Skip to main content
. 2010 Mar 16;192(10):2491–2502. doi: 10.1128/JB.00035-10

TABLE 4.

Genes of M. smegmatis with an identified SigF-dependent promoter consensus

Expression category Locus Gene product Microarray analysis
 PRODORIC promoter analysis
Exponential phase
 Stationary phase
 Promoter sequence (5′ → 3′) Positionb PWM scorec
Ratioa P value Ratio P value
Strong SigF-dependent gene expressione in exponential and/or stationary phase MSMEG_0266 Arginine decarboxylase 0.39 0.051 0.17 2.58E−04 GTCG-N17-GGGAT 160 NF
MSMEG_0267 Esterase 0.32 0.05 0.14 4.86E−04 GTTT-N15-GGGTA 27 14.68
MSMEG_0451 Oxidoreductase, FAD-linked 0.12 1.12E−03 0.11 9.94E−05 GTTC-N19-GGGCC 49 NF
MSMEG_0670 FAD-dependent oxidoreductase 0.38 0.05 0.22 5.90E−03 GGTT-N16-GGGTA 9 12.99
MSMEG_0671 S-(Hydroxymethyl)glutathione dehydrogenase 0.29 0.049 0.07 1.96E−07 GTTT-N15-GGGTA 47 14.64
MSMEG_0672 Conserved hypothetical protein 0.19 2.29E−03 0.04 9.03E−06 GTTT-N15-GGGTA 50 14.58
MSMEG_0697 Integral membrane protein 0.18 4.43E−03 0.04 1.48E−06 GTTT-N16-GGGAA 58 13.79
MSMEG_1076 Conserved hypothetical protein 0.05 7.61E−06 0.03 4.16E−06 GTTT-N16-GGGTA 50 14.28
MSMEG_1097 Glycosyl transferase, group 2 family protein 0.05 4.74E−05 0.03 1.09E−06 GTGT-N15-GGGTT 11 NF
MSMEG_1112 Aconitate hydratase 0.36 0.06 0.19 6.42E−03 GTTT-N16-GGGAA 8 13.84
MSMEG_1131 Tryptophan-rich sensory protein 0.29 0.04 0.82 0.63 GTGT-N16-GGGTA 9 12.95
MSMEG_1315 Small conductance mechanosensitive ion channel family protein 0.46 0.026 0.29 1.59E−03 GTTG-N17-GGGTA 11 13.8
MSMEG_1758 Hypothetical protein 0.26 5.15E−03 0.09 1.06E−04 GTTT-N16-GGGTA 8 14.25
MSMEG_1766 Conserved hypothetical protein 0.57 0.1 0.15 3.66E−04 GTTT-N16-GGGAA 32 13.75
MSMEG_1770d Conserved hypothetical protein 0.04 1.28E−07 0.01 2.50E−07 GTTT-N16-GGGCA 64 13.74
MSMEG_1771 Methylase, putative 0.08 2.49E−04 0.04 3.18E−06 GTTT-N15-GGGTA 29 14.6
MSMEG_1773 Conserved hypothetical protein 0.19 9.80E−03 0.34 2.73E−03 GTTT-N15-GGGAA 11 14.13
MSMEG_1774 Conserved hypothetical protein 0.1 1.06E−03 0.03 5.55E−06 GTTT-N16-GGGTA 64 14.31
MSMEG_1775 Cytochrome P450 monooxygenase 0.34 0.07 0.09 1.07E−04 GTTT-N15-GGGTA 9 14.62
MSMEG_1777 UsfY protein 0.15 1.44E−03 0.05 1.13E−05 GTTT-N16-GGGTA 69 14.31
MSMEG_1782 Oxidoreductase, short chain dehydrogenase/reductase 0.19 9.73E−03 0.04 7.39E−06 GTTT-N15-GGGTA 221 14.16
MSMEG_1787 RsbW protein 0.5 0.04 0.45 8.18E−03 GTTT-N17-GGGTA 56 14.76
MSMEG_1792 Conserved hypothetical protein 0.44 0.11 0.16 5.01E−04 GGGT-N14-GGGCA 268 NF
MSMEG_1794 Dehydrogenase 0.31 0.047 0.09 7.03E−05 GTGT-N17-GGGTA 15 13.28
MSMEG_1801 Hypothetical protein 0.49 0.19 0.18 2.68E−03 GGTG-N18-GGGAA 173 NF
