WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection
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Abstract
The most powerful approach to detect distant homologues of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we applied a powerful sequence-based procedure to identify distant homologues of viral proteins. It relies on three principles: (1) traces of sequence similarity can persist beyond the significance cutoff of homology detection programmes; (2) candidate homologues 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 homologues can be validated using highly sensitive profile–profile comparison. As a test case, this approach was applied to a protein without known homologues, encoded by ORF4 of Lake Sinai viruses (which infect bees). We discovered that the ORF4 protein contains a domain that has homologues in proteins from >20 taxa of viruses infecting arthropods. We called this domain ‘widespread, intriguing, versatile’ (WIV), because it is found in proteins with a wide variety of functions and within varied domain contexts. For example, WIV is found in the NSs protein of tospoviruses, a global threat to food security, which infect plants as well as their arthropod vectors; in the RNA2 ORF1-encoded protein of chronic bee paralysis virus, a widespread virus of bees; and in various proteins of cypoviruses, which infect the silkworm Bombyx mori. Structural modelling with AlphaFold indicated that the WIV domain has a previously unknown fold, and bibliographical evidence suggests that it facilitates infection of arthropods.
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Zhu, F., Li, D., Song, D., Huo, S., Ma, S., Lü, P., Liu, X., Yao, Q., & Chen, K. (2020) · Journal of Proteomics · doi:10.1016/j.jprot.2020.103802 · Cited by 10 · see citing works
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A new cypovirus from the Japanese peppered moth, Biston robustus
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Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Keegan, R. M., Simpkin, A. J., & Rigden, D. J. (2024) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798324009380 · Cited by 12 · see citing works
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In the AlphaFold era, when is experimental phasing of protein crystals still required?Preprint
Keegan, R. M., Simpkin, A. J., & Rigden, D. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.19.604295
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- Authors
- Karlin, D. G.
- Affiliations
- Humboldt-Universität zu Berlin (DE)
- Corresponding author
- Karlin, David G.
- ORCID
- Karlin, David G.
- Venue
- Journal of General Virology
- Publisher
- Microbiology Society
- Published
- 2024-01-09
- Volume
- 105
- Issue
- 1
- ISSN
- 0022-1317 (ISSN-L)
- 1465-2099
- OpenAlex
- W4390706080
- Cited by
- 8
- References
- 108
- Citations by year
- 2026: 3 · 2025: 1 · 2024: 4
- FWCI
- 1.09
- Type
- journal article
- Language
- en
- Open access
- green
- dx.doi.org
- Licence
- cc-by
- Locations
- Journal of General Virology (publishedVersion)
- Preprints.org (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Virus Research Studies
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Keywords
- arthropod viruses, Lake Sinai virus, chronic bee paralysis virus, Bombyx mori, protein structure prediction, AlphaFold
- MeSH terms
- Protein Domains, Animals, Arthropod Vectors, Arthropods, Bees, Reoviridae, Bombyx, Viral Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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