Table 6.

ςB-independent stress gene induction inB. subtilisa

GenebFunction or nearest homolog (E value)Regulatory protein or sigma factorOperon structureInduction ratio
wtsigB
PredictedValidatedEtOHHeatSaltEtOHHeatSalt
Induction by EtOH, heat, and salt shock
murGUndecaprenyl-PP-MURNAC-pentapeptide-UDPGlCNAc GlCNAc transferasem2.52.72.32.92.22.5
sacCLevanase (EC 3.2.1.65 )CcpA, LevRm3.24.43.24.14.44.9
yugJButanol dehydrogenase (EC 1.1.1.-), C. acetobutylicum(1e-97)m3.76.75.16.35.02.7
yutGLow temperature requirement C protein,B. halodurans(4e-51)m2.28.43.93.07.62.4
ywoAProbable bacitracin transport permease BcrC,B. licheniformis(4e-17)m2.53.12.04.12.52.4
ywnFUnknown conserved protein, B. halodurans(6e-05)m4.75.05.96.03.53.1
ywaCGTP pyrophosphokinase, B. halodurans(4e-36)m2.43.22.34.32.95.1
Induction by EtOH and heat shock
groESClass I heat shock protein (chaperonin)HrcA1st+7.2111.016161.6
groELClass I heat shock protein (chaperonin)2nd+5.0141.311181.9
yhfAUnknown conserved protein, B. halodurans(1e-41)2nd2.53.71.32.83.41.3
yhfIUnknown conserved protein, B. halodurans(2e-59)1st2.62.71.13.42.60.8
yhfJLipoate-protein ligase, B. halodurans(e-136)2nd2.83.21.23.32.80.8
yhfKUnknown conserved protein BH1520, B. halodurans(3e-32)3rd3.33.01.95.22.81.3
yitWdTDP-4-keto-l-rhamnose reductase RmlD, S. mutans(3e-31)m3.22.91.24.02.71.2
yjbGOligopeptidase F homolog, B. subtilis(<3e-180)m4.34.11.84.62.81.2
ykuVUnknown conserved protein, B. halodurans(1e-59)m2.63.11.32.52.60.8
yoeBNo similaritym7.4201.5176.00.7
yqkFOxidoreductase BH1011, B. halodurans(e-102)m6.74.01.86.92.81.1
yqiGNADH oxidase, T. brockii(2e-45)m2.54.61.75.15.41.6
hrcAcTranscriptional repressor of class I heat shock genesHrcA1st+5.27.856.87.68.6
grpEHeat shock protein (HSP-70 cofactor)2nd+2.83.91.84.94.32.8
dnaKcMolecular chaperone3rd+1.45.51.83.26.43.7
yvrD3-Hydroxybutyrate dehydrogenase, S. meliloti(1e-30)m3.14.82.44.04.31.5
iolSIon channel homolog YccK, B. subtilis(3e-94)m2.63.11.83.93.21.0
Induction by heat shock
ycnDNADPH-flavin oxidoreductase, B. halodurans(4e-49)m1.44.12.11.94.11.6
yjeAPeptidoglycan GlcNAc deacetylase,Streptococcus pneumoniae(1e-48)m0.66.20.60.96.60.7
clpEATP-dependent Clp protease-like (class III stress gene)CtsRm+1.0121.22.3154.4
yqjMNADH oxidase, B. halodurans(e-126)m1.66.51.42.35.41.1
yrkFORF H0532, Halobacterium sp. (5e-13)3rd1.29.02.85.76.11.8
yrkEHypothetical protein, Staphylococcus aureus(5e-36)2nd1.04.72.23.13.51.2
yrkDHypothetical protein, S. aureus(5e-14)1st0.83.51.52.83.41.1
Induction by EtOH shock
ygaCUnknown conserved protein BH3193, B. halodurans(6e-28)m3.11.22.33.21.22.8
yhcXNitrilase-related protein, D. radiodurans(1e-32)2nd3.82.52.23.91.81.2
yhgBNo similarity1st3.41.12.03.71.01.7
ykgBHypothetical protein YadB, L. lactis(1e-60)m4.91.91.63.81.80.7
yktCmyo-Inositol-1(or 4)-monophosphatase homolog, B. subtilis(e-153)1st3.41.62.73.41.31.1
