Table 4. Pathway and regulator enrichment for Shewanella W3-18-1 in carbon-limited chemostat co-culture with lactate as the sole source of carbon.
| Pathway/regulon enrichment | P-valuea |
|---|---|
| Genes displaying ⩾2-fold increase in mRNA abundance relative to the axenic state | |
| Amino acids biosynthesis: argC, aroF, asnB, cysD, cysJ, glnA, hisD, hisG, lysC, tyrA | 0.0001 |
| Metabolism of inorganic nutrients: cysD, cysJ, glnA, nrfA | 0.0063 |
| Phospholipase: pldA | 0.0130 |
| Alanine degradation: ald | 0.0133 |
| Nitrogen assimilation, NtrC regulon: amtB, glnA, glnK, SputW3181_0223 | 0.0001 |
| Tryptophan biosynthesis, TrpR regulon: aroF, tyrA | 0.0043 |
| Genes displaying ⩾2-fold decrease in mRNA abundance relative to the axenic state | |
| Aspartate super-pathway: asd, lysA, metA, metB, metC, metE, metH, metK, metL | 0.0001 |
| Threonine degradation: ilvA, ilvC, ilvD, ilvG, ilvH, ilvI | 0.0002 |
| Tryptophan biosynthesis: trpA, trpB, trpCF, trpD, trpE, trpG | 0.0002 |
| Fatty acid and lipids degradation: fadA, fadB, fadE, fadI, fadJ, glpD, SputW3181_1978, SputW3181_2433 | 0.0004 |
| Homoserine and methionine biosynthesis: asd, metA, metB, metC, metE, metE, metH, metL | 0.0069 |
| Isoleucine and valine biosynthesis: asd, ilvA, ilvC, ilvD, ilvG, ilvH, ilvI, metL | 0.0106 |
| B12 biosynthesis and uptake: cobC, cobS, cobT, cobU, btuC, btuD | 0.0237 |
| Thiamin biosynthesis thiC, thiDE, thiF, thiH | 0.0237 |
| Superpathway of chorismate metabolism: aroE, pheA, trpA, trpB, trpCF, trpD, trpE, trpG, ubiC | 0.0276 |
| Methylglyoxal detoxification: dldD, gloB | 0.0286 |
| Methionine biosynthesis, MetJ regulon: btuB, metA, metB, metE, metF, metH, metK, metL, metR, metT, metY, msrA, SputW3181_0088, SputW3181_0089, SputW3181_1636, SputW3181_2707 | 0.0000 |
| Fatty acid degradation, PsrA regulon: etfQ, fadA, fadB, fadE, fadH, fadI, fadJ, psrA, SputW3181_1978, SputW3181_2146 | 0.0004 |
| Methionine biosynthesis, MetR regulon: metC, metE, metR | 0.0058 |
| Fatty acid degradation, FadR regulon: fadI, fadJ, fadL | 0.01319 |
| Lactate utilization, LlldR regulon: lldE, lldF | 0.03802 |
a
P-value represents the probability that the number of genes associated with a specific pathway/regulon occurs by chance.