Table 1.
Converged mutations identified in P. putida from pCA TALEs, FA TALEs, pCA + FA TALEs, or glucose ALEs. See Supplementary Data File 1 for a list of all identified mutations.
| Gene name (Locus ID)a | Mutation typeb (unique counts) | Gene annotation(s)c | Experiment(s) in which mutations were identifiedd |
|---|---|---|---|
| gacS (PP_1650) | SNP (7), DEL (3) | sensor protein GacS | pCA, FA, pCA + FA, Glucose |
| oprB-II (PP_1445) | SNP (2), DEL (1) | carbohydrate-selective porin | pCA + FA, Glucose |
| uvrY | SNP (6), INS (1) | BarA/UvrY two-component system response regulator | pCA, FA, pCA + FA, Glucose |
| sucA (PP_4189) | SNP (7) | 2-oxoglutarate dehydrogenase subunit E1 | pCA, FA, pCA + FA |
| rho (PP_5214) | SNP (10) | transcription termination factor Rho | pCA, FA, pCA + FA |
| PP_3350 | SNP (6), DEL (12), INS/DUP (3), INS (1) | hypothetical protein | pCA, FA, pCA + FA |
| ttgB (PP_1385) | SNP (6) | efflux pump membrane protein TtgB | pCA, pCA + FA |
| accD (PP_1996) | SNP (3) | acetyl-CoA carboxylase carboxyltransferase subunit beta | pCA, FA, pCA + FA |
| accA (PP_1607) | SNP (2) | acetyl-CoA carboxylase carboxyltransferase subunit alpha | pCA |
| PP_5245, kefB-III (PP_5246) | SNP (2) | AraC family transcriptional regulator/glutathione-regulated potassium/H+ antiporter | pCA, FA, pCA + FA |
| kefB-III (PP_5246) | SNP (4) | AraC family transcriptional regulator/glutathione-regulated potassium/H+ antiporter | pCA, pCA + FA |
| fleQ (PP_4373) | SNP (6), DEL (1) | transcriptional regulator FleQ | FA, pCA + FA, Glucose |
| dnaK (PP_4727) | SNP (2) | chaperone protein DnaK | FA |
| wbpL (PP_1804) | SNP (1), INS (2) | glycosyl transferase WbpL | pCA |
| PP_1060, PP_1061 | SNP (2) | glutamate synthase large subunit/ATP-dependent DNA helicase | pCA, pCA + FA |
| rpoN (PP_0952) | INS (1), DEL (1) | RNA polymerase sigma-54 factor | pCA + FA |
| sdhA (PP_4191) | SNP (1) | succinate dehydrogenase flavoprotein subunit | pCA + FA |
| oxyR (PP_5309) | SNP (1), INS/DUP (1) | oxidative and nitrosative stress transcriptional dual regulator | pCA + FA, Glucose |
Locus identifiers (IDs) are provided from the NCBI Prokaryotic Genome Annotation Pipeline Version 4.10 (Oct. 2019).
Mutation type abbreviations: SNP, single nucleotide polymorphism; INS, insertion; DEL, deletion; DUP: duplication. The number in parentheses indicates the unique number of counts this type of mutation was observed across the re-sequenced samples, in either a population or isolate.
Annotations assigned from NCBI Reference Genome NC_002947.4.
Experiment abbreviations: pCA, TALE in p-coumaric acid; FA, TALE in ferulic acid; pCA + FA, TALE in equal mass mixture of p-coumaric acid and ferulic acid; Glucose, ALE in glucose.