Table 1.
Effect of mutations in SL1 on plaque production
| Virus name | Mutation recovered | Intended effect of mutation on SL1 | Plaque diameter (mm)a |
|---|---|---|---|
| SL1 stem mutants | |||
| MHV-A59 1000 | WT | 2.37 ± 0.05 | |
| SL1-A | G14C/G15U/G17C | Destroys base pairing in the upper region of the stem | Not viable |
| SL1-B | C28G/C29A/C30G | Destroys base pairing in the upper region of the stem | 1.82 ± 0.04 |
| SLI-AB | C28G/C29A/C30G G14C/G15U/G17C | Maintains base pairing in the upper region of the stem | 2.16 ± 0.04 |
| SL1-C | G6C/A7U/G8C | Destroys base pairing in the lower region of the stem | 1.55 ± 0.03 |
| SL1-D | C37G/U38A/C39G | Destroys base pairing in the lower region of the stem | 1.77 ± 0.05 |
| SL1-CD | G6C/A7U/G8C | Maintains base pairing in the lower region of the stem | Not viable |
| C37G/U38A/C39G | |||
| Cytidine deletion mutants | |||
| MHV-A59 1000 | WT | 2.14 ± 0.06 | |
| SL1-ΔC16 | ΔC16 | Removes a bulged C from the upper region of the stem | 2.03 ± 0.05 |
| SL1-ΔC19/C20 | ΔC19/C20 | Removes two bulged Cs from the upper region of the stem | 2.08 ± 0.09 |
| SL1-ΔC16/C19/C20 | ΔC16/C19/C20 | Removes all bulges from the upper region of the stem | 1.87 ± 0.06 |
| SL1-ΔA35 mutant and second-site suppressor mutants | |||
| MHV-A59 1000 | WT | 2.74 ± 0.06 | |
| SL1-ΔA35-PL6-ps1 | ΔA35/3′A29G | Removed bulged A from the lower region of the stem | 2.47 ± 0.09 |
| SL1-ΔA35-PL6-ps2 | ΔA35/G10A/3′A29G | Removed bulged A from the lower region of the stem | 2.53 ± 0.08 |
| SL1-ΔA35-PL12-ps2 | ΔA35/C34U/3′A78G | Removed bulged A from the lower region of the stem | 2.13 ± 0.08 |
| SL1-ΔA35-PL4-ps1 | ΔA35/U33C/3′A29G | Removed bulged A from the lower region of the stem | 2.57 ± 0.09 |
| SL1-ΔA35-PL1-ps1 | ΔA35/A36U/3′A29G | Removed bulged A from the lower region of the stem | 2.46 ± 0.07 |
| SL1-ΔA35-PL3-ps1 | ΔA35/C37U/3′A29G | Removed bulged A from the lower region of the stem | 2.80 ± 0.10 |
| SL1-ΔA35-PL14-ps1 | ΔA35/C37U/3′A78G | Removed bulged A from the lower region of the stem | 2.54 ± 0.07 |
| Mutants that target the lower SL1 stem | |||
| MHV-A59 1000 | WT | 2.2 ± 0.05 | |
| SL1-A5G/U40C | A5G/U40C | Increased stability of lower stem | Not viable |
| SL1-U40C | U40C | Control for A5G/U40C | 2.1 ± 0.06 |
| SL1-A5G | A5G | Control for A5G/U40C | 1.8 ± 0.06 |
| SL1-A5C/U40C | A5C/U40C | Control for A5G/U40C | 2.1 ± 0.06 |
| SL1-A7G/U38C | WT | Increased stability of the lower region of the stem | Unstable |
Data are from four separate experiments. A WT MHV-A59 is included for comparison with each experiment.
a
Plaque diameters were calculated as an average of at least 50 plaques, as described previously.21