TABLE 4.
Key mutations for final endpoint clones of S. aureus TCH1516 after tolerance adaptive laboratory evolution in RPMI+ to nafcillin (SNFR)
| Genea | Specific function | Mutation | Protein and nucleotide changeb |
Strain(s) |
|---|---|---|---|---|
| mecA | Beta-lactam-inducible penicillin-binding protein |
SNP | D586Y (GAT→TAT) | 7, 9, 13, 15, 17, 23 |
| SNP | V488F (GTT→TTT) | 19 | ||
| rpoD (sigA) | DNA-directed RNA polymerase sigma subunit |
SNP | A187T (GCA→ACA) | 13 |
| SNP | A194V (GCA→GTA) | 19 | ||
| gdpP | Cyclic di-AMP phosphodiesterase |
SNP | N182K (AAC→AAG) | 9 |
| SNP | S222F (TCC→TTC) | 23 | ||
| ywtF | Putative transcriptional regulator |
DEL | Coding (235/1218 nt) | 7 |
| SNP | Y121* (TAC→TAG) | 15 | ||
| SNP | D214N (GAC→AAC) | 19 | ||
| codY | CodY family transcriptional regulator |
SNP | S204L (TCA→TTA) | 9 |
| SNP | K205N (AAA→AAT) | 15 | ||
| cdaA | Cyclic di-AMP synthase | SNP | W76C (TGG→TGC) | 7 |
| SNP | Q55H (CAG→CAT) | 13 | ||
| SNP | A80S (GCT→TCT) | 17 | ||
| ssaA2_4 | Staphylococcal secretory antigen |
SNP | W70* (TGG→TAG) | 9 |
| SNP | C45Y (TGT→TAT) | 15 | ||
| SNP | G65V (GGC→GTC) | 17 | ||
| oatA (oatA_2) | O-Acetyltransferase | SNP | G451S (GGT→AGT) | 7 |
| DEL | Coding (1239-1250/1812 nt) | 9 | ||
| DEL | Coding (29/1812 nt) | 13 | ||
| DEL | Coding (1327/1812 nt) | 15 | ||
| SNP | E341* (GAA→TAA) | 19 | ||
| vraS | Sensor histidine kinase | SNP | G92V (GGC→GTC) | 7 |
| SNP | V66L (GTA→CTA) | 17, 19, 23 | ||
| RS08710 | Heme uptake protein MmpL11 | DEL | Coding (2065-2067/2280 nt) | 7, 19 |
a
The gene nomenclature provided by prokka annotation, reflected in the mutation analysis, is shown in the parentheses. The gene locus tag corresponds to USA300HOU_RSXXXXX.
b
An asterisk indicates that a mutation led to a stop codon being formed.