Table 1.
Mutations that occurred in the strains isolated from the evolution experiment
| Gene | Genomic coordinate | Nucleotide change | Effect of nucleotide change | Frequency (%) | Time | Description |
|---|---|---|---|---|---|---|
| – | 257,908 | G → A | 5 | T5 | IS1 non-coding | |
| frmR (1) | 379,625 | A → C | V(86) → G | 5 | T7 | Formaldehyde repressor |
| frmR (2) | 379,821 | − 1:C | Q(21) → frameshift | 5 | T7 | |
| gltA | 754,123 | C → T | E(116) → K | 10 | T4 | Citrate synthase |
| plsX (1) | 1,148,440 | − 1:A | Q(274)KS → QRA STOP | 10 | T3 | Fatty acid/phospholipid synthesis protein |
| plsX (2) | 1,148,491 | G → T | G(291) → C | 10 | T4 | |
| fabF (1) | 1,152,159 | T → G | F(74) → C | 48 | T3 | Component of 3-oxoacyl-ACP synthase II |
| fabF (2) | 1,152,159 | C → T | wt | 5 | T4 | |
| marC (1) | 1,618,245 | A → T | stop → frameshift | 10 | T4 | Inner membrane protein |
| marC (2) | 1,618,498 | − 7:ATCGCTA | I(135) → stop | 10 | T2 | |
| marC (3) | 1,618,805 | − 1:T | M(35) → stop | 48 | T3 | |
| yffS | 2,564,930 | G → T | A → A (silent) | 5 | T3 | CPZ-55 prophage; uncharacterized protein |
| yfgO | 2,615,421 | G → A | A(154) → V | 5 | T2 | Function unknown, predicted membrane permease |
| iscR | 2,661,812 | T → A | H(107) → L | 10 | T5 | Iron–sulfur cluster regulator |
| srmB | 2,713,364 | G → A | D(157) → N | 10 | T2 | SrmB is a DEAD-box protein with RNA helicase activity that facilitates an early step in the assembly of the 50S subunit of the ribosome |
| PyghB | 3,153,480 | − 15 | 33 | T4 | Required, with yqjA, for membrane integrity | |
| trkH | 4,033,611 | G → A | G(156) → D | 10 | T5 | TrkH is a potassium ion transporter |
| rraA (1) | 4,119,044 | A → T | V(96) → E | 10 | T4 | RraA inhibits ribonuclease E activity by binding to and masking the C-terminal RNA binding domain of RNase E |
| rraA (2) | 4,119,138 | C → T | G(67) → S | 5 | T4 | |
| plsB | 4,255,502 | T → C | Q(322) → R | 5 | T2 | Membrane-bound glycerol-3-phosphate acyltransferase catalyzes the first committed step in phospholipid biosynthesis |
| Rob (1) | 4,634,494 | C → A | G(273) → stop | 5 | T5 | Transcriptional regulator implied in solvent tolerance |
| Rob (2) | 4,635,002 | + 1:T | Y(103) → stop | 10 | T6 | |
| Rob (3) | 4,635,168 | + 1:G | H(48) → frameshift | 19 | T6 | |
| creC | 4,637,267 | T → G | L (191) → W | 5 | T5 | Carbon source responsive sensor kinase |
Protein functions are taken from ecocyc.org. For genes with alternative mutations, the numbering behind the gene name refers to the mutation name provided in Fig. 2