TABLE 3.
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 |
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.