Table 2.
Genes significantly differentially regulated in response to diacetate and lactate effects and the interaction of the organic acids as determined by ANOVA model B
| Organic acid effect | Strain(s) | No. of genes witha: |
Selected differentially transcribed genes or gene setsb |
|||
|---|---|---|---|---|---|---|
| Increased transcription | Decreased transcription | Gene sets | Increased transcription | Decreased transcription | ||
| Acetate | H7858 | 79 | 116 | Positive enrichment for transcription and 16 transcriptional regulators (lmo2243 [adaA], lmo2128 [malR]), most also with significant lactate effects; glycolysis-related genes increased (fbp, pdhA, mannose-6-phosphate isomerase H7858_2275) and decreased (pfk, gap, pgk) | ||
| F6854 | 0 | 0 | ||||
| H7858 and F6854 | 0 | 0 | ||||
| Lactate | H7858 | 100 | 114 | Positive enrichment for transcription (lmo1496 [greA]) and protein fate (low-temp requirement lmo0215, peptidase lmo1393) | ||
| F6854 | 105 | 108 | Positive enrichment for the PrfA regulon (lmo0205 [plcB], lmo0422 [inlA]) | |||
| H7858 and F6854 | 15 | 12 | lmo1770 (purQ), lmo2085 (sdrD), phosphotransferase system IIA lactose/cellobiose component gene lmo2685, ribosomal protein genes (rpmAF), lmo2524 (fabZ) | lmo0967 (relA), lmo2243 (adaA), lmo2662 (rpiB), lmo1806 (acpP), lmo2727 (lrp) | ||
| Interaction | H7858 | 157 | 317 | Positive enrichment for the CodY regulon (lmo0565 [hisH], lmo0689 [cheV], lmo0714 [fliG]) | codY, branched-chain amino acid biosynthesis genes (ilvBN, leuA) | |
| F6854 | 58 | 151 | Positive enrichment for the PrfA regulon (inlA) and purine biosynthesis; negative enrichment for the Hpr gene set (lmo2192 [oppF], lmo0593) | |||
| H7858 and F6854 | 8 | 32 | lmo0002 (dnaN), lmo0890 (rsbS), lmo1975 (dinP), zinc transporter gene lmo1446 (zurM), oxidoreductase gene lmo2163 (gfo) | Biosynthesis-related genes (lmo1547 [mreC], lmo2526 [murA], lmo1591 [argC]), lmo2622 (rplN) | ||
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 presence of the organic acid had a numerically positive effect on gene transcription.
Bold phrases describe sets of genes that were significantly enriched (P < 0.05, false-discovery rate, <30%) by GSEA. Specific genes or gene groups that appeared relevant due to membership in a overrepresented group (e.g., functional groups, regulon, regulated operons, etc.) or in a group functionally related to pathways affected by organic acid treatments were included.