MSMEG_1802 ChaB protein 0.24 5.03E−03 0.1 8.96E−05 GTTT-N16-GGGCA 63 13.6
MSMEG_2112 Secreted protein 0.23 4.48E−03 0.31 3.52E−03 GTTT-N15-GGGTA 24 14.75
MSMEG_2337 Isopentenyl-diphosphate delta-isomerase, type 2 0.21 3.50E−03 0.16 3.83E−04 GGTG-N15-GGGTA 67 NF
MSMEG_2347d Phytoene dehydrogenase 0.49 0.06 0.23 9.98E−04 GTTT-N16-GGGTA 97 14.4
MSMEG_2415 Hemerythrin HHE cation binding region 0.25 3.78E−03 0.08 1.12E−05 GTTG-N15-GGGTA 61 13.42
MSMEG_2830 ISMsm4, transposase 0.41 8.50E−03 0.54 5.29E−03 GGTT-N16-GGGTG 209 NF
MSMEG_2913 Hydrolase 0.36 0.042 0.1 1.36E−04 GTTT-N15-GGGTA 3 14.64
MSMEG_2927d ABC transporter, permease protein OpuCB 0.17 6.18E−04 0.11 3.14E−04 GTTT-N16-GGGTA 39 14.23
MSMEG_2958 Conserved hypothetical protein 0.17 3.78E−03 0.03 2.48E−06 GTTC-N15-GGGTA 24 13.34
MSMEG_3022d Transglycosylase-associated protein 0.05 5.77E−06 0.05 1.65E−05 GTTT-N16-GGGTA 30 14.34
MSMEG_3082 Soul heme binding protein 0.72 7.33E−03 0.44 5.67E−03 GCTT-N16-GGGTA 67 12.94
MSMEG_3141d Conserved domain protein 0.43 0.033 0.4 0.022 GTGT-N16-GGGTA 29 12.94
MSMEG_3255 DoxX subfamily, putative 0.02 6.01E−08 0.01 8.94E−08 GTTT-N15-GGGAA 36 14.09
MSMEG_3304 Succinate semialdehyde dehydrogenase 0.44 0.06 0.08 1.73E−07 GTGT-N15-GGGTA 25 13.24
MSMEG_3439 Hypothetical protein 0.15 4.30E−03 0.11 3.21E−04 GTTT-N15-CGGTA 59 NF
MSMEG_3443 Hypothetical protein 0.41 1.21E−03 0.47 0.026 GTTT-N15-GGGAT 45 NF
MSMEG_3536 Sugar transport protein 0.56 0.07 0.29 1.33E−05 GTGG-N16-GGGTA 134 NF
MSMEG_3543 Soluble secreted antigen MPT53 0.28 0.015 0.09 1.14E−04 GTTT-N16-GGGAA 138 13.68
MSMEG_3673 4-Alpha-glucanotransferase 0.55 0.08 0.38 3.26E−03 GTTT-N16-GGGCA 195 13.61
MSMEG_4195 Conserved hypothetical protein 0.58 0.017 0.42 9.23E−03 GTTT-N15-GGGTA 60 14.07
MSMEG_5189 Oxidoreductase 0.31 6.13E−03 0.42 0.013 GGTT-N16-GGGTA 25 12.93
MSMEG_5343 Conserved hypothetical protein 0.38 0.06 0.2 1.35E−03 GTTT-N16-GGCTA 35 NF
MSMEG_5402 Dehydrogenase DhgA 0.21 3.45E−03 0.18 9.24E−04 GTTT-N15-GGGTA 8 14.69
MSMEG_5543 Hypothetical protein 0.03 7.87E−07 0.02 9.61E−07 GTTT-N17-GGGTA 77 15.01
MSMEG_5550 Protein-glutamate methylesterase 0.29 3.07E−03 0.35 9.26E−03 GTTT-N15-GGGTA 20 14.58
MSMEG_5617 Immunogenic protein MPT63 0.02 5.65E−11 0.04 4.26E−06 GTTT-N15-GGGTA 70 14.65
MSMEG_6211 Hypothetical protein 0.13 1.15E−03 0.06 4.79E−05 GGTT-N15-GGGTA 9 13.19
MSMEG_6212 Hemerythrin HHE cation binding domain subfamily 0.05 2.87E−05 0.02 3.65E−07 GTTT-N15-GGGTA 51 14.64
MSMEG_6213 Manganese-containing catalase 0.31 0.039 0.06 1.20E−05 GTTT-N15-GGGTA 40 14.57
MSMEG_6232 Catalase KatA 0.3 0.049 0.05 1.93E−06 GTTT-N16-GGGAA 67 13.78
