Karlin, D. (2024). WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection. Journal of General Virology, 105(1).
Karlin, D. (2024). WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection. Journal of General Virology, 105(1).
Karlin, D. (2024). WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection. Journal of General Virology, 105(1).
Karlin, D. (2024). WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection. Journal of General Virology, 105(1).
Abstract
Today, the most powerful approach to detect distant homologs of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we developed a powerful sequence-based procedure to identify distant homologs of viral proteins. It relies on 3 main principles: 1) Traces of sequence similarity with a protein can persist beyond the significance cutoff of homology detection programs; 2) Candidate homologs can be identified among proteins with weak sequence similarity to the query, by using "contextual" information, e.g. taxonomy or type of host infected; 3) These candidate homologs can be validated using highly sensitive profile-profile comparison.As a test case, we applied our approach to a protein without known homologs, ORF4 of Lake Sinai virus (which infects bees). We discovered that ORF4 is composed of a domain that has homologs in proteins from >20 taxa of viruses infecting arthropods. We called it “Widespread, Intriguing, Versatile” (WIV) domain because it is found in proteins with a wide variety of domain organizations and functions. For example, WIV is encoded by the NSs protein of tospoviruses, a global threat to food security, which infect plants through arthropod vectors; by the protein encoded by RNA2 ORF1 of chronic bee paralysis virus, a widespread virus of bees; and by various proteins of cypoviruses, which infect the silkworm bombyx mori. WIV has a previously unknown structural fold, according to Alphafold predictions. In some viral species, WIV facilitates infection of arthropods, according to bibliographical evidence
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