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A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions
Published on: July 18, 2013
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Investigating the Human Host-ssRNA Virus Interaction Landscape Using the SMEAGOL Toolbox
Avantika Lal1, Mariana Galvao Ferrarini2,3, Andreas J Gruber4
1Insitro, South San Francisco, CA 94080, USA.
Viruses
|July 27, 2022
Summary
Most RNA viruses interact with human RNA-binding proteins (RBPs). Analyzing viral genomes revealed specific RBP motif enrichment or depletion, indicating selection pressures. A new tool, SMEAGOL, aids future research and antiviral target discovery.
Area of Science:
- Virology
- Computational Biology
- Genomics
Background:
- Viruses utilize host cell machinery, including RNA-binding proteins (RBPs), for replication.
- The specific interactions between viral genomes and host RBPs are largely uncharacterized for most viruses.
Purpose of the Study:
- To investigate the interaction landscape between single-stranded RNA (ssRNA) viruses and human RBPs.
- To identify potential selection pressures shaping these virus-host interactions.
Main Methods:
- Analysis of 197 ssRNA viral genome sequences.
- Computational identification of motifs recognized by human RBPs within viral genomes.
- Development of the SMEAGOL computational toolbox.
Main Results:
- The majority of analyzed ssRNA viral genomes showed significant enrichment or depletion of motifs for specific human RBPs.
- These findings suggest evolutionary selection acting on RBP-virus genome interactions.
Conclusions:
- Viral genomes are shaped by interactions with host RBPs.
- The SMEAGOL toolbox provides a resource for future studies on ssRNA virus-host interactions.
- Understanding these interactions can aid in identifying novel antiviral drug targets.
