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Article

Investigating the Human Host—ssRNA Virus Interaction Landscape Using the SMEAGOL Toolbox

1
Insitro, South San Francisco, CA 94080, USA
2
Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
3
Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, 69622 Villeurbanne, France
4
Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
*
Author to whom correspondence should be addressed.
Academic Editors: Franziska Hufsky, Alba Pérez-Cataluña, Walter Randazzo, Gloria Sanchez, Fernando González-Candelas and Manja Marz
Viruses 2022, 14(7), 1436; https://doi.org/10.3390/v14071436
Received: 27 April 2022 / Revised: 19 June 2022 / Accepted: 24 June 2022 / Published: 29 June 2022
(This article belongs to the Special Issue Virus Bioinformatics 2022)
Viruses have evolved numerous mechanisms to exploit the molecular machinery of their host cells, including the broad spectrum of host RNA-binding proteins (RBPs). However, the RBP interactomes of most viruses are largely unknown. To shed light on the interaction landscape of RNA viruses with human host cell RBPs, we have analysed 197 single-stranded RNA (ssRNA) viral genome sequences and found that the majority of ssRNA virus genomes are significantly enriched or depleted in motifs for specific human RBPs, suggesting selection pressure on these interactions. To facilitate tailored investigations and the analysis of genomes sequenced in future, we have released our methodology as a fast and user-friendly computational toolbox named SMEAGOL. Our resources will contribute to future studies of specific ssRNA virus—host cell interactions and support the identification of antiviral drug targets. View Full-Text
Keywords: RNA virus genome; RNA-binding protein; virus-host interaction; toolbox RNA virus genome; RNA-binding protein; virus-host interaction; toolbox
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MDPI and ACS Style

Lal, A.; Galvao Ferrarini, M.; Gruber, A.J. Investigating the Human Host—ssRNA Virus Interaction Landscape Using the SMEAGOL Toolbox. Viruses 2022, 14, 1436. https://doi.org/10.3390/v14071436

AMA Style

Lal A, Galvao Ferrarini M, Gruber AJ. Investigating the Human Host—ssRNA Virus Interaction Landscape Using the SMEAGOL Toolbox. Viruses. 2022; 14(7):1436. https://doi.org/10.3390/v14071436

Chicago/Turabian Style

Lal, Avantika, Mariana Galvao Ferrarini, and Andreas J. Gruber. 2022. "Investigating the Human Host—ssRNA Virus Interaction Landscape Using the SMEAGOL Toolbox" Viruses 14, no. 7: 1436. https://doi.org/10.3390/v14071436

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