Table 1.
Groups of genes with similar transcription patterns across organic acid treatments as determined by ANOVA model A
| Transcription patternb | Strain(s) | No. of genes witha: |
Selected differentially transcribed genesc |
||
|---|---|---|---|---|---|
| Increased transcription | Decreased transcription | Increased transcription | Decreased transcription | ||
| A, G | H7858 | 271 | 377 | Ribosomal protein genes (rpmJ, rpsHS, rplPC), toxic ion resistance genes (lmo1967 and lmo1977), mannose ABC transporter genes (lmo1997, lmo2001 [manSL]), regulator gene lmo2003, zinc-containing alcohol dehydrogenase genes (lmo0773, lmo2573) | Biosynthesis of cofactor genes (lmo1556 [hemC], lmo0224, lmo0225 [folPB]) , fatty acid metabolism genes (lmo1806, lmo1807 [acpP, fabG]), iron ABC transport genes (lmo1957, lmo1959), oxidative stress genes (lmo0983 [gpxA], lmo0669 [ydaD]), glycolysis genes (pgk, gap, gapR), pyruvate dehydrogenase gene (lmo1053 [pdhB]), two-component response regulator genes (lmo1021, lmo1377, lmo2500), ABC-2 transport protein gene lmo0742 |
| F6854 | 0 | 0 | |||
| B, H | H7858 | 32 | 45 | Pentose phosphate epimerase gene (lmo0499 [rpe]), cytochrome d oxidase subunit gene (lmo2718 [cydA]) | lmo0001 (dnaA), lmo0243 (sigH), bkd operon member lmo1372 (lpdA), potassium sensor gene lmo2679 (kdpD), putative acetyltransferase genes (lmo0353, lmo0652) |
| F6854 | 201 | 295 | lmo0433 (inlA), two-component system genes (lmo2500 and -1 [phoRP]), sugar ABC transporter genes (fructose transporter genes lmo0357, lmo0426, and lmo2137 [fruA]), prophage genes (lmo2283, lmo2284, lmo2286, and lmo2293), zinc-containing alcohol dehydrogenase genes (lmo0773, lmo2573) | Motility genes (cheA, flgDE, fliM), lmo0894, lmo0896 ([rsbWX]), cation transporter genes (lmo2087, lmo2575, lmo0990), menaquinone biosynthesis genes (menBDF), peroxidase gene (lmo0983 [gpxA]), acetate kinase genes (lmo1168 and lmo1581), ABC-2 transport protein gene lmo0742 | |
| H7858 and F6854 | 7 | 7 | Regulatory protein gene (lmo0168 [abrB]), DNA damage-inducible protein gene (lmo1975 [dinP]), oxidoreductase gene (lmo2163 [gfo]), ATP-binding ABC component gene (lmo2192 [oppF]), glucose-6-phosphate isomerase gene (lmo2367 [pgi]) | 2 prophage genes (lmo0113, lmo0124), glucose kinase gene (lmo1339 [gki]) | |
| C, I | H7858 | 31 | 40 | Acetolactate synthase gene (lmo2006 [alsS]), MATE pump gene lmo2725, TetR-like repressor gene lmo2088 | lmo1985 (ilvN), lmo2483 (hprK) |
| F6854 | 14 | 8 | Fructose phosphotransferase system component gene (lmo2135 [fruA]), transcription antiterminator gene (lmo2138), lmo1055 (pdhD) | lmo1531 (queA) | |
| H7858 and F6854 | 0 | 2 | Glutamine synthetase repressor gene lmo1298, putative ABC permease gene lmo1746 | ||
| D, J | H7858 | 0 | 0 | ||
| F6854 | 12 | 80 | Transcriptional regulator gene (lmo2493 [czrA]) | Amino acid genes (lmo1985 [ilvN], lmo1587 [argF], lmo1591 [argC]), fatty acid gene (bkd operon member lmo1373), nucleotide metabolism gene (lmo0192 [purR]), energy metabolism gene (lmo1171 [adhE]) | |
| E, K | H7858 | 24 | 13 | Hemolysin genes (lmo0202 [hly], lmo2738), pyruvate dehydrogenase repressor gene (lmo0948), transcriptional regulator genes (H7858_1021.1 and H7858_0866) | Potassium-transporting ATPase subunit gene (lmo2680 [kdpE]), MerR family transcriptional regulator gene (lmo2728) |
| F6854 | 0 | 0 | |||
| F, L | H7858 | 36 | 114 | lmo0714 (fliG) in the CodY gene set, lmo1246 (deaD), lmo1566 (citC), acetyl-CoA carboxylase gene (lmo1573 [accD]), lmo2582 (vicK) | Regulatory protein genes (lmo0893 [rsbV], lmo0895 [sigB], lmo1280 [codY]), lactate dehydrogenase gene (lmo0210 [ldh]) |
| F6854 | 0 | 0 | |||
Genes were considered significantly differentially expressed if they had a fold change of >1.5 and adjusted (for multiple comparisons) P value of <0.05. Genes in a cluster were described as having increased transcription if the average transcription expression of the cluster increased from control (CTRL) treatment to the combination treatment (PLSDA).
Transcription patterns in the same row of Fig. 2 are presented together. This combines patterns that show the same relative trends in either increased or decreased differential transcription across treatments.
Genes that appeared relevant due to membership in an overrepresented group (e.g., functional groups, regulated operons, etc.) or in a group functionally related to pathways elaborated in the text were included.