MSMEG_6305 Conserved hypothetical protein 0.31 0.028 0.12 1.11E−04 GTTT-N16-GGGCA 8 13.55
MSMEG_6467 Starvation-induced DNA-protecting protein 0.04 2.65E−05 0.03 3.62E−06 GTTC-N16-GGGCA 100 NF
MSMEG_6541 Anti-sigma factor antagonist 0.8 0.033 0.5 2.45E−03 GTTT-N15-GGGTA 282 14.54
MSMEG_6665 Integral membrane protein 0.18 3.16E−03 0.13 1.88E−04 GTTT-N15-GGGAA 8 14.07
MSMEG_6751 Hypothetical protein 0.59 0.08 0.22 3.54E−04 GGTT-N15-GGGTA 9 13.17
MSMEG_6768 Halogenase 0.66 0.1 0.37 0.047 GCTT-N16-GGGTA 9 12.88
SigF-dependent gene expressionf in exponential and/or stationary phase MSMEG_0686 Oxidoreductase 0.85 0.019 0.72 0.013 GTTT-N15-GGGTA 8 14.65
MSMEG_1204d 3-Oxoacyl-[acyl-carrier-protein] synthase 2 0.89 0.03 1.08 0.08 GTTC-N15-GGGTA 128 13.27
MSMEG_1360d Endonuclease/exonuclease/phosphatase 0.92 0.19 0.75 0.032 GTGT-N15-GGGTA 14 13.25
MSMEG_1477d Major facilitator superfamily 0.74 0.1 0.61 0.01 GTGT-N16-GGGTA 122 12.93
MSMEG_1807 Acetyl-/propionyl-coenzyme A carboxylase alpha chain 0.98 0.76 0.8 2.16E−03 GGTT-N17-GGGTA 294 13.33
MSMEG_1848 Formate dehydrogenase-O, major subunit 0.6 0.013 0.57 0.42 GGTT-N15-GGGTA 8 13.22
MSMEG_1853 Na+/H+ antiporter NhaA 0.69 0.026 0.66 0.023 GTTT-N15-GGGTA 99 14.73
MSMEG_2775 Na+/H+ antiporter NhaA 0.94 0.035 1.02 0.84 GTTT-N16-GGGCA 183 13.56
MSMEG_3046 Carbamoyl-phosphate synthase, small subunit 1.08 0.6 0.81 4.42E−03 GTTT-N16-GGGAA 206 13.72
MSMEG_3312 Hemerythrin HHE cation binding domain subfamily 0.74 0.08 0.56 0.025 GTTT-N15-GGGTA 26 14.58
MSMEG_3563d Drug transporter 1.14 0.83 0.61 5.64E−03 GTTT-N16-GGGTA 114 14.21
MSMEG_3621 NADH dehydrogenase 0.96 0.44 0.82 0.025 GTTG-N15-GGGTA 98 13.36
MSMEG_3689d Sodium:solute symporter 1.06 0.037 0.96 0.36 GTTT-N16-GGGAA 96 13.72
MSMEG_4831 Transcriptional regulator, TetR family protein 1.32 0.018 1.18 0.35 GTTG-N16-GGGTA 232 12.98
MSMEG_4918 1,4-Alpha-glucan branching enzyme 0.6 0.027 0.52 0.022 GGTT-N15-GGGTA 172 13.2
MSMEG_5328 Conserved hypothetical protein 0.7 0.013 0.61 0.05 GTTT-N16-GGGAA 48 13.72
MSMEG_5554 Antar domain protein 0.9 0.3 1.11 9.33E−03 GTTG-N15-GGGTA 231 13.33
MSMEG_5661 ABC transporter ATP binding protein 1.1 0.81 0.64 0.028 GTTT-N16-GGGAA 39 13.7
MSMEG_5710 Hypothetical protein 0.9 0.015 0.93 0.43 GTTT-N16-GGGCA 211 12.99
MSMEG_6515d Trehalose synthase 0.68 3.70E−03 0.63 0.018 GTGT-N16-GGGTA 10 12.88
MSMEG_6676 Probable conserved transmembrane protein 0.54 9.69E−03 0.68 0.1 GTTC-N16-GGGTA 162 13.12
MSMEG_6739 Hypothetical protein 0.79 0.06 0.62 0.03 GTTT-N16-GGGTA 63 13.63
MSMEG_6822 Beta-lactamase 0.79 9.46E−03 0.55 0.039 GTTT-N16-GGGTA 46 14.2
