TABLE 2.
Differential expression of acid-evolved strains compared to ancestral strain W3110
| Regulation of expression | Genes in the indicated straina |
|||
|---|---|---|---|---|
| B11-1 | F9-2 | F11-1 | H9-1 | |
| Upregulated ≥4-fold | citCDEFGX, dcuAB, srlABDE, tdcBCDEFG, ttdAB, ykgEFG | norVW, ykgEFG | {glpABC glpD glpFK glpTQ}, nirBD, ykgEG | fdnGH, {glpABC, glpTQ}, ykgEF |
| Downregulated ≥4-fold | {ariR, bhsA}, {argO, lysA, lysC}, cysACDHIJNPUW, {gadABCE, mdtEJ}, nrdHI, sufABC, yhiM, ymdF | dmsABC, fdnG, frdABCD, ΔgadBCEW, ΔhdeABD, hyaABCDEF, hybABO, hypABCD, napDF, narIJUYZ, nikABCDE, nrfAC, ybaST, yhiM, ynaIJ, ynfEFGKO | {argO, lysA, lysC, lysP}, ΔgadABCEWX, ΔhdeABD, ΔmdtEF, sufABCD, ybaST, ycaC, yciFG, yhiM, ymdF | appABC, {argO, lysA, lysC}, {gadABCEWX, hdeA, mdtEF, slp}, hyaABCDEF, osmEY, otsAB, sufABCDES, ybaST, yciFG, yhiM, ymdF |
a
Selected genes and regulons from Table S2 representing all genes upregulated or downregulated ≥4-fold relative to expression levels in W3110 and fitting the criterion of a P value of <0.001 as assessed by negative binomial tests in DESeq. RNA was isolated from bacteria cultured to log phase in LBKmal broth, pH 4.8. Delta symbols indicate gene deletions (Table S1). Genes within braces (boldface) are grouped together based on functional relevance.