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
▼
Show Figures
Figure 1
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- Supplementary File 1:
ZIP-Document (ZIP, 42496 KiB)
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 StyleLal, 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
Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.