No significant SigF-dependent gene expressiong observed under standard growth conditions MSMEG_0191 BadF/BadG/BcrA/BcrD ATPase family 1.32 0.54 1.08 0.53 GTTT-N17-GGGAA 64 14.21
MSMEG_0362 Amidohydrolase 2 0.97 0.55 1.18 0.22 GTTC-N17-GGGTA 69 13.43
MSMEG_0430 ISMsm4, transposase No data No data GTTT-N16-GGGAA 155 13.75
MSMEG_0522 pp24 protein 1.01 0.86 0.78 0.09 GTTT-N15-GGGTA 34 14.61
MSMEG_0681 P450 heme-thiolate protein 1.03 0.56 1 0.99 GTTT-N16-GGGCA 45 13.02
MSMEG_0849 Oxygenase 1.26 0.6 0.99 0.62 GTGT-N17-GGGTA 102 13.29
MSMEG_1055 Hexapeptide transferase family protein No data No data GTTG-N17-GGGTA 37 13.45
MSMEG_1145 Virulence factor Mce family protein 0.97 0.22 1.15 0.43 GTTT-N15-GGGGA 214 12.9
MSMEG_1222 ISMsm6, transposase 1.07 0.77 1.09 0.36 GTGT-N15-GGGTA 8 13.11
MSMEG_1295 Transthyretin 0.76 0.06 0.8 0.08 GTGT-N16-GGGTA 160 12.86
MSMEG_1332 Conserved hypothetical protein 1.03 0.55 1.29 0.12 GTTT-N17-GGGCA 161 14.24
MSMEG_1435 Ribosomal protein S10 1.01 0.94 0.86 0.5 GTTC-N15-GGGTA 257 13.24
MSMEG_1440 Ribosomal protein S19 65.48 0.39 0.82 0.29 GTGT-N15-GGGTA 354 13.17
MSMEG_1698 Putative ammonia monooxygenase superfamily 1.93 0.33 1 0.96 GTTT-N15-GGGTA 8 14.54
MSMEG_1742 Oxidoreductase 0.73 0.19 0.9 0.08 GTTT-N15-GGGTA 89 14.63
MSMEG_1784 Type I topoisomerase 0.9 0.22 0.85 0.12 GTGT-N16-GGGTA 183 12.91
MSMEG_1844 Conserved hypothetical protein 0.85 0.35 0.88 0.44 GTTT-N15-GGGTA 24 14.6
MSMEG_1919 Transcription factor WhiB 0.85 0.08 0.86 0.37 GCTT-N16-GGGTA 199 12.95
MSMEG_2200d Formyltetrahydrofolate deformylase 1 0.91 0.97 0.71 GTTT-N15-GGGTA 237 14.6
MSMEG_2335 Hexapeptide transferase family protein 1.02 0.53 1.08 0.1 GTTG-N17-GGGTA 37 13.45
MSMEG_2425 Ammonium transporter 1.33 0.22 1.02 0.76 GTTC-N15-GGGTA 238 13.25
MSMEG_2466 Glutaryl coenzyme A dehydrogenase 1.17 0.17 0.96 0.79 GTTC-N17-GGGTA 174 13.44
MSMEG_2780 Uroporphyrinogen decarboxylase 1.05 0.6 1.02 0.71 GTTT-N15-GGGCA 92 13.91
MSMEG_2804 Two-component system sensor kinase 0.92 0.07 1.13 0.18 GTTG-N16-GGGTA 39 13.13
MSMEG_2837 Nitrate reductase NarB 0.86 0.2 0.8 0.73 GTTT-N16-GGGTA 42 14.26
MSMEG_2938 Acyl coenzyme A thioesterase II 1.04 0.49 1.18 0.35 GTCT-N15-GGGTA 60 13.09
MSMEG_3026 Conserved hypothetical protein 1.12 0.08 1 1 GTTC-N15-GGGTA 51 13.35
MSMEG_3205 Histidinol dehydrogenase 1.13 0.07 1.13 0.47 GCTT-N15-GGGTA 201 13.15
MSMEG_3289 gp61 protein 0.82 0.23 0.68 0.12 GTTT-N15-GGGTA 29 14.68
MSMEG_3610 Conserved hypothetical protein 1.03 0.26 1.29 0.13 GTTG-N15-GGGTA 73 13.29
MSMEG_3611 d-Xylulose 5-phosphate/d-fructose 6-phosphate phosphoketolase 1.01 0.97 0.73 0.05 GGTT-N15-GGGTA 68 13.29
