Coronavirus 5′ UTR
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The first 150 to 200 nucleotides within the 5′ UTR of Alphacoronaviruses are highly structured and shown to be conserved on the structural level. The 5′ UTRs are predicted to contain three conserved stem-loops:[3]
- SL1 is important for viral replication, most likely playing a role in the template-switch of viral subgenomic RNA (sgRNA) transcription. Mutations of the upper part of SL1 seem to have a higher impact of viral replication level.
- SL2 is crucial for viral viability. Nucleotides are interchangeable as long as the structure remains stable. Disrupting any G-C pairing causes major defects in viral replication.
- SL4 is hypothesised to play a role in directing subgenomic RNA synthesis during viral replication.
Downstream of SL4 lies SL5, which overlaps with the first ORF of the viral genome. The three terminal loops of SL5 contain a conserved sequence 5′-UUCCGU-3′
and are thought to act as the packaging signal.[2]
Similar to Alphacoronavirus, the first 150 to 200 nucleotides within the Betacoronavirus 5′ UTR are highly structured and contains three conserved stem-loops (SL1, SL2 and SL4).
Similar to other Sarbecoviruses, the 5′ UTR of
The 5′ UTR of Gammacoronaviruses is similar to the 5′ UTRs of Alpha- and Betacoronaviruses, as they also contain three helices denoted as SL1, SL2 and SL4. Further, in a subset of Gammacoronaviruses a third stem-loop, SL3, is observed. SL1 and SL2 have major impacts of the level of viral replication, whereas SL4 is hypothesized to play a role as a "spacer" during the template-switch of sgRNA synthesis.
The 5′UTR of
See also
- Coronavirus 3′ UTR
- Coronavirus 3′ UTR pseudoknot
- Coronavirus 3′ stem-loop II-like motif (s2m)
- Coronavirus frameshifting stimulation element
- Coronavirus packaging signal