TABLE 2.
Target gene candidates for 24 B. subtilis two-component regulatory systemsa
| System | No. of genes | Upregulated genesb | Downregulated genes |
|---|---|---|---|
| CitS-CitT | 5 | (citS), citT, citM, yflN, yxiO | |
| DesK-DesR | 26 | des, (desK), desR, yorV, yvfU, yvfT, yvfS, yvfR, hisZ | ydbH, yesL, yesM, yfiI, yjdC, yjdD, yjdE, yjdF, yrxA, rbsR, rbsK, rbsD, rbsA, rbsC, rbsB, ywoG, licC |
| LytS-LytT | 6 | (ysbB), (ysbA), lytT, (lytS), ywjC | ywbH |
| YbdK-YbdJ | 9 | ybdJ, (ybdK), purC, purN, purH, ald | ykoM, ysfC, ysfD |
| YcbA-YcbB | 19 | ybgH, (ycbA), ycbB, lctE, sunA | ybbC, ndhF, ybcT, ybdB, ykzH, yoxA, lpd, bkdR, ysfC, ysfD, rbsB, hutH, hutU, hutI |
| YcbM-YcbL | 4 | ycbL, (ycbM), ysfC, ysfD | |
| YccG-YccH | 5 | (yccG), yccH, natA, natB, yccK | |
| YclK-YclJ | 30 | gerKB, yclH, yclI, yclJ, (yclK), yfiY, ykcB, ykcC, ykuO, pyrR, yngA, yngB, yngC, ysfC, ysfD, yukL, dhbB, dhbA, fhuD | acoA, acoB, acoC, acoL, yvdK, yvdH, atpD, atpA, atpE, qoxC, qoxB |
| YdbF-YdbG | 76 | ydbG, (ydbF), (ydbH), yhcP, yjcP, yqaS, mcpA, mcpB, flgK, flgM | feuC, ybbC, adaA, ndhF, ybcH, ybcL, ybdJ, ybdL, ybfF, ybfH, ycxB, ycxD, ycsO, ydaO, yesZ, yisZ, cotY, yjiA, yjiC, yjmG, xpf, xkdM, ykzH, pksI, ymaB, yngK, yoxD, yoaB, yoaJ, yoaV, yozH, yozJ, yobS, yobW, yqhB, yqfT, yqbE, yqbA, yqaL, yqaJ, yrkP, yrkO, yrdN, cypA, yrpE, sigZ, yraK, yrrD, sspA, yteQ, ytkD, ytaB, glgP, paiA, yurH, yvsH, yvaG, yvaP, opuCD, yvbG, araE, yvfA, yvoE, yvoA, ywrA, yycD |
| YdfH-YdfI | 29 | ydfE, (ydfH), ydfI, ydfJ, ydfT, ydgJ, ydjM, ykuD, pyrR, proJ, proH, yqjD, ysbA, rbsR, rbsK, rbsD, rbsA, rbsC, rbsB, licC, yydH | lctE, lctP, yqxL, ywcJ, ywbH, cydC, cydB, cydA |
| YesM-YesN | 21 | (yesM), yesN, (yesO), (yesP), (yesQ), (yesR), (yesS), (yesT), (yesU), (yesV), (yesW), (yesX), (yesY), (yesZ), (yetA), (lplA), (lplB), opuBD | yjdD, yjdE, licC |
| YfiJ-YfiK | 31 | (yfiJ), yfiK | ybdB, argC, argJ, argB, argD, carA, carB, argF, yjaZ, appF, appB, ykfA, yoeB, yqiZ, leuC, leuB, leuA, ilvN, ilvB, ytzD, argH, argG, yutL, thrB, hom, yxbC, yxbB, yxnB, yxaM |
| YhcY-YhcZ | 8 | (yhcY), yhcZ, yknU, bglS, licT, yxiP, yycE | yjdD |
| YkoH-YkoG | 26 | ybdJ, yclH, yclI, ykcB, ykcC, htrA, ykmA, ykoG, (ykoH), (ykoI), (ykoJ), ykoS, ykoT, yngA, yngB, yngC, yocH, yoqN, yqjD, ytlI, yvtB, yvtA, yvpB, yvpA, galE, yybQ | |
| YrkQ-YrkP | 11 | yjcE, ykcB, ykcC, yqaQ, yqaI, (yrkR), (yrkQ), yrkP, yrkO, yrkN, ywmG | |
| YtsB-YtsA | 9 | slp, yrkR, yrkQ, yrkP, (ytsD), (ytsC), (ytsB), ytsA, yvcR | |