MSMEG_3672 Transporter, small multidrug resistance (SMR) family 1.12 0.41 1 0.96 GTTC-N17-GGGTA 62 13.43
MSMEG_3811 Universal stress protein family, putative 0.85 0.21 1.15 0.26 GTTG-N15-GGGTA 1 13.38
MSMEG_3822 Regulatory protein GntR, HTH 1.01 0.92 1.08 0.63 GTCT-N15-GGGTA 28 13.22
MSMEG_3918 Hypothetical protein 0.97 0.58 1.19 0.13 GTTT-N17-GGGTA 75 14.57
MSMEG_4070d Transcriptional regulator, TetR family, putative 0.98 0.87 1.18 0.35 GTGT-N16-GGGTA 69 12.94
MSMEG_4232 UDP-N-acetylmuramoylalanyl-d-glutamate-2,6-diaminopimelate ligase 1.16 0.06 1.1 0.32 GTCT-N16-GGGTA 232 12.87
MSMEG_4270 Adenosine kinase 1.1 0.14 1.2 0.13 GTTG-N16-GGGTA 246 13.08
MSMEG_4405 Putative ECF sigma factor RpoE1 1.03 0.68 0.99 0.94 GCTT-N15-GGGTA 234 13.1
MSMEG_4427 Transmembrane efflux pump 1.11 0.47 1.15 0.35 GTTC-N15-GGGAA 279 12.87
MSMEG_4441 Cupin domain protein 1.58 0.35 1 0.99 GTCT-N17-GGGTA 147 13.3
MSMEG_4633 Peptidase S9, prolyl oligopeptidase 1.33 0.12 1.04 0.81 GTTT-N16-GGGTA 95 14.16
MSMEG_4707 Nonheme bromoperoxidase BPO-A2 0.47 0.06 0.9 0.87 GTTT-N15-GGGTA 35 13.94
MSMEG_4737 Conserved hypothetical protein 1.1 0.45 1.27 0.3 GTTT-N15-GGGCA 97 13.39
MSMEG_5011 Hypothetical protein 1.06 0.53 1.18 0.19 GGTT-N15-GGGTA 42 13.22
MSMEG_5376 Conserved hypothetical protein 1.59 0.28 1.3 0.23 GTGT-N17-GGGTA 99 13.34
MSMEG_5434 Hypothetical protein 0.95 0.61 0.85 0.57 GGTT-N15-GGGTA 119 13.16
MSMEG_5499 Conserved hypothetical protein 1.26 0.32 1.46 0.35 GTTT-N16-GGGCA 197 13.53
MSMEG_5559 Metabolite/sugar transport protein 0.87 0.43 0.84 0.08 GTTT-N16-GGGTA 39 14.12
MSMEG_5580d Ku protein 1 0.98 1.15 0.18 GTTT-N16-GGGTA 9 13.67
MSMEG_5754 gp41 protein 1.02 0.34 1 0.98 GTTG-N15-GGGAA 301 12.87
MSMEG_5773 Fatty acid desaturase 0.97 0.49 1.09 0.32 GTGT-N17-GGGTA 177 13.63
MSMEG_5872 DNA binding response regulator PhoP 1 0.96 1.2 0.05 GTTT-N17-GGGTA 71 14.75
MSMEG_5907 Acyl coenzyme A dehydrogenase 1.09 0.29 1.12 0.28 GGTT-N15-GGGTA 181 13.21
MSMEG_6091 Negative regulator of genetic competence ClpC/MecB 1.01 0.82 1.12 0.18 GTTG-N15-GGGTA 136 13.42
MSMEG_6199 Transcription factor WhiB 1.23 0.1 1.29 0.19 GCTT-N15-GGGTA 23 13.14
MSMEG_6427 Superoxide dismutase (Mn) 0.91 0.24 1.02 0.45 GGTT-N17-GGGTA 120 13.3
MSMEG_6847 Conserved hypothetical protein 0.93 0.49 1.17 0.22 GTTG-N15-GGGAA 280 12.84
a

ΔsigF strain/wild-type gene expression ratio.

b

Base pairs between end of −10 promoter element and annotated start codon.

c

PWM, position weight matrix. NF, not found.

d

SigF promoter site previously proposed by Provvedi et al. (28).

e

P < 0.05, >2-fold difference between wild type and ΔsigF strain.

f

P < 0.05.

g

P > 0.05.