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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.