Questions discussed:
Chapter 5 part C (sections 5.22-5.31)
1. We have previously discussed structural and nonstructural proteins, but coronaviruses also express “accessory proteins.” What do the accessory proteins do? When are they “optional”?
2. What mechanism allows polyprotein ORF1ab to be made instead of just ORF1a? Go to the betacoronavirus page of ViralZone and look up which nonstructural proteins within ORF1ab are suggested to have a function in host modulation.
3. Several SARS-CoV-2 genes were shown to modulate host interferon responses in a Nature Communication paper called “Activation and evasion of type I interferon responses by SARS-CoV-2.” Which SARS-CoV-2 gene products were able to block the induction of an IFN-beta luciferase reporter (fig 2C)? Which SARS-CoV-2 gene products were able to block the induction of an ISRE luciferase reporter (fig 5A)?
4. Draw a diagram of the SARS-CoV-2 genome. Your drawing should look similar to fig. 5.4. However, add the following features to your drawing: the leader sequence, transcriptional regulatory sequences (TRS-L and multiple TRS-B). Explain a) how there can be various sizes of (-) ssRNA and b) how every sgRNA would have a leader sequence.
5. Most coronavirus sgRNAs are translated as a single protein. However, others can encode two proteins. The mechanism for coding the N and 9b proteins from one sgRNA involves two start codons: one “weak” and one “strong”. What is the optimal Kozak sequence? Who was this sequence named after? How different is the “weak” start codon from “optimal” Kozak sequence?
Certain amino acids are thought to be essential for ExoN to provide coronaviruses with proofreading capability. Why is there a need for proofreading in coronaviruses? What chemical property (under physiological pH) do the R chains of the amino acids in the proofreading motif have? If those amino acids were replaced with alanines, what property do the R chains then have?
