Inter-subunit interactions of the Autographa californica M nucleopolyhedrovirus RNA polymerase

Identification of Key Genes Involved in Resistance to Early Stage of BmNPV Infection in Silkworms

Bombyx mori nucleopolyhedrovirus (BmNPV) is one of the most serious pathogens restricting the sustainable development of the sericulture industry. Currently, there is no effective treatment for BmNPV infection in silkworms, and the mechanism underlying BmNPV resistance in silkworms is also not clear. In this study, comparative transcriptome analyses were carried out in midguts of two silkworm varieties, namely BaiyuN, which is a resistance variety, and Baiyu, which is a susceptible variety, at five different time points (i.e., 0, 1, 3, 6, and 9 h) post-BmNPV infection to detect the early-stage transcriptional changes in these silkworms. In total, 1911 and 1577 differentially expressed genes (DEGs) were identified in the Baiyu and BaiyuN varieties, respectively, involving a total of 48 metabolic pathways. Of these pathways, eight were shared by the Baiyu and BaiyuN varieties in response to BmNPV infection. Notably, four genes (i.e., BGIBMGA08815, BGIBMGA003935, BGIBMGA003571, BGIBMGA010059) were upregulated in the Baiyu variety while downregulated in the BaiyuN variety. The inhibited expression of these four genes in the resistant variety highlighted their potential roles in the resistance of early-stage viral replication. Thus, our study provided a new avenue for the further study of the mechanism underlying BmNPV infection in silkworms and the potential treatment of BmNPV infection.

CRISPR/Cas9-Mediated Disruption of the lef8 and lef9 to Inhibit Nucleopolyhedrovirus Replication in Silkworms

Bombyx mori nucleopolyhedrovirus (BmNPV) is a pathogen that causes severe disease in silkworms. In a previous study, we demonstrated that by using the CRISPR/Cas9 system to disrupt the BmNPV ie-1 and me53 genes, transgenic silkworms showed resistance to BmNPV infection. Here, we used the same strategy to simultaneously target lef8 and lef9, which are essential for BmNPV replication. A PCR assay confirmed that double-stranded breaks were induced in viral DNA at targeted sequences in BmNPV-infected transgenic silkworms that expressed small guide RNAs (sgRNAs) and Cas9. Bioassays and qPCR showed that replication of BmNPV and mortality were significantly reduced in the transgenic silkworms in comparison with the control groups. Microscopy showed degradation of midgut cells in the BmNPV-infected wild type silkworms, but not in the transgenic silkworms. These results demonstrated that transgenic silkworms using the CRISPR/Cas9 system to disrupt BmNPV lef8 and lef9 genes could successfully prevent BmNPV infection. Our research not only provides more alternative targets for the CRISPR antiviral system, but also aims to provide new ideas for the application of virus infection research and the control of insect pests.

Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes

Baculoviruses are a group of insect viruses with large circular dsDNA genomes exploited in numerous biotechnological applications, such as the biological control of agricultural pests, the expression of recombinant proteins or the gene delivery of therapeutic sequences in mammals, among others. Their genomes encode between 80 and 200 proteins, of which 38 are shared by all reported species. Thanks to multi-omic studies, there is remarkable information about the baculoviral proteome and the temporality in the virus gene expression. This allows some functional elements of the genome to be very well described, such as promoters and open reading frames. However, less information is available about the transcription termination signals and, consequently, there are still imprecisions about what are the limits of the transcriptional units present in the baculovirus genomes and how is the processing of the 3′ end of viral mRNA. Regarding to this, in this review we provide an update about the characteristics of DNA signals involved in this process and we contribute to their correct prediction through an exhaustive analysis that involves bibliography information, data mining, RNA structure and a comprehensive study of the core gene 3′ ends from 180 baculovirus genomes.

The study of the phiKZ phage non-canonical non-virion RNA polymerase

Non-canonical multisubunit DNA-dependent RNA-polymerases (RNAP) form a new group of the main transcription enzymes, which have only distinct homology to the catalytic subunits of canonical RNAPs of bacteria, archaea and eukaryotes. One of the rare non-canonical RNAP, which was partially biochemically characterized, is non-virion RNAP (nvRNAP) encoded by Pseudomonas phage phiKZ. PhiKZ nvRNAP consists of five subunits, four of which are homologs of β and β' subunit of bacterial RNAP, and the fifth subunits with unknown function. To understand the role of the fifth subunit in phiKZ nvRNAP, we created co-expression system allowing to get recombinant full five-subunit (5s) and four-subunit (4s) complexes and performed their comparison. The 5s recombinant complex is active on phage promoters in vitro as the native nvRNAP. The 4s complex cannot extend RNA, so 4s complex is not a catalytically active core of phiKZ nvRNAP. Thus, the phiKZ fifth subunit is not only a promoter-recognition subunit, but it plays an important role in the formation of active phiKZ nvRNAP.