ypiAα-Acetolactate synthase Als, L. lactis(9e-34)1st4.22.21.96.71.01.8
yrzFNo similarity1st3.21.92.33.71.82.1
yrzGNo similarity2nd3.11.62.65.61.72.4
ytkLNo similaritym3.82.42.03.11.30.9
ytxKUnknown conserved protein BH3193, B. halodurans(3e-76)m3.61.20.95.91.30.7
yuaENo similaritym4.32.52.26.51.91.5
yvqHPhage shock protein A, E. coli(8e-07)2nd3.61.10.6231.20.9
yvqINo similarity1st3.41.61.3161.50.9
yvgWCation-transporting ATPase, P type (PacS) PAB0626, P. abyssim3.51.41.04.01.60.8
ureBUrease (gamma subunit) (EC 3.5.1.5 )SigA, SigH1st3.80.80.83.20.70.6
ureAUrease (beta subunit) (EC 3.5.1.5 )Cod, GlnR2nd4.41.31.43.51.00.9
Induction by salt shock
yaaNTellurite resistance protein, R. sphaeroides(2e-50)SigW2nd1.41.34.72.21.25.7
sigWRNA polymerase ECF type sigma factorSigW1st1.30.83.31.40.73.7
ybbMAnti-ς factor of SigW2nd1.20.64.22.71.28.6
ybfARibosomal protein S18 alanine acetyltransferase homolog, A. fulgidus (1e-06)m2.21.93.73.82.16.0
opuAAcGlycine betaine ABC transporter (ATP-binding protein)SigA1st+0.30.42.20.60.43.6
opuABcGlycine betaine ABC transporter (permease)2nd+0.80.91.90.70.72.9
opuACGlycine betaine ABC transporter (glycine betaine-binding protein)3rd+0.30.63.20.60.54.0
ydbSUnknown conserved protein, B. halodurans(3e-28)SigW1st2.11.36.72.81.35.3
ydbTUnknown conserved protein BH1721, B. halodurans(9e-68)2nd1.40.87.12.20.74.9
ydjFPhage shock protein A, D. radiodurans(4e-20)SigWm2.30.99.13.91.114
ydjGUnknown conserved protein, B. halodurans(6e-74)SigW1st1.21.15.52.41.39.6
ydjHUnknown conserved protein, B. halodurans(2e-11)2nd1.51.53.01.81.34.5
ydjIUnknown conserved protein, B. halodurans(4e-5)3rd0.91.04.11.71.07.8
ydjONo similaritySigW3rd1.00.74.21.00.75.3
ydjPBromide peroxidase, S. aureofaciens(1e-18)2nd1.81.55.91.41.25.9
yeaANo similarity1st1.41.24.81.21.14.8
spoOMSporulation control proteinSigHm3.70.86.14.20.96.6
yhaUPutative transmembrane transport protein,S. coelicolor(8e-65)3rd0.90.97.30.80.74.5
yhaTcHypothetical protein YrvC,B. subtilis(4e-49)2nd1.11.03.71.21.22.6
yhaSNo similarity1st1.61.6201.71.512
yhgDTranscriptional regulator (TetR/AcrR family),B. halodurans(8e-32)m1.11.65.30.61.411
yjoBFtsH, Helicobacter pylori(2e-20)SigWm3.61.3152.21.013
ykrLProbable protease HtpX, E. coli(2e-51)m1.21.16.92.41.512
yknWUnknown conserved protein, B. halodurans(4e-20)SigW1st1.00.67.52.40.811
yknXcATP-binding cassette transporter-like protein TptB, S. cristatus(5e-23)2nd0.40.70.70.90.90.6
yknYPutative ABC transporter YvrO, B. subtilis(3e-75)3rd1.20.63.43.20.85.5
yndNGlutathione transferase FosB (EC 2.5.1.18 ),S. epidermidis (8e-48)Potential SigWm1.31.14.52.21.16.4
proJGlutamate 5-kinaseSigA2nd+1.31.34.91.21.24.4
proHPyrroline-5-carboxylate reductase1st+1.41.24.61.10.94.1
yoaFNo similarityPotential SigWm0.30.53.20.70.76.4
yobJNo similaritySig Wm1.20.55.23.90.910
yocLNo similarity2nd1.00.83.31.01.06.3
