TABLE 2.
Genotypes and characteristics of complementation-independent ϕXG4J isolates
| Genetic changes found in viable strainsa |
No. of independent isolates | Suppressing phenotypeb | Structural/genetic characteristicsc | |
|---|---|---|---|---|
| Nucleotide change | Coat protein amino acidd | |||
| T1044C | L14P | 2 | Pinprick | F-J contact site |
| G1067T | G22C | 1 | Pinprick | J protein suppressor† |
| G1129T | E42D* | 3 | Pinprick | F-J contact site |
| A1134G | D44G | 1 | Pinprick | F-J contact site |
| G1214T | V71F* | 2 | Pinprick | J protein suppressor† |
| Internal scaffolding (B) suppressor† | ||||
| B/J protein binding pocket | ||||
| C1220T | H73Y* | 2 | Pinprick | B/J protein binding pocket |
| A1613G | T204A* | 2 | Pinprick | J protein suppressor† |
| External scaffolding (D) suppressor† | ||||
| A991G | 2 | Pinprick | J-F intercistronic region | |
| G993T | 1 | Pinprick | J-F intercistronic region | |
| G993C | 1 | Pinprick | J-F intercistronic region | |
| 991–1011 duplicated (+21) | None | 5 | Medium | J-F intercistronic region |
| 991–1014 duplicated (+24) | None | 1 | Medium | J-F intercistronic region |
| 991–1202 duplicated (+210) | E42D | 1 | Medium | J-F intercistronic region |
Single base changes in gene F, which encodes the viral coat protein. The nucleotide substitutions are reported with the wild-type nucleotide, the position within the published sequence (69), and the substituted nucleotide. The amino acid substitutions conferred by the mutation are reported with the wild-type amino acid, the position within the protein, and the substituted amino acid. In some strains, a portion of the J-F intercistronic region and 5′ end of the downstream F gene was duplicated. The duplicated nucleotides are numbered. The number within the parentheses refers to the duplication’s length.
The suppressing phenotype reflects plating efficiencies and plaque morphologies. Phenotypes: pinprick, forms weak fuzzy pinprick plaques without exogenous complementation by the cloned ϕX174 J gene at an ∼10−1 frequency (uncomplemented titer/complemented titer); medium, forms clear distinct plaques, but smaller than the wild type. Uncomplemented and complemented titers are comparable.
Information regarding the coat protein amino acids in the virion atomic structure (15, 16) and/or other phenotypes associated with the mutation. †, Mutations previously isolated as suppressors of mutant J proteins (24), mutant internal scaffolding proteins (62), or mutant external scaffolding proteins (31, 33, 35).
*, Missense mutations that were also isolated independently in cis with the 991–1011 (+21) duplication.