Table 2S: Transcriptome data summary for genes of the CzrA, ArsR, CueR, PerR and Fur regulons.

gene / description / fold induction1
Ag(I) / As(V) / Cd(II) / Ni(II) / Zn(II) / Cu(II)
CzrA Regulon2
czcD / cation efflux; K+or H+ antiport / 21.0 / 86.2 / 28.7 / 67.7 / 45.3 / 6.6
trkA / modulator of czcD function / 8.5 / 37.7 / 14.2 / 33.2 / 27.5 / 5.1
cadA / Cd(II) efflux P-type ATPase / 4.9 / 49.8 / 9.8 / 21.7 / 29.7 / 3.9
ArsR Regulon3
arsR / metalloregulator / 231.8 / 384.4 / 294.2 / 1.52 / 14.6 / 2.8
yqcK / unknown / 88.6 / 117.8 / 147.7 / 1.1 / 1.4 / 2.9
arsB / arsenite efflux, ACR3 homolog / 156.0 / 271.7 / 44.3 / 1.2 / 5.6 / 2.5
arsC / arsenate reductase / 122.7 / 198.6 / 128.1 / 1.0 / 4.1 / 2.7
CueR Regulon4
copZ / Cu chaperone / 14.8 / 1.3 / 23.8 / 1.0 / 2.4 / 15.0
copA / Cu efflux P-type ATPase / 18.8 / 1.6 / 28.1 / 1.0 / 1.8 / 8.8
PerR Regulon5
mrgA / dps homolog / 43.1 / 149.5 / 10.6 / 0.8 / 1.2 / 4.6
katA / catalase / 79.9 / 129.9 / 11.7 / 0.8 / 0.7 / 10.8
zosA / Zn(II) uptake; P-type ATPase / 13.0 / 37.0 / 9.4 / 1.0 / 1.1 / 0.3
perR / metalloregulator / 3.6 / 2.6 / 2.2 / 0.9 / 1.3 / 1.7
fur / metalloregulator / 1.9 / 1.3 / 1.3 / 0.4 / 0.9 / 1.3
ahpC / alkyl hydroperoxide reductase / 4.9 / 5.8 / 1.8 / 0.8 / 0.9 / 5.6
ahpF / alkyl hydroperoxide reductase / 3.5 / 5.7 / 1.3 / 0.8 / 1.0 / 5.2
hemA / heme biosynthesis / 3.9 / 6.2 / 2.8 / 0.8 / 1.0 / 1.8
hemX / heme biosynthesis / 2.2 / 1.7 / 2.4 / 0.7 / 1.0 / 1.3
hemC / heme biosynthesis / 1.4 / 2.1 / 2.3 / 0.7 / 1.0 / 1.3
hemD / heme biosynthesis / 1.3 / 1.8 / 2.6 / 0.8 / 1.2 / 1.4
hemB / heme biosynthesis / 1.1 / 1.7 / 2.2 / 0.9 / 1.0 / 1.4
hemL / heme biosynthesis / 0.9 / 1.3 / 1.8 / 0.9 / 1.1 / 1.4
Fur Regulon6
ykuN / flavodoxin / 0.9 / 0.8 / 0.1 / 0.8 / 0.2 / 16.3
ykuO / unknown / 0.3 / 0.3 / 0.1 / 0.3 / 0.2 / 33.9
ykuP / flavodoxin / 0.4 / 0.4 / 0.2 / 0.5 / 0.3 / 22.0
dhbA / Corynebactin biosynthesis / 0.4 / 0.3 / 0.2 / 0.9 / 0.7 / 29.1
dhbBx / Corynebactin biosynthesis / 0.6 / 0.4 / 0.3 / 0.7 / 0.8 / 13.1
dhbC / Corynebactin biosynthesis / 0.7 / 1.5 / 0.3 / 1.0 / 0.6 / 13.8
dhbE / Corynebactin biosynthesis / 0.6 / 0.5 / 0.2 / 1.0 / 0.6 / 16.3
dhbF / Corynebactin biosynthesis / 0.9 / 0.8 / 0.2 / 1.0 / 0.7 / 8.9
feuA / Corynebactin and Enterobactin uptake; ABC-transporter / 0.5 / 0.6 / 0.2 / 0.7 / 0.5 / 9.8
feuB / Corynebactin and Enterobactin uptake; ABC-transporter / 0.7 / 2.5 / 0.5 / 0.7 / 0.6 / 4.5
feuC / Corynebactin and Enterobactin uptake; ABC-transporter / 0.5 / 0.4 / 0.4 / 0.6 / 0.5 / 7.8
fhuB / ferric hydroxamate uptake; ABC-transporter / 0.2 / 0.2 / 0.1 / 0.6 / 0.3 / 8.9
fhuC / ferric hydroxamate uptake; ABC-transporter / 0.3 / 0.3 / 0.3 / 0.6 / 0.6 / 5.8
fhuD / ferric hydroxamate uptake; binding protein / 0.2 / 0.1 / 0.1 / 0.3 / 0.4 / 19.4
fhuG / ferric hydroxamate uptake; ABC-transporter / 0.2 / 0.2 / 0.3 / 0.6 / 0.5 / 7.3
ybbB / AraC type regulator / 0.4 / 1.0 / 0.1 / 0.4 / 0.3 / 5.6
yclN / predicted siderophore uptake; ABC-transporter / 0.2 / 0.2 / 0.2 / 0.5 / 0.5 / 10.7
yclO / predicted siderophore uptake; ABC-transporter / 0.2 / 0.1 / 0.3 / 0.5 / 0.5 / 12.2
yclP / predicted siderophore uptake; ABC-transporter / 0.2 / 0.2 / 0.3 / 0.5 / 0.6 / 12.1
yclQ / predicted siderophore uptake; ABC-transporter / 0.3 / 0.2 / 0.4 / 0.6 / 0.6 / 12.6
ydbN / unknown / 1.0 / 0.8 / 0.1 / 0.9 / 0.5 / 5.2
yfhA / Schizokinin, Arthrobactin uptake; ABC-transporter / 0.4 / 0.3 / 0.3 / 0.7 / 0.4 / 5.2
yfhC / similar to nitroreductase / 0.5 / 0.6 / 0.4 / 0.7 / 0.6 / 5.1
yfiY / Schizokinin, Arthrobactin uptake; binding protein / 0.5 / 0.1 / 0.3 / 0.8 / 1.0 / 10.0
yfmCx / Ferric citrate uptake / 0.3 / 0.3 / 0.3 / 0.6 / 0.7 / 5.3
yhfQ / siderophore uptake; binding protein / 0.3 / 0.3 / 0.2 / 0.5 / 0.4 / 8.0
yuiI / similar to esterase / 0.4 / 0.3 / 0.2 / 0.5 / 0.6 / 16.0
yukL / unknown / 1.0 / 1.0 / 1.0 / 1.2 / 1.0 / 5.0
yusV / ATPase component for YfiYZYfhA and FeuABC / 0.2 / 0.1 / 0.1 / 0.3 / 0.4 / 7.2
ywbL / Fe transport; FTS3 homolog / 0.2 / 0.1 / 0.2 / 0.4 / 0.4 / 6.2
ywbM / Fe transport; FTS3 homolog / 0.2 / 0.2 / 0.3 / 0.5 / 0.5 / 8.3
yxeB / Ferrioxamine uptake; binding protein / 0.2 / 0.1 / 0.2 / 0.4 / 0.3 / 11.6
MntR Regulon7
mntA / Mn(II) uptake; ABC-transporter / 0.8 / 0.3 / 0.1 / 0.8 / 0.8 / 1.1
mntB / Mn(II) uptake; ABC-transporter / 0.9 / 0.5 / 0.1 / 0.8 / 0.6 / 1.3
mntC / Mn(II) uptake; ABC-transporter / 1.0 / 0.8 / 0.1 / 0.8 / 1.0 / 1.3
mntD / Mn(II) uptake; ABC-transporter / 0.9 / 0.9 / 0.1 / 0.9 / 0.6 / 1.3
mntH / Mn(II) uptake, NRAMP homolog / 1.0 / 0.6 / 0.1 / 0.8 / 1.0 / 1.4