| YufL-YufM | 98 | ybbC, ybbD, ybbE, ybbF, ybbH, ybbI, ybbJ, ybbK, ybfT, ycbP, nin, nucA, yckF, yckG, ycxB, ydfL, rapH, yfjU, ygxB, yhfS, yhfT, yhfU, comK, yhxD, yjgD, smf, yodF, yopY, yopX, yopW, yqjD, sinI, comGG, comGF, comGE, comGD, comGC, comGB, comGA, comEC, comEA, comER, comC, ysbA, ytxD, ccpA, (yufL), yufM, comFC, comFB, comFA, ywpJ, ywpH, ywkA, ywfM, yweA, licH, licC, licB, aldY, galE, yxiQ, bglH, yyaF | lctP, yhfB, pyrB, pyrC, pyrAA, pyrAB, pyrDII, pyrD, pyrE, yosO, yonB, yomU, yolF, yqjI, ythP, mcpB, yukL, yukM, dhbB, dhbC, dhbA, yvfC, yvfB, yvfA, yveR, yveQ, yveP, yveN, yveM, yveL, ywcJ, cydC, cydB, cydA |
| YvcQ-YvcP | 47 | yhaS, clpE, mreBH, yorK, yorI, yorG, yorF, yorE, yorA, yoqS, yoqL, yoqH, yoqD, yoqB, yoqA, yopZ, yopX, yonO, yonN, yonB, yomX, yomW, yomU, yomT, yomS, yomO, yomM, yomG, yomD, araM, araD, araB, araA, ytzE, ytsD, ytsC, yvqI, (yvcS), (yvcR), (yvcQ), yvcP, yvcB, yxdM, yxdL, yxaH | yukL, fliT |
| YvfT-YvfU | 10 | yocE, yvfU, (yvfT), yvfS, yvfR | ydaD, ydaS, yqgZ, yrpC, dhbB |
| YvqB-YvqA | 9 | ygxB, yjgD, htrA, yvtB, yvtA, yvqA | yjdC, yjdD, yjdE |
| YvqE-YvqC | 31 | yacD, cysK, ycsF, ycsG, ycsJ, ydhE, yhcY, yhcZ, yhdA, yhdB, yhdC, yjcL, ypuA, yqjD, gerAB, yvqC, (yvqE), yvqF, yvqG, yvqH, yvqI, yvrK, yvrL, yxjN, yxjM, yxjL, pepT, bglS, licT, yxiP, yycE | |
| YvrG-YvrH | 43 | ycbN, yfhI, yfhK, csbB, yfhO, yheN, wprA, yisO, yisW, ykcB, ykcC, ykfD, yocH, sunT, sunA, yokF, yokE, ypzC, yqjD, pstB2, pstA, (yvrG), yvrH, dltA, galE, yxiM, yxiL, yxiK, yxiJ, yxiI, yxzG, yxiH, yxiG, yxiF, yxxG, wapA, yxdL | ycdA, yorF, yrkO, yrhH, lytC, lytB |
| YxdK-YxdJ | 9 | ydbP, acoA, yqjD, yxdM, yxdL, (yxdK), yxdJ | glpT, yjdE |
| YxjM-YxjL | 28 | yhcY, yhcZ, yhdA, yhfO, yqjL, yqjD, yvqC, yvqE, yvqF, yvqG, yvqH, yvqI, yvrK, yxjN, yxjL, bglS, licT, yxiP, yycE | glpT, ycbK, yjdC, yjdE, pyrAB, pyrD, pyrE, yojI, ywhP |
a
RNA preparation and DNA microarray experiments were repeated until the two best quality hybridization profiles were obtained. The expression ratio for each gene was taken as the average of two ratios obtained from the hybridization profiles shown. The target gene candidates exhibited greater than fourfold upregulation or downregulation and are listed in clockwise order starting at the chromosomal location of oriC.
b
The genes in bold were cloned into plasmid pDG148 and overexpressed up on the addition of IPTG. The underlined genes are known target genes of the respective two-component systems. Transcription of the genes in parentheses can be induced by IPTG due to pMUTIN integration into sensor kinase genes without a response to overproduction of the cognate response regulator genes.