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Published on: February 27, 2021
An overlapping essential gene in the Potyviridae
Betty Y-W Chung1, W Allen Miller, John F Atkins
1BioSciences Institute, University College Cork, Cork, Ireland.
Summary
Researchers discovered a hidden gene, pipo, within the Potyviridae family of plant viruses. This essential gene, translated via ribosomal frameshifting, is crucial for viral survival and reveals potential for other undiscovered viral genes.
Area of Science:
- Virology
- Molecular Biology
- Bioinformatics
Background:
- The Potyviridae family comprises over 30% of known plant viruses, many with significant agricultural impact.
- Potyviridae viruses possess a positive-sense RNA genome (~10 kb) with a single large open reading frame (ORF) encoding a polyprotein.
- This polyprotein is proteolytically cleaved into approximately 10 mature functional proteins.
Purpose of the Study:
- To identify and characterize novel genetic elements within the Potyviridae viral genome.
- To investigate the function and expression mechanism of a newly discovered short open reading frame (sORF).
Main Methods:
- Bioinformatic analysis to identify conserved ORFs with coding signatures.
- Site-directed mutagenesis to assess the impact of the sORF on viral viability.
- Immunoblotting using specific antisera to detect protein expression in planta.
Main Results:
- Discovery of a conserved sORF, termed pipo, located within the P3 cistron and translated in the +2 reading frame.
- Mutations disrupting PIPO protein expression were lethal to Turnip mosaic potyvirus, indicating its essentiality.
- Detection of an ~25-kDa PIPO-fusion product in planta, suggesting expression via ribosomal frameshifting or transcriptional slippage.
Conclusions:
- The PIPO protein, expressed as a P3-PIPO fusion, is essential for Potyviridae virus viability.
- This discovery highlights the potential for hidden, overlapping genes in viral genomes and other organisms.
- The MLOGD software package is a valuable tool for identifying such cryptic genetic elements.
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