Supplementary Material: Table S3
Table S3. class U: Genes induced by heat shock1 – (no obvious B promoter)
Fold-inductionGene / 3' / 10' / 20' / Predicted Function2 or Comments
appD / 0.83 / 14.7 / 1.67 / oligopeptide transport
= appF / 0.58 / 11.6 / 1.31
=appA / 0.74 / 4.28 / 2.26
=appB / 0.76 / 3.75 / 0.85
=appC / 0.83 / 3.72 / 1.05
amhX / 1.34 / 6.74 / 1.86 / aminohydrolase
cydA / 4.83 / 5.21 / 6.70 / cytochrome bd ubiquinol oxidase (subunit I); no signal in 2 expts.
gerCA / 0.64 / 8.07 / 2.03 / menaquinone biosynthesis (heptaprenyl diphosphate synthase component)
(gerCB, gerCC not induced)
gntR / 10.9 / 2.96 / 1.57 / transcriptional repressor of the gluconate operon
=gntK / 8.18 / 4.72 / 1.52 / gluconate kinase (gntP no signal)
=gntZ / 1.81 / 2.23 / 0.79 / 6-phosphogluconate dehydrogenase
ilvB / 0.29 / 8.30 / 2.19 / isoleucine, valine biosynthesis
=ilvN / 0.23 / 6.48 / 1.55
=ilvC / 0.55 / 4.45 / 2.65
=leuA / 0.81 / 2.17 / 1.44
=leuB / 0.31 / 2.36 / 1.42
=leuC / 0.37 / 1.56 / 1.68
=leuD / 0.53 / 0.82 / 1.58
murC / 5.61 / 1.98 / 1.34 / UDP-N-acetylmuramate-alanine ligase (upstream, codirectional with PB-ytxG)
nrgB / 4.19 / 6.07 / 4.07 / nrgA – no signal
opuBA / 0.56 / 2.00 / 1.86 / choline ABC transporter (osmotic stress)
=opuBB / 3.49 / 1.77 / 4.52
=opuBC / 9.38 / 1.52 / 3.40
=opuBD / 9.46 / -- / 4.42 / operon convergent with yvaQ – but that gene not induced
phoA / 3.71 / 10.8 / 5.29 / alkaline phosphatase A
sacV / 4.90 / 5.20 / 4.17 / regulator of the levansucrase gene
spoIIR / 11.6 / -- / -- / required for processing of pro-E
=ywlB / 9.74 / 1.79 / --
ssuD / 8.16 / 2.21 / 1.49 / desulfonation of aliphatic sulfonates (aka ygcA); ssuC also weakly induced but ssuB has no signal, ssuA no induction.
ybfB / 1.58 / 17.7 / 2.03 / unknown, integral membrane protein
yceB / 3.29 / 8.05 / 5.52 / unknown; similar to alkanal monooxygenase (paralogs=YwcH, YtmO, YvbT)
yceK / 2.04 / 7.46 / 2.79 / similar to transcriptional regulator (ArsR family); divergent from the opuA operon.
ycgJ / 1.75 / 5.76 / 6.23 / unknown conserved
yclA / 7.68 / 2.76 / 2.65 / similar to transcriptional regulator (LysR family)
ydcN / 0.55 / 2.19 / 1.83 / transcriptional regulator (phage-related; Xre family) in 'prophage 2'
=ydcM / 0.77 / 3.07 / 2.78 / similar to immunity region protein in prophage
=ydcL / 1.29 / 4.57 / 4.22 / similar to phage integrase – this operon is diverg. from sacV
yfjR / 1.22 / 4.78 / 6.85 / similar to 3-hydroxyisobutyrate dehydrogenase
yfkF / 5.35 / 1.24 / 1.59 / similar to multidrug-efflux transporter (convergent with yfkH, table 4)
yjcI / 1.30 / 4.23 / 5.02 / cystathione gamma-synthase (S-box regulon) = metB
=yjcJ / 1.62 / 3.48 / 5.50 / cystathione beta-lyase (S-box regulon) = metC
yjlB / 11.4 / 2.43 / 2.11 / unknown
yoaD / 1.00 / 6.12 / 4.67 / similar to phosphoglycerate dehydrogenase (convergent with yoxC operon; Table 3)
=yoaC / 1.08 / 4.31 / 3.44 / similar to xylulokinase (S-box regulon)
=yoaB / 2.25 / -- / 2.47 / unknown (S-box regulon)
yoeB / 12.7 / 18.2 / 10.9 / unknown
yomZ / 1.87 / 4.05 / 6.46 / unknown
=yonA / 1.83 / 3.70 / 4.37 / unknown
yqaB / 4.08 / 6.22 / 4.27 / similar to phage-related protein
yqiK / 1.64 / 4.06 / 4.52 / similar to glycerophosphodiester phosphodiesterase
yqkE / 1.72 / 3.99 / 5.14 / 74 aa, unknown
yqjM / 3.36 / 18.5 / 14.8 / unknown, similar to NADH-dependent flavin oxidoreductase
=yqjL / 7.50 / 15.5 / 7.74 / unknown
yrhH / 9.95 / 27.0 / 11.6 / similar to methyltransferase
=yrhI / 8.84 / 31.2 / 6.41 / similar to transcriptional regulator (TetR/AcrR family)
=yrhJ / 8.96 / 27.6 / 7.94 / similar to cytochrome P450 /NADPH-cytochrome P450 reductase
ytiA / 6.91 / 1.37 / 1.90 / 84 amino acids
ytzE / 3.48 / 7.08 / 8.01 / similar to transcriptional regulator (DeoR family)
yugS / 7.57 / 17.6 / 3.54 / integral membrane protein (YhdP family; 4 paralogs)
=yugU / 13.7 / 2.30 / 2.05 / (no data on yugT)
yumD / 9.45 / 7.07 / 0.85 / similar to GMP reductase
yutK / 16.9 / 2.81 / 4.06 / Na+ / nucleoside cotransporter
yuxJ / 2.58 / 5.23 / 5.72 / similar to multidrug-efflux transporter
ywfB / 4.32 / 8.60 / 4.74 / unknown, ywfC not strongly induced
yxaB / 12.4 / 4.78 / 2.24 / unknown
yxeI / 3.31 / 7.47 / 5.01 / similar to penicillin amidase
1 This list contains those genes from sets # 2 and #3.
2 Functional annotations are derived from the SubtiList database (32).