Construction and Application of a Protein Interaction Map for White Spot Syndrome Virus (WSSV)

White spot syndrome virus (WSSV) is currently the most serious global threat for cultured shrimp production. Although its large, double-stranded DNA genome has been completely characterized, most putative protein functions remain obscure. To provide more informative knowledge about this virus, a proteomic-scale network of WSSV-WSSV protein interactions was carried out using a comprehensive yeast two-hybrid analysis. An array of yeast transformants containing each WSSV open reading frame fused with GAL4 DNA binding domain and GAL4 activation domain was constructed yielding 187 bait and 182 prey constructs, respectively. On screening of ∼28,000 pairwise combinations, 710 interactions were obtained from 143 baits. An independent coimmunoprecipitation assay (co-IP) was performed to validate the selected protein interaction pairs identified from the yeast two-hybrid approach. The program Cytoscape was employed to create a WSSV protein–protein interaction (PPI) network. The topology of the WSSV PPI network was based on the Barabási-Albert model and consisted of a scale-free network that resembled other established viral protein interaction networks. Using the RNA interference approach, knocking down either of two candidate hub proteins gave shrimp more protection against WSSV than knocking down a nonhub gene. The WSSV protein interaction map established in this study provides novel guidance for further studies on shrimp viral pathogenesis, host-viral protein interaction and potential targets for therapeutic and preventative antiviral strategies in shrimp aquaculture.White spot syndrome virus (WSSV)¹ is the causative agent of white spot disease (WSD) and is one of the most serious viral pathogens that threaten the shrimp culture industry worldwide. Because WSD causes rapid and high mortality up to 100% within 3–10 days after viral infection (1), it causes dramatic economic losses on farms. WSSV is a large enveloped, ovoid to bacilliform, double-stranded DNA (dsDNA) virus with a genome of ∼300 kb (See reviews in (2, 3)). The WSSV genome has been completely characterized for isolates from Thailand (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"AF369029","term_id":"58866698","term_text":"AF369029"}}AF369029), China (accession number {"type":"entrez-nucleotide","attrs":{"text":"AF332093","term_id":"721172032","term_text":"AF332093"}}AF332093) and Taiwan (accession number {"type":"entrez-nucleotide","attrs":{"text":"AF440570","term_id":"19481591","term_text":"AF440570"}}AF440570). To expand its basic genetic information, various genomic and proteomic approaches have been applied to gain more insight into the molecular mechanisms of WSSV pathogenesis (See reviews in (2, 3)). However, the roles of most of the WSSV proteins still remain to be elucidated. This is due to the fact that many of its putative open reading frames (ORFs) lack homology to known proteins in the database. Protein–protein interaction studies can provide a valuable framework for understanding the roles of protein functions. Interaction studies of WSSV proteins have particularly focused on viral structural proteins (4–15). However, so far there has been no report on a protein–protein interaction (PPI) network for WSSV or any other crustacean virus. By contrast, several PPI networks for cellular organisms such as Saccharomyces cerevisiae (16, 17), Helicobacter pylori (18), Drosophila melanogaster (19), Caenarhabitis elegans (20), Plasmodium falciparum (21), and Homo sapiens (22, 23) and pathogens such as bacteriophage T7 (24), vaccinia virus (25), hepatitis C virus (26), and herpesviruses (27–29) have already been established. Therefore, the present study aimed to obtain a more fundamental understanding of WSSV protein interactions. A comprehensive yeast two-hybrid assay was employed to generate viral fusion proteins with DNA binding (BD) and activation (AD) domains in an array format that effectively allowed searching every possible binary interaction in WSSV. The interaction results from the yeast two-hybrid assays were subsequently validated by coimmunoprecipitation (co-IP). Topological properties of the WSSV PPI network were assessed and compared with previously published viral networks. Candidate viral hub proteins with high numbers of interacting partners were identified in this study and their significance was investigated using an RNA interference approach.     

Co-interactive DNA-binding between a novel, immunophilin-like shrimp protein and VP15 nucleocapsid protein of white spot syndrome virus

White spot syndrome virus (WSSV) is one of the most serious pathogens of penaeid shrimp. Although its genome has been completely characterized, the functions of most of its putative proteins are not yet known. It has been suggested that the major nucleocapsid protein VP15 is involved in packaging of the WSSV genome during virion formation. However, little is known in its relationship with shrimp host cells. Using the yeast two-hybrid approach to screen a shrimp lymphoid organ (LO) cDNA library for proteins that might interact with VP15, a protein named PmFKBP46 was identified. It had high sequence similarity to a 46 kDa-immunophilin called FKBP46 from the lepidopteran Spodoptera frugiperda (the fall armyworm). The full length PmFKBP46 consisted of a 1,257-nucleotide open reading frame with a deduced amino acid sequence of 418 residues containing a putative FKBP-PPIase domain in the C-terminal region. Results from a GST pull-down assay and histological co-localization revealed that VP15 physically interacted with PmFKBP46 and that both proteins shared the same subcellular location in the nucleus. An electrophoretic mobility shift assay indicated that PmFKBP46 possessed DNA-binding activity and functionally co-interacted with VP15 in DNA binding. The overall results suggested that host PmFKBP46 might be involved in genome packaging by viral VP15 during virion assembly.     

Cloning and characterization of a caspase gene from black tiger shrimp (Penaeus monodon)-infected with white spot syndrome virus (WSSV)

A black tiger shrimp (Penaeus monodon) caspase cDNA homologue (PmCasp) has been identified from a hemocyte library using a previously identified caspase homologue from the banana shrimp (Penaeus merguiensis) as a probe. The full-length PmCasp was 1202bp with a 954bp open reading frame, encoding 317 amino acids. The deduced protein contained a potential active site (QACRG pentapeptide) conserved in most caspases. It had 83% identity with caspase of P. merguiensis and 30% identity with drICE protein of Drosophila melanogaster, and it exhibited caspase-3 activity in vitro. PmCasp was cloned and expressed in Escherichia coli and a rabbit polyclonal antiserum was produced. In Western blots, the antiserum reacted with purified recombinant PmCasp and with lysates of E. coli containing the expressed plasmid. In crude protein extracts from normal shrimp, the antiserum reacted with 36 and 26kDa bands likely to correspond to inactive pro-caspase and its proteolytic intermediate form, respectively. PmCasp expression was measured in normal shrimp and in white spot syndrome virus (WSSV)-infected shrimp at 24 and 48h post-injection (p.i.) by semi-quantitative RT-PCR, Western blot analysis, and immunohistochemistry. Semi-quantitative RT-PCR analysis revealed up-regulation of PmCasp at 48h p.i. and expression remained high up to the moribund state. These results were supported by Western blot analysis showing increased PmCasp protein levels at 24 and 48h p.i. when compared to normal control shrimp. Immunohistochemical analysis of gills from the WSSV-infected shrimp revealed immunoreactivity localized in the cytoplasm of both normal and apparently apoptotic cells. In summary, a caspase-3 like gene is conserved in P. monodon and is up-regulated after WSSV infection.