Divergent Antiviral Mechanisms of Two Viperin Homeologs in a Recurrent Polyploid Fish

Abstract

Polyploidy and subsequent diploidization provide genomic opportunities for evolutionary innovations and adaptation. The researches on duplicated gene evolutionary fates in recurrent polyploids have seriously lagged behind that in paleopolyploids with diploidized genomes. Moreover, the antiviral mechanisms of Viperin remain largely unclear in fish. Here, we elaborate the distinct antiviral mechanisms of two viperin homeologs (Cgviperin-A and Cgviperin-B) in auto-allo-hexaploid gibel carp (Carassius gibelio). First, Cgviperin-A and Cgviperin-B showed differential and biased expression patterns in gibel carp adult tissues. Subsequently, using co-immunoprecipitation (Co-IP) screening analysis, both CgViperin-A and CgViperin-B were found to interact with crucian carp (C. auratus) herpesvirus (CaHV) open reading frame 46 right (ORF46R) protein, a negative herpesvirus regulator of host interferon (IFN) production, and to promote the proteasomal degradation of ORF46R via decreasing K63-linked ubiquitination. Additionally, CgViperin-B also mediated ORF46R degradation through autophagosome pathway, which was absent in CgViperin-A. Moreover, we found that the N-terminal α-helix domain was necessary for the localization of CgViperin-A and CgViperin-B at the endoplasmic reticulum (ER), and the C-terminal domain of CgViperin-A and CgViperin-B was indispensable for the interaction with degradation of ORF46R. Therefore, the current findings clarify the divergent antiviral mechanisms of the duplicated viperin homeologs in a recurrent polyploid fish, which will shed light on the evolution of teleost duplicated genes.

Two Duplicated Ptpn6 Homeologs Cooperatively and Negatively Regulate RLR-Mediated IFN Response in Hexaploid Gibel Carp

“…Each Cgptpn6 homeolog with three alleles was confirmed by FISH. Consistent with our previous studies (35,36), three green Cgptpn6-A signals and three red Cgptpn6-B signals were located on the three different chromosomes when simultaneously using Cgptpn6-A-BAC-DNA and Cgptpn6-B-BAC-DNA as probes respectively (Figure 1B). Syntenic alignment showed that gibel carp chromosome CgA16 and CgB16 both retained approximately 60% of the analyzed homologous genes in zebrafish chromosome 16 and had a conserved gene block (styk1-phc1-atn1-mlf2-ptpn6).…”

“…Numerous examples have proven that homeolog biased expression seems to be a rule rather than an exception (30). In our previous studies, homeolog bias occurred differently in different tissues (35,36,50); for example, Cgviperin-A was expressed higher than Cgviperin-B in the spleen and liver, whereas in the gill, the transcripts of Cgviperin-B were more abundant than Cgviperin-A (36). However, Cgptpn6-A was dominant in the 12 adult tissues (Figure 2), and poly I:C, poly dA:dT, and SVCV all induced higher upregulated expression of Cgptpn6-A relative to Cgptpn6-B (Figure 3).…”

“…Compared to the crucian carp genome, CaMAVS, CaMITA and CaIRF3 localize in A subgenome, while CaTBK1 and CaATG14 belong to B subgenome. The plasmids containing CaIFN-luc and ISRE-Luc in pGL3-Basic luciferase reporter vectors were constructed as described previously (36). The primers including the restriction enzyme cutting sites used for plasmid construction were also listed in Supplementary Table 1.…”

“…Although the evolutionary fates of duplicated genes have been well elaborated in plant polyploids, only a few studies on recurrent animal polyploids have been reported due to the difficulties in discriminating the different homeologs/alleles of duplicated genes. We had recently elaborated the divergent functions of duplicated foxl2 and viperin homeologs in gibel carp (35,36). However, no single model or ideal could explain all evolutionary ways and fates of duplicate genes (30,33,37).…”

“…Gibel carp, which is widely distributed across the Eurasian continent (38)(39)(40)(41)(42)(43), has been recognized as an evolutional hexaploid with over 150 chromosomes in comparison with tetraploid goldfish (C. auratus) with 100 chromosomes (44)(45)(46). Analyses of several conserved genes suggests that two extra rounds of polyploidy, an early allopolyploidy and a later autopolyploidy, had taken place during gibel carp evolution (35,36,(47)(48)(49)(50). Disease resistance breeding has become an important hotspot in the current research landscape.…”