Table 2.
Recurring Mutations Identified across the ALE Endpoint Strains.
| Gene | Specific Function | Category | Mutation | Protein Change | Strain Number(s) |
|---|---|---|---|---|---|
| pyrE/rph | Orotate phosphoribosyltransferase/RNase PH | M | 82-bp deletion | Frameshift | 1, 2, 3, 4, 5, 7, 9, 10 |
| rpoC | RNA polymerase subunit | R | SNP | A734V (GCG→GTG) | 1, 2 |
| SNP | Q1367* (CAG→TAG) | 5, 7, 10 | |||
| pykF | Pyruvate kinase I | M | SNP | ydhZ/pykF intergenic (−498/−59) | 3 |
| SNP | T278S (ACC→TCC) | 10 | |||
| SNP | K286* (AAA→TAA) | 4, 5, 7 | |||
| rne | Ribonuclease E | R | SNP | D415N (GAC→AAC) | 6/8 |
| SNP | H243Y (CAT→TAT) | 3 | |||
| SNP | G124S (GGT→AGT) | 9 | |||
| SNP | V19A (GTA→GCA) | 2 | |||
| ygaH/mprA | L-Valine efflux transporter/MprA repressor | R | SNP | Intergenic (+77/−14) | 6/8 |
| SNP | Intergenic (+80/−11) | 10 | |||
| SNP | Intergenic (+81/−10) | 4, 5 | |||
| mlaE | Phospholipid ABC transporter | C | SNP | L107F (TTG→TTT) | 4, 5, 7 |
| yfdI | Predicted inner membrane protein | C | 1-bp insertion | Frameshift (519/1,332 nt) | 8 |
| SNP | Q186* (CAA→TAA) | 6 | |||
| 1-bp deletion | Frameshift (1,274/1,332 nt) | 3 | |||
| nagC | PTS regulator | C | SNP | C264S (TGC→AGC) | 6/8 |
| 1-bp deletion | Frameshift (218/1,221 nt) | 2 | |||
| hns/tdk | H-NS regulator/thymidine kinase | R | SNP | Intergenic (−22/−583) | 6/8 |
| Insertion sequence | Intergenic (−111/−486) | 9 | |||
| hfq | RNA binding protein | R | SNP | D9A (GAT→GCT) | 1, 7 |
| nagA | N-acetylglucosamine-6-phosphate deacetylase | C | SNP | G265D (GGC→GAC) | 2 |
| 21-bp deletion | In-frame (381 − 401/1,149 nt) | 1 | |||
| secD | Membrane protein channel component | C | SNP | R181L (CGC→CTC) | 8 |
| SNP | G499G (GGC→GGT) | 2 | |||
| dinQ/arsR | Toxic membrane peptide/metal-responsive regulator | C | SNP | Intergenic (−209/−486) | 8 |
| 1-bp deletion | Intergenic (−305/−390) | 3 | |||
| ilvL/ilvX | Leader peptide regulating isoleucine and valine biosynthesis operons | M | Double SNP | Intergenic (+47/−39) | 6 |
| SNP | Intergenic (+48/−39) | 8 |
M, metabolic; R, regulatory; C, cell envelope.