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Table 1 Modules and sub-modules found in the B. subtilis glucose-responding regulatory network.

From: Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli

Module Physiological function Genes
M1 Heat shock response acoR(↓), alsS(↑), arfM, alsR, ydiH, cydC(↑), dnaK(↓), grpE(↓), lctP(↑), hrcA, resD, groEL(↓), groES(↓)
  Carbon catabolism glpK(↓), glpP, ahrC, rocR, iolR, araB(↓), araN(↓), acuB(↓), galK(↓), msmX(↓), pta(↓), bglH(↓), bglP(↓), yxiE(↓), licA(↓), licB(↓), licC(↓), licH(↓), treA(↓), treP(↓), ccpA, iolC(↓), iolF(↓), iolH(↓), iolI(↓), ccpB, xylR, xylA(↑), araR, treR, licR, licT, levD(↓), levE(↓), levR, sigL, rocA(↑), ydjK(↓), rbsA(↓), rbsB(↓), rbsC(↓), rbsD(↓), rbsK(↓), rbsR(↓)
M2 Endospore formation citG(↓), codY, dppE(↓), hag(↑), abrB, sigH, spoVG(↓), yxnB(↓)
  Sporulation dltA(↑), dltB(↑), dltD(↑), dltE(↑), mcpB(↑), yjcP(↑), yvyC(↓), sigD
MM1 Sporulation sigX, spo0A
M3 Prespore formation comA, yvrH, wprA(↓), degQ(↓), wapA(↑), sacA(↓), sacP(↓), degU, sacT, sacY, tenA, yveB(↓), sigG, gerKA(↓), ybxH(↓), sspD(↑), spoVAD(↓), spoVAC(↑), sspJ(↓), sspM(↑), adhB(↓), yraG(↓), yraE(↓), yraD(↓), yndE(↑), ylaJ(↓), sspN(↓)
  Spore formation ctsR, bofC(↓), csbX(↑), sigF, spoVT, sigB, clpP(↓), rsbW(↓), ydaE(↓), ydhK(↓), yjgB(↑), gcaD(↑), yycD(↓), ysnF(↓), ypuB(↑), yoxB(↓), yotK(↑), yqhQ(↓), spoIIQ(↑), yfhD(↓), yfhE(↓), yhcM(↓), yqzG(↓)
MM2 Glycerophospholipid metabolism glpQ(↓), glpT(↓), phoP
M4 Hexuronate metabolism exuR, mmgA(↓), yjmC(↓)
M5 Nitrogen metabolism glnR, glnA(↑), glnP(↑), kipR, tnrA, ykoL(↓), ykzB(↑)
  Spore coat formation gerE, spoIIIC, spoIVCB, cotB(↓), cotC(↓), cotV(↓), cotW(↓), cotT(↓), cgeA(↓), cgeB(↓), cotZ(↓), sspG(↓), cgeC(↓), yurS(↓), yoaN(↑), yjcB(↓), spoVFA(↓), yisZ(↓), ykvP(↓), ykvQ(↓), ylbD(↓), ylbE(↓), cotS(↓), ywrJ(↓), ytxO(↓), ytcC(↓), ytaA(↓), yqfQ(↓), yodH(↓), yngK(↓), ymaG(↓), spsA(↓), spsI(↓), ycsF(↓), spoIIID, ylbO, yhcO(↓), yhcP(↓), ypqA(↓), ysnD(↓)
M6 SOS response lexA, ybaK(↓), aprX(↓), yozM(↓), yozL(↑)
  Prospore formation spoIIIAC(↓), yqfZ(↓), sigE, usd(↓), mbl(↑), yheD(↓), yjcA(↓), yncD(↓), yngE(↓), yngG(↓), ywdL(↓)
MM3 Glycolysis cggR, eno(↑), pgk(↑), pgm(↑)
MM4 Nitrogen assimilation fnr, narG(↓), narH(↑)
M7 Competence comK, comGB(↑), cspB(↓), yhjC(↓), yhcD(↑), ssb(↑), rpsF(↑), rpsR(↑)
MM5 Peroxide stress ahpC(↓), ahpF(↓), perR
MM6 PTS-glucose system glcT, ptsG(↑), ptsI(↑)
MM7 Amine and polyamine degradation bltD(↓), bltR, mta
MM8 Extracytoplasmic sigY, yxlC(↓), yxlE(↓)
MM9 Aspartate catabolism ansB(↓), ansR
MM10 N/A lmrA, yxaH(↓)
MM11 N/A fur, ydhU(↓)
MM12 N/A rok, yydH(↓)
MM13 Sorbitol catabolism gutB(↓), gutR
MM14 Purine metabolism purQ(↑), purr
MM15 N/A birA, ytbQ(↑)
MM16 N/A yufM, ywkB(↑)
MM17 N/A appC(↓), hpr
MM18 Lactose catabolism lacA(↓), lacR
M8 Extracytoplasmic sigW, yceC(↓), yceD(↑), yceF(↓), ydjH(↓)
M9 Cysteine biosynthesis cysK(↓), ytmI(↓), ytmJ(↓), ytmK(↑), ytmL(↓), ytnI(↓), ytnM(↓), yrzC, ytlI
  1. We found 9 modules and 18 mini-modules (MM), the latter defined as a module comprising only genes in the same operon or a simple regulon, with just a few members. Up-regulated genes are indicated by an up-arrow (↑), whereas a down-arrow (↓) indicates a down-regulated gene; genes without an arrow were not significantly detected in microarray. Physiological functions are discussed in the text. A module tagged 'N/A' means that currently not enough information exists to make a functional assignment.