yocMSmall heat shock protein HspC, B. japonicum(2e-9)1st0.81.13.60.81.05.7
yozOHypothetical protein YjqA, B. subtilis (7e-10)Potential SigWm0.60.66.10.60.66.4
yqfBNo similarityPotential SigW3rd1.21.03.91.61.26.2
yqfAProtein of unknown function ORF1, B. megaterium(1e-151)2nd1.70.9242.81.122
yqeZNo similarity1st1.30.9171.81.017
yrkAIntegral membrane protein with hemolysin domain, C. jejuni(1e-73)m0.90.89.41.11.116
yteJUnknown conserved protein, B. halodurans(3e-31)SigW2nd1.31.03.44.11.05.3
yteIProteinase IV, A. aeolicus(1e-37)1st2.40.93.65.30.84.7
ythQABC transporter (permease), B. halodurans (6e-05)Potential SigW2nd1.51.13.42.31.24.7
ytgBABC transporter, ATP-binding protein (TroB),T. pallidum(6e-79)2nd0.80.83.70.91.110
ytgAABC transporter, periplasmic binding protein (TroA), T. pallidum(9e-63)1st0.91.04.20.91.110
yuaIProbable acetyltransferase, D. radiodurans(1e-15)SigW3rd2.50.8347.02.162
yuaGEpidermal surface antigen, B. halodurans(4e-78)2nd3.60.9577.21.968
yuaFNo similarity1st1.71.0142.71.220
gbsBgAlcohol dehydrogenaseSigA2nd+1.01.12.01.01.23.8
gbsAGlycine betaine aldehyde dehydrogenase1st+1.01.74.61.22.115
mrpBNa+/H+ antiporter BH1318, B. halodurans(2e-26)2nd+0.81.73.10.71.66.9
opuBDcCholine ABC transporter (membrane protein)SigA4th+1.21.22.60.91.24.2
opuBCcCholine ABC transporter (choline-binding protein)3rd+0.60.72.90.81.09.4
opuBBCholine ABC transporter (membrane protein)2nd+0.91.03.01.01.05.3
opuBACholine ABC transporter (ATP-binding protein)1st+0.50.73.30.71.012
opuCDcGlycine betaine/carnitine/choline ABC transporter (membrane protein)SigA4th+4.30.82.60.30.83.2
opuCCGlycine betaine/carnitine/choline ABC transporter (binding protein)3rd+0.30.7150.51.028
opuCBGlycine betaine/carnitine/choline ABC transporter (membrane protein)2nd+0.70.99.81.21.116
opuCAGlycine betaine/carnitine/choline ABC transporter (ATP-binding protein)1st+0.40.9130.40.915
yvlDUnknown conserved protein, B. halodurans(4e-23)SigW4th1.51.26.02.71.39.3
yvlCcUnknown conserved protein BH3592,B. halodurans(3e-11)3rd0.91.32.31.21.12.9
yvlBUnknown conserved protein, B. halodurans(4e-63)2nd2.71.37.23.41.211
yvlANo similarity1st2.01.36.13.11.39.2
yxjIHypothetical protein SCGD3.06, S. coelicolor(2e-05)SigWm1.10.53.21.20.64.8
ahpFAlkyl hydroperoxide reductase (large subunit) (EC 1.6.99.3 )2nd+0.91.73.71.01.63.6
ahpCcAlkyl hydroperoxide reductase (small subunit)SigA1st+0.72.12.81.02.03.4
  • a See Table 1, footnotes b through e, and Table 2, footnote b, for explanations of data presentation.

  • b Genes are sorted according to their order in the B. subtilis genome. Genes previously known to be induced by the stimulus are shown in bold. EtOH, ethanol.

  • c Operon internal genes that do not meet the stringent expression criteria are included here if the flanking genes display ςB-dependent expression or if the operon structure has been proven by Northern blot analysis.