Table 4.
Significantly changed TFAs under isobutanol condition predicted by GTRNetwork reconstructed gene regulatory network The reconstructed gene regulatory network includes 381 potential new regulatory links, the 16 significantly changed TFAs predicted by original RegulonDB data from Brynildsen's paper [39] are not included.
| TF | Function | Target Genes |
|---|---|---|
| ArgR | Arginine catabolism | argA, gltF, argE, argH, rimP, rbfA, truB, rpsO, pnp, nusA, infB, hisP, gltD, gltB, carB, artP, artI, artQ, artM, artJ, hisJ, hisQ, metY, astE, astB, astD, astA, astC, hisM, argB, argC, argD, argF, argG, argI, argR, carA |
| AscG | Arbutin-salicin-cellibiose transport and utilization | ascB, ascF, ascG, htpG, prpR, clpB, dnaJ, dnaK, tpke11, groL, groS, grpE, hslU, hslV, ybbN, lipB, ybeD, lnt, ybeX, ybeY, ybeZ |
| CysB | Novobiocin resistance, sulfur utilization, and sulfonate-sulfur catabolism | tauA, tauB, tauC, ssuC, ssuD, ssuA, ssuE, hslJ, cbl, tauD, ssuB, cysP, cysU, cysW, cysN, cysM, cysK, cysJ, cysI, cysH, cysD, cysC, cysB, cysA, gsiA, gsiB, gsiC, gsiD, iaaA, yciW, ydjN, yeeD, yeeE |
| Lrp | Leucine-responsive regulatory protein | lhgO, alaT, alaU, alaV, gltT, gltU, gltV, gltW, ileT, ileU, ileV, micF, rrfA, rrfB, rrfC, rrfD, rrfE, rrfG, rrfH, rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, rrlH, rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, rrsH, rrfF, thrV, csiD, ilvX, adhE, aroA, fimA, fimC, fimD, fimE, fimF, fimG, fimH, gabT, gcvH, gltB, gltD, ilvA, ilvD, ilvE, ilvH, ilvH, ilvI, ilvM, kbl, livF, livG, livH, livJ, livK, livM, lrp, lysU, malT, ompC, ompF, oppA, oppB, oppC, oppD, oppF, osmC, sdaA, serA, serC, tdh, argO, ilvL, gabD, gabP, osmY, hdeA, hdeB, yhiD, dadA, dadX, gcvT, gltF, stpA, gcvP, aidB, fimI, yeiL, yojI, gdhA, ilvG_1, ilvG_2, thrA, thrB, thrC, thrL |
| MarA | Multiple antibiotic resistance | pqiB, pqiA, ybaO, nfsB, micF, slp, dctR, acrB, acrA, marB, marR, marA, inaA, rfaY, rfaZ, yhiD, hdeB, hdeA, rob, zwf, fumC, fpr, nfo, poxB, purA, putA, sodA, tolC, ygiA, ygiB, ygiC, ltaE, ybjT, talA, tktB, phr, ybgA, yhbW |
| MetJ | Methionine biosynthesis and transport | metF, metK, metL, metR, yeiB, folE, ahpC, ahpF, metQ, metN, metI, metA, metB, metC, metE |
| NadR | NAD biosynthesis | nadA, pnuC, pncB, nadB |
Bolded genes have significant changes in expression according to Brynildson's paper [39]. Underlined genes are predicted new regulatory target genes of the TF from GTRNetwork.