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Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2
Getong Liu1,2, Hengyi Jiang1,2, Dongrong Chen1,2
1Shanghai Pudong Hospital, Fudan University Pudong Medical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China.
Nucleic Acids Research
|January 31, 2024
Summary
Researchers discovered 39 Hammerhead-variant ribozymes (CoV-HHRz) in the SARS-CoV-2 genome. These ribozymes are conserved across variants and may play a role in viral RNA processing and replication.
Area of Science:
- Virology
- Molecular Biology
- Biochemistry
Background:
- The COVID-19 pandemic, caused by the SARS-CoV-2 virus, necessitates a deeper understanding of its genome and biological mechanisms.
- Despite extensive research, no ribozymes have been previously identified within the SARS-CoV-2 genome.
Purpose of the Study:
- To identify and characterize novel ribozyme sequences within the SARS-CoV-2 genome.
- To investigate the potential in vitro and in vivo activity of these identified ribozymes.
Main Methods:
- Bioinformatic analysis to identify Hammerhead-variant ribozyme sequences (CoV-HHRz) in the SARS-CoV-2 genome.
- In vitro biochemical assays to assess ribozyme cleavage activity, including pH and ion dependency.
- Comparison of CoV-HHRz conservation across SARS-CoV-2 variants and other coronaviruses.
- Correlation of CoV-HHRz cleavage sites with known subgenomic RNA (sgRNA) breakpoints using transcriptome data.
Main Results:
- Identification of 39 Hammerhead-variant ribozyme sequences (CoV-HHRz) highly conserved within SARS-CoV-2 variants.
- CoV-HHRz exhibit typical ribozyme characteristics, including pH and ion-dependent cleavage, with optimal activity in the presence of Mn2+.
- Cleavage sites of four CoV-HHRz align with breakpoints of expressed sgRNAs in SARS-CoV-2, suggesting potential in vivo function.
- These ribozymes are implicated in processing sgRNAs for ORF7b, ORF 10, and ORF1ab nsp13, crucial for viral packaging and lifecycle.
Conclusions:
- The discovery of CoV-HHRz in SARS-CoV-2 expands our understanding of viral RNA processing mechanisms.
- These ribozymes are conserved within SARS-CoV-2 variants and show potential for in vivo activity in sgRNA processing.
- CoV-HHRz may represent a novel target for antiviral strategies against SARS-CoV-2.
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