1 Fold induction by 3 min. metal stress at OD600=0.3 in LB medium at the following concentrations: 10 mM Ag(II); 10 mM As(V); 10 mM Cd(II); 10 mM Cu(II); 500 mM Ni(II) or 300 mM Zn(II).

2CzrA regulon as defined in this manuscript.

3ArsR regulon as previously reported (Sato and Kobayashi, 1998).

4CueR regulon as previously reported (Gaballa et al., 2003).

5Only katA and mrgA expression data were used in the construction of Fig. 3. These genes have previously been shown to be the most highly induced genes of the PerR regulon and are therefore accurate indicators of PerR derepression (Helmann et al., 2003; Herbig and Helmann, 2001). The complete PerR regulon is shown here.

6Fur regulon as previously reported (Baichoo et al., 2002).

7MntR regulon as previously reported (Que and Helmann, 2000).

References

Baichoo, N., Wang, T., Ye, R., and Helmann, J.D. (2002) Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon. Mol Microbiol 45: 1613-1629.

Gaballa, A., Cao, M., and Helmann, J.D. (2003) Two MerR homologues that affect copper induction of the Bacillus subtilis copZA operon. Microbiology 149: 3413-3421.

Helmann, J.D., Wu, M.F., Gaballa, A., Kobel, P.A., Morshedi, M.M., Fawcett, P., and Paddon, C. (2003) The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors. J Bacteriol 185: 243-253.

Herbig, A.F., and Helmann, J.D. (2001) Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA. Mol Microbiol 41: 849-859.

Que, Q., and Helmann, J.D. (2000) Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins. Mol Microbiol 35: 1454-1468.

Sato, T., and Kobayashi, Y. (1998) The ars operon in the skin element of Bacillus subtilis confers resistance to arsenate and arsenite. J Bacteriol 180: 1655-1661.