Introduction to Baculovirus Molecular Biology

The development of baculovirus expression vector systems has accompanied a rapid expansion of our knowledge about the genes, their function and regulation in insect cells. Classification of these viruses has also been refined as we learn more about differences in gene content between isolates, how this affects virus structure and their replication in insect larvae. Baculovirus gene expression occurs in an ordered cascade, regulated by early, late and very late gene promoters. There is now a detailed knowledge of these promoter elements and how they interact first with host cell-encoded RNA polymerases and later with virus-encoded enzymes. The composition of this virus RNA polymerase is known. The virus replication process culminates in the very high level expression of both polyhedrin and p10 gene products in the latter stages of infection. It has also been realized that the insect host cell has innate defenses against baculoviruses in the form of an apoptotic response to virus invasion. Baculoviruses counter this by encoding apoptotic-suppressors, which also appear to have a role in determining the host range of the virus. Also of importance to our understanding of baculovirus expression systems is how the virus can accumulate mutations within genes that affect recombinant protein yield in cell culture. The summary in this chapter is not exhaustive, but should provide a good preparation to those wishing to use this highly successful gene expression system.

Molecular characterization of nucleopolyhedrovirus of three lepidopteran pests using late expression factor-8 gene

A PCR based method for detection of viral DNA in nucleopolyhedrovirus of three lepidopterans, Spodoptera litura, Amsacta albistriga and Helicoverpa armigera, was developed by employing the late expression factor-8 (lef-8) gene of three NPV using specific primers. The amplicons of 689, 699 and 665 bp were amplified, respectively, and the nucleotide sequences were submitted to GenBank and the accession numbers were obtained. The sequences of lef-8 gene of S. litura NPV and H. armigera NPV matched with those of their respective references in the GenBank database, thereby confirming their identity, however, the sequence of A. albistriga NPV was the first sequence submitted to the GenBank database. The sequence similarity analysis between the three lef-8 gene of NPV sequenced in the present study revealed that there was no significant similarity between them, however A. albistriga NPV and S. litura NPV were found to be closely related. CLUSTAL alignment of the sequences generated revealed general relatedness among NPVs lef-8 gene. The study confirmed that lef-8 gene can be used for quick and correct discriminatory identification of insect viruses.

Direct interactions between bidensovirus BmDNV-Z proteins and midgut proteins from the virus target Bombyx mori

In this study we aimed to identify the protein-protein interactions between Bombyx mori midgut and the bidensovirus BmDNV-Z via a yeast two-hybrid (Y2H) system. To achieve this we constructed a Gal4 activation domain fusion library that expresses the host genes and Gal4 DNA binding domain fusion bait vectors that express BmDNV-Z genes. Y2H assay revealed 15 potential interactions between host and viral proteins. To verify the interactions, we modified and reconstructed a pair of bimolecular fluorescence complementation (BiFC) vectors and achieved the co-expressions of the candidate host genes and viral genes in insect culture cells. The BiFC assay confirmed the specificity of the interactions including B. mori 35 kDa protease and two BmDNV-Z proteins encoded by VD1-ORF2 and VD2-ORF1; B. mori transgelin and BmDNV-Z protein encoded by VD2-ORF3; and B. mori serine protease precursor and BmDNV-Z encoded by VD2-ORF3 in vitro. Our findings revealed that the specific host midgut proteins are involved in the interactions between B. mori and BmDNV-Z, which will facilitate our understanding of the molecular mechanisms of BmDNV-Z infection.

Use of bacterial artificial chromosomes in baculovirus research and recombinant protein expression: current trends and future perspectives

The baculovirus expression system is one of the most successful and widely used eukaryotic protein expression methods. This short review will summarise the role of bacterial artificial chromosomes (BACS) as an enabling technology for the modification of the virus genome. For many years baculovirus genomes have been maintained in E. coli as bacterial artificial chromosomes, and foreign genes have been inserted using a transposition-based system. However, with recent advances in molecular biology techniques, particularly targeting reverse engineering of the baculovirus genome by recombineering, new frontiers in protein expression are being addressed. In particular, BACs have facilitated the propagation of disabled virus genomes that allow high throughput protein expression. Furthermore, improvement in the selection of recombinant viral genomes inserted into BACS has enabled the expression of multiprotein complexes by iterative recombineering of the baculovirus genome.

Effect of ac68 knockout and lef3 leading sequence disruption on viral propagation

Orf68 (ac68) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is identified to be an early gene, but its transcription start site remains unknown. The coding sequence of ac68 overlaps 280-bp leading sequence and 159-bp coding sequence of lef3 (ac67). In this study, the transcription start site of ac68 was determined by 5' RACE analysis to be 18 nucleotides upstream from the start codon. In order to investigate the effect of ac68 deletion on virus propagation, we generated a bacmid with an ac68 knockout by deleting 360-bp inside the ac68 gene, which also deleted 220-bp leading sequence of lef3. Production of infectious budded virus and formation of nucleocapsids and occlusion bodies exhibited wild-type patterns of virus propagation in Sf-9 cells infected with the mutant bacmid. The result demonstrated that ac68 was not an essential gene for viral propagation which was confirmed by further deletion of ac68, and disruption of the lef3 leading sequence did not affect viral propagation. Ac68 was the second auxiliary gene discovered besides Ac133 (alk-exo) among the 30 core genes of AcMNPV.

