEAD-box protein 3 (DDX3) and poly(A)-binding protein 1 (PABP1) are identified as key factors in regulating CI translation of JEV via their interactions with DB2 and sHP-SL RNA structures. Mechanistically, it is revealed that DDX3 binds to both 5'UTR and 3'UTR of the JEV genome to establish a closed-loop architecture and recruit eIF4G/eIF4A to form the DDX3/PABP1/eIF4G/eIF4A tetrameric complex via its interaction with PABP1, thereby recruiting the ribosomal 43S preinitiation complex (PIC) to the 5'-end of the JEV genome to start translation. These findings demonstrate a noncanonical translation strategy employed by JEV and further reveal the regulatory roles of DDX3 and PABP1 in this mechanism. These results expand the knowledge of the translation initiation regulation in flaviviruses under the state of host translational shutoff, which provides a conserved antiviral target against orthoflavivirus.

Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and in silico modelling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA in solution forms a modular architecture composed of three distinct structural domains (I-III). Two regions within domain III are represented in tertiary interactions to form an H-type pseudoknot. Computational modelling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many Pestivirus species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.

Recent Advances on the Bovine Viral Diarrhea Virus Molecular Pathogenesis, Immune Response, and Vaccines Development

The bovine viral diarrhea virus (BVDV) consists of two species and various subspecies of closely related viruses of varying antigenicity, cytopathology, and virulence-induced pathogenesis. Despite the great ongoing efforts to control and prevent BVDV outbreaks and the emergence of new variants, outbreaks still reported throughout the world. In this review, we are focusing on the molecular biology of BVDV, its molecular pathogenesis, and the immune response of the host against the viral infection. Special attention was paid to discuss some immune evasion strategies adopted by the BVDV to hijack the host immune system to ensure the success of virus replication. Vaccination is one of the main strategies for prophylaxis and contributes to the control and eradication of many viral diseases including BVDV. We discussed the recent advances of various types of currently available classical and modern BVDV vaccines. However, with the emergence of new strains and variants of the virus, it is urgent to find some other novel targets for BVDV vaccines that may overcome the drawbacks of some of the currently used vaccines. Effective vaccination strategy mainly based on the preparation of vaccines from the homologous circulating strains. The BVDV-E2 protein plays important role in viral infection and pathogenesis. We mapped some important potential neutralizing epitopes among some BVDV genomes especially the E2 protein. These novel epitopes could be promising targets against the currently circulating strains of BVDV. More research is needed to further explore the actual roles of these epitopes as novel targets for the development of novel vaccines against BVDV. These potential vaccines may contribute to the global eradication campaign of the BVDV.

Delivery of antisense peptide nucleic acid by gold nanoparticles for the inhibition of virus replication

Aim: We aim to use peptide nucleic acid (PNA) for antisense therapy against bovine viral diarrhea virus (BVDV), a surrogate model of human hepatitis C virus, and introduce an optimal approach for delivering PNA into the cell. Materials & methods: PNA was designed for hybridization to the 5'-untranslated region of BVDV RNA in order to form a heteroduplex structure and inhibit the translation and replication of virus. Gold nanoparticles (AuNPs) were used as a delivery system for PNA. Results: The cellular uptake of PNA-AuNPs and inhibition of BVDV infection in the middle stage of viral replication were found. Conclusion: Further research is warranted to develop AuNPs as a potential vehicle for delivering PNA in order to remove viruses from the infected cells.

[Construction of the pIRES2-ZsGreen1 eukaryotic expression vector of Factor Ⅸ gene and expression in HEK-293 cells]

Objective: To construct pIRES2-ZsGreen1/F Ⅸ expression vector, using the pcDNA/FⅨ plasmid containing FⅨ cDNA as template, and express in HEK-293 cells. Methods: The total ORF of F Ⅸ gene was amplified from pcDNA/F Ⅸ plasmid, then the amplified fragment was clonded into the pIRES2-ZsGreen1 vector using the Infusion enzyme. The positive clones of eukaryotic expression vector of pIRES2-ZsGreen1/F Ⅸ were screened and expanded after transfection, then were constructed and confirmed by PCR and sequencing. Transient expression experiments were performed using HEK-293 cells transfected with the expression vectors and observed the expression of ZsGreen1 protein by confocal laser microscope. The relative expression levels of FⅨ mRNA, protein and FⅨ activity (FⅨ∶C) were detected by real time PCR (RT-PCR), immunofluorescence microscopy, One-Stage method, respectively. Results: The expression vector, pIRES2-ZsGreen1/F Ⅸ, was successfully constructed and expressed in HEK-293 cells. RT-PCR detected the expression of F Ⅸ mRNA in HEK-293 cells and the immunofluorescence microscopy showed FⅨ protein distributed in the surrounding of nucleus. FⅨ∶C of cell lysates and cell culture fluid transfected with the expression vectors were (92.03 ± 0.29)% and (86.89 ± 8.78)%, respectively; while both F Ⅸ∶C of cell lysates and cell culture fluid transfected with or without the expression vectors were 0. Conclusion: The experimental results showed the expression vector, pIRES2-ZsGreen1/FⅨ, was successfully constructed , which provided experiment basement for the follow study on the location, function and molecular pathology of hemophilia B.

Standing your ground to exoribonucleases: Function of Flavivirus long non-coding RNAs

Members of the Flaviviridae (e.g., Dengue virus, West Nile virus, and Hepatitis C virus) contain a positive-sense RNA genome that encodes a large polyprotein. It is now also clear most if not all of these viruses also produce an abundant subgenomic long non-coding RNA. These non-coding RNAs, which are called subgenomic flavivirus RNAs (sfRNAs) or Xrn1-resistant RNAs (xrRNAs), are stable decay intermediates generated from the viral genomic RNA through the stalling of the cellular exoribonuclease Xrn1 at highly structured regions. Several functions of these flavivirus long non-coding RNAs have been revealed in recent years. The generation of these sfRNAs/xrRNAs from viral transcripts results in the repression of Xrn1 and the dysregulation of cellular mRNA stability. The abundant sfRNAs also serve directly as a decoy for important cellular protein regulators of the interferon and RNA interference antiviral pathways. Thus the generation of long non-coding RNAs from flaviviruses, hepaciviruses and pestiviruses likely disrupts aspects of innate immunity and may directly contribute to viral replication, cytopathology and pathogenesis.