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. 2009 Apr 17;191(12):3869–3880. doi: 10.1128/JB.00113-09

TABLE 3.

Genes with ≥3-fold change in mRNA levelsa

cg designation NCgl designation Gene name Description of (putative) product Avg mRNA ratio (ΔcitAB strain mRNA/wt mRNA)
cg0089 NCgl0067 citA Sensor histidine kinase 0.00
cg0090 NCgl0068 citB Response regulator 0.00
cg3125 NCgl2724 tctA Tricarboxylate transport membrane protein 0.04
cg3126 NCgl2725 tctB Tricarboxylate transport membrane protein 0.01
cg3127 NCgl2726 tctC Tricarboxylate binding protein 0.02
cg2380 NCgl2088 14-kDa membrane protein 0.03
cg0088 NCgl0066 citH Citrate transporter 0.04
cg1376 NCgl1173 ssuD1 Sulfonatase (alkanesulfonate monooxygenase) 0.10
cg1377 NCgl1174 ssuC Aliphatic sulfonate transmembrane ABC transporter protein 0.04
cg1379 NCgl1175 ssuB Aliphatic sulfonate ATP binding ABC transporter protein 0.10
cg1380 NCgl1176 ssuA Aliphatic sulfonate binding protein 0.20
cg3226 NCgl2816 l-Lactate permease 0.05
cg3227 NCgl2817 lldD Quinone-dependent l-lactate dehydrogenase 0.15
cg3308 NCgl2881 rpsF 30S ribosomal protein S6 0.09
cg0810 NCgl0676 Hypothetical protein 0.09
cg1628 NCgl1383 Hydrolase of the α/β superfamily 0.12
cg1581 NCgl1341 argJ Bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein 0.14
cg1582 NCgl1342 argB N-Acetylglutamate kinase 0.18
cg1583 NCgl1343 argD Acetylornithine aminotransferase 0.27
cg3026 NCgl2635 mrpD Subunit D of multisubunit Na+/H+ antiporter 0.19
cg3027 NCgl2636 mrpE Subunit E of multisubunit Na+/H+ antiporter 0.15
cg3028 NCgl2637 mrpF Subunit F of multisubunit Na+/H+ antiporter 0.24
cg3029 NCgl2638 mrpG Subunit G of multisubunit Na+/H+ antiporter 0.23
cg1156 NCgl0975 ssuD2 Monooxygenase for sulfonate utilization 0.19
cg1451 NCgl1235 serA Phosphoglycerate dehydrogenase 0.22
cg0576 NCgl0471 rpoB Subunit β of DNA-directed RNA polymerase 0.23
cg2894 NCgl2523 Drug resistance-related transcriptional repressor 0.24
cg1364 NCgl1161 atpF Subunit B of ATP synthase 0.26
cg2157 NCgl1892 terC Tellurium resistance membrane protein 0.30
cg1151 NCgl0972 seuA Monooxygenase for sulfonate ester utilization 0.30
cg1386 NCgl1182 fixA Subunit β of putative electron transfer flavoprotein 0.30
cg0653 NCgl0538 rpsK 30S ribosomal protein S11 0.31
cg1147 NCgl0968 ssuI Flavin mononucleotide binding protein required for sulfonate and sulfonate ester utilization 0.32
cg1349 NCgl1147 Membrane protein containing CBS domain 0.33
cg0825 NCgl0689 fabG 3-Ketoacyl-(acyl carrier protein) reductase 0.35
cg0882 NCgl0738 Hypothetical protein 0.36
cg3420 NCgl2983 sigM RNA polymerase σ factor of ECF subfamily 2.37
cg2069 NCgl1774 psp1 Putative secreted protein 2.50
cg3351 NCgl2920 nagI Gentisate 1,2-dioxygenase 2.56
cg2630 NCgl2314 pcaG Subunit α of protocatechuate dioxygenase 2.57
cg2966 NCgl2588 Phenol 2-monooxygenase 2.71
cg1255 NCgl1060 HNH endonuclease 2.87
cg0638 NCgl0524 HD superfamily hydrolase 3.09
cg3216 NCgl2808 gntP Gluconate permease 3.10
cg2504 NCgl2201 Hypothetical protein 3.14
cg2181 NCgl1915 Secreted component of ABC-type peptide transport system 3.26
cg2182 NCgl1916 Permease component of ABC-type peptide transport system 3.46
cg2183 NCgl1917 Permease component of ABC-type peptide transport system 3.71
cg2184 NCgl1918 ATPase component of ABC-type peptide transport system; contains duplicated ATPase domains 4.41
cg3151 NCgl2131 tnp2b Transposase 3.56
cg0759 prpD2 Methylcitrate dehydratase 3.63
cg0760 NCgl0629 prpB2 Methylisocitrate lyase 9.11
cg0762 NCgl0630 prpC2 Methylcitrate synthase 11.05
cg2938 NCgl2563 Permease component of ABC-type dipeptide/oligopeptide/nickel transport system 3.93
cg2940 NCgl2565 ATPase component of ABC-type transport system; contains duplicated ATPase domains 3.69
cg2836 NCgl2476 sucD Subunit α of succinyl-CoA synthetase 4.92
cg2837 NCgl2477 sucC Subunit β of succinyl-CoA synthetase 3.82
cg3047 NCgl2656 ackA Acetate kinase 4.00
cg3048 NCgl2657 pta Phosphotransacetylase 5.43
cg0961 NCgl0805 metA Homoserine O-acetyltransferase 4.89
cg2426 tnp2d Transposase 5.32
cg1612 NCgl1368 Acetyltransferase 5.69
cg2610 NCgl2294 Secreted component of ABC-type dipeptide/oligopeptide/nickel transport system 6.19
cg3107 NCgl2709 adhA Zn-dependent alcohol dehydrogenase 9.21
cg3195 NCgl2787 Flavin-containing monooxygenase 26.82
a

For the genes listed, the mRNA level in the ΔcitAB strain was altered ≥3-fold compared to the mRNA level in the wild type (wt) in at least three of four independent experiments after the growth of the strains in CGXII minimal medium containing 50 mM citrate and 50 mM glucose as carbon sources. The table includes those genes for which the mean mRNA ratio showed at least a twofold change (increase or decrease) and had a P value of ≤0.05. The mRNA ratios shown are mean values from three to four independent DNA microarray experiments starting from independent cultures. mRNA was prepared from cells in the exponential growth phase. CBS, cystathionine-β-synthase; ECF, extracytoplasmic function; succinyl-CoA, succinyl coenzyme A.