Evolutionary selection of pestivirus variants with altered or no microRNA dependency
Open Access
- 6 May 2020
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 48 (10), 5555-5571
- https://doi.org/10.1093/nar/gkaa300
Abstract
Host microRNA (miRNA) dependency is a hallmark of the human pathogen hepatitis C virus (HCV) and was also described for the related pestiviruses, which are important livestock pathogens. The liver-specific miR-122 binds within the HCV 5′ untranslated region (UTR), whereas the broadly expressed let-7 and miR-17 families bind two sites (S1 and S2, respectively) in the pestiviral 3′ UTR. Here, we dissected the mechanism of miRNA dependency of the pestivirus bovine viral diarrhea virus (BVDV). Argonaute 2 (AGO2) and miR-17 binding were essential for viral replication, whereas let-7 binding was mainly required for full translational efficiency. Furthermore, using seed site randomized genomes and evolutionary selection experiments, we found that tropism could be redirected to different miRNAs. AGO cross-linking and immunoprecipitation (CLIP) experiments and miRNA antagonism demonstrated that these alternative variants bound and depended on the corresponding miRNAs. Interestingly, we also identified miRNA-independent variants that were obtained through acquisition of compensatory mutations near the genomic 3′ terminus. Rescue experiments demonstrated that miRNA binding and 3′ mutagenesis contribute to replication through mutually exclusive mechanisms. Altogether, our findings suggest that pestiviruses, although capable of miRNA-independent replication, took advantage of miRNAs as essential host factors, suggesting a favorable path during evolutionary adaptation.Funding Information
- Faculty of Health and Medical Sciences, University of Copenhagen
- Department of Infectious Diseases, Hvidovre Hospital
- European Research Council (802899)
- Independent Research Fund Denmark (4004-00598, 6110-00595, 6111-00314)
- Novo Nordisk Foundation (NNF14OC0012533, NNF15OC0017404, 0058443)
- Lundbeck Foundation (R221-2016-1455, R192-2015-1154)
- Innovation Fund Denmark (3040-00001B)
- Weimann Foundation
- Department of Immunology and Microbiology, University of Copenhagen
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