Identification of protein-protein interactions of the occlusion-derived virus-associated proteins of Helicoverpa armigera nucleopolyhedrovirus

The purpose of this study was to identify protein-protein interactions among the components of the occlusion-derived virus (ODV) of Helicoverpa armigera nucleopolyhedrovirus (HearNPV), a group II alphabaculovirus in the family Baculoviridae. To achieve this, 39 selected genes of potential ODV structural proteins were cloned and expressed in the Gal4 yeast two-hybrid (Y2H) system. The direct-cross Y2H assays identified 22 interactions comprising 13 binary interactions [HA9-ODV-EC43, ODV-E56-38K, ODV-E56-PIF3, LEF3-helicase, LEF3-alkaline nuclease (AN), GP41-38K, GP41-HA90, 38K-PIF3, 38K-PIF2, VP80-HA100, ODV-E66-PIF3, ODV-E66-PIF2 and PIF3-PIF2] and nine self-associations (IE1, HA44, LEF3, HA66, GP41, CG30, 38K, PIF3 and P24). Five of these interactions - LEF3-helicase and LEF3-AN, and the self-associations of IE1, LEF3 and 38K - have been reported previously in Autographa californica multiple nucleopolyhedrovirus. As HA44 and HA100 were two newly identified ODV proteins of group II viruses, their interactions were further confirmed. The self-association of HA44 was verified with a His pull-down assay and the interaction of VP80-HA100 was confirmed by a co-immunoprecipitation assay. A summary of the protein-protein interactions of baculoviruses reported so far, comprising 68 interactions with 45 viral proteins and five host proteins, is presented, which will facilitate our understanding of the molecular mechanisms of baculovirus infection.

Characterization of LEF4 ligand binding property and its role as part of baculoviral transcription machinery

Late expression factor 4 (LEF4) is one of the four identified subunits of Autographa californica nucleopolyhedrosis virus (AcNPV) encoded RNA polymerase that carries out transcription from viral late and very late promoters. This 464-amino acid baculovirus-encoded protein also harbors 5' mRNA capping activity that includes RNA 5' triphosphatase, nucleoside triphosphatase, and guanylyltransferase activities. Hydrolysis of 5' triphosphate RNA and free NTPs is metal ion dependent property of the protein. In the present communication, we describe the structural changes in the recombinant LEF4 protein following ligand binding. Metal ion binding causes some alteration in the conformation around aromatic amino acids whereas there is no effect on tryptophan fluorescence on GTP binding in absence and presence of metal ion. It is found that GTP and divalent cation cofactor produce some prominent changes in the secondary structure of the protein. Electrophoretic mobility shift assay (EMSA) shows that LEF4 is the probable factor that acts as anchor to dock the viral RNA polymerase on the very late polyhedrin promoter (Ppolh) facilitated by other factors.

Autographa californica multiple nucleopolyhedrovirus 38K is a novel nucleocapsid protein that interacts with VP1054, VP39, VP80, and itself

It has been shown that the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) 38K (ac98) is required for nucleocapsid assembly. However, the exact role of 38K in nucleocapsid assembly remains unknown. In the present study, we investigated the relationship between 38K and the nucleocapsid. Western blotting using polyclonal antibodies raised against 38K revealed that 38K was expressed in the late phase of infection in AcMNPV-infected Spodoptera frugiperda cells and copurified with budded virus (BV) and occlusion-derived virus (ODV). Biochemical fractionation of BV and ODV into the nucleocapsid and envelope components followed by Western blotting showed that 38K was associated with the nucleocapsids. Immunoelectron microscopic analysis revealed that 38K was specifically localized to the nucleocapsids in infected cells and appeared to be distributed over the cylindrical capsid sheath of nucleocapsid. Yeast two-hybrid assays were performed to examine potential interactions between 38K and nine known nucleocapsid shell-associated proteins (PP78/83, PCNA, VP1054, FP25, VLF-1, VP39, BV/ODV-C42, VP80, and P24), three non-nucleocapsid shell-associated proteins (P6.9, PP31, and BV/ODV-E26), and itself. The results revealed that 38K interacted with the nucleocapsid proteins VP1054, VP39, VP80, and 38K itself. These interactions were confirmed by coimmunoprecipitation assays in vivo. These data demonstrate that 38K is a novel nucleocapsid protein and provide a rationale for why 38K is essential for nucleocapsid assembly.