TABLE 2.
Genome-wide comparison of mRNA levels in C. glutamicum wild type and the ΔrosR mutant using DNA microarrays
The mRNA ratios represent mean values from three independent microarray experiments starting from independent cultures (see “Experimental Procedures”). The strains were cultivated in CGXII minimal medium with 4% (w/v) glucose, and mRNA was isolated in the exponential growth phase. The table includes those genes that showed a ≥2-fold changed mRNA level (increased or decreased) in at least two of the three experiments and that had a p value ≤ 0.05 (exception is gluD; here only one experiment was evaluable). The genes are ordered according to their position on the genome. The mRNA ratios for the genes narJ and gluD were marked with an asterisk, as the mRNA ratio (narJ) or the p value (gluD) were not within the defined range. However, these genes were included, as they are part of operons of which all other genes fulfilled the selected criteria.
| Accession no. | Gene | Annotation | mRNA ratio DrosR/WT |
|---|---|---|---|
| Genes with a decreased mRNA level in strain DrosR | |||
| cg0416 | Secreted protein carrying a eukaryotic domain | 0.24 | |
| cg0415 | ptpA2 | Low molecular weight phosphotyrosine protein phosphatase | 0.32 |
| cg1109 | porB | Anion-specific porin precursor | 0.46 |
| cg1324 | rosR | Transcriptional regulator of MarR family | 0.00 |
| cg1345 | narK | Putative nitrate/nitrite antiporter | 0.34 |
| cg1344 | narG | Respiratory nitrate reductase, α-subunit | 0.31 |
| cg1343 | narH | Respiratory nitrate reductase, β-subunit | 0.43 |
| cg1342 | narJ | Respiratory nitrate reductase, δ-subunit | 0.55* |
| cg1341 | narI | Respiratory nitrate reductase, γ-subunit | 0.42 |
| cg1382 | glgE | Putative α-amylase | 0.49 |
| cg1671 | Putative membrane-associated GTPase | 0.42 | |
| cg2136 | gluA | ABC transporter for glutamate, ATP-binding protein | 0.39 |
| cg2137 | gluB | ABC transporter for glutamate, secreted glutamate-binding protein | 0.36 |
| cg2138 | gluC | ABC transporter for glutamate, permease | 0.37 |
| cg2139 | gluD | ABC transporter for glutamate, permease | 0.29* |
| cg2649 | Secreted penicillin-binding protein | 0.39 | |
| cg2773 | Uncharacterized protein with SCP/PR1 domain | 0.32 | |
| Genes with an increased mRNA level in strain DrosR | |||
| cg0072 | Membrane protein of unknown function | 189.00 | |
| cg0144 | rbtT | Putative arabinitol or ribitol transporter | 2.25 |
| cg0292 | tnp16a | Transposase (ISCg16a) | 2.17 |
| cg0364 | Membrane protein | 3.51 | |
| cg0384 | rluC1 | Ribosomal large subunit, pseudouridine synthase C | 2.57 |
| cg0408 | Membrane protein | 2.82 | |
| cg0823 | Putative monooxygenase | 69.95 | |
| cg0824 | tnp5a | Transposase (ISCg5a) | 3.10 |
| cg1001 | mscL | Large conductance mechanosensitive channel | 2.24 |
| cg1150 | Putative NAD(P)H-dependent FMN reductase | 169.08 | |
| cg1255 | HNH endonuclease | 3.48 | |
| cg1322 | Putative polyisoprenoid-binding protein | 20.66 | |
| cg1426 | Protein of glutathione S-transferase family | 26.02 | |
| cg1848 | Luciferase-like monooxygenase | 22.24 | |
| cg1850 | Putative FMN reductase | 419.73 | |
| cg2329 | Luciferase-like monooxygenase | 140.65 | |
| cg2426 | tnp2d | Transposase (ISCg2d) | 4.14 |
| cg2485 | phoD | Secreted alkaline phosphatase precursor | 2.31 |
| cg2504 | Protein of unknown function | 4.93 | |
| cg2599 | Pirin-related protein | 3.68 | |
| cg2759 | tnp15b | Transposase (ISCg15b) | 2.87 |
| cg2844 | pstA | ABC transporter for phosphate uptake, permease component | 3.51 |
| cg2914 | tnp5b | Transposase (ISCg5b) | 3.51 |
| cg2953 | xylC | Putative benzaldehyde dehydrogenase | 2.13 |
| cg3004 | gabD1 | Putative succinate semialdehyde dehydrogenase | 2.34 |
| cg3084 | Putative flavin-containing monooxygenase | 40.64 | |
| cg3085 | Luciferase-like monooxygenase | 2.46 | |
| cg3258 | rluC2 | Putative pseudouridine synthase | 2.38 |
| cg3272 | Membrane protein (putative Fe2+/Mn2+ transporter) | 2.67 | |
| cg3273 | Protein of unknown function | 2.38 | |
| cg3274 | Site-specific recombinase (resolvase) fragment | 3.69 | |
| cg3284 | cgtS9 | Two-component histidine kinase CgtS9 | 198.14 |
| cg3288 | Hypothetical protein predicted by Glimmer | 2.58 | |
| cg3289 | Putative thiol-disulfide isomerase | 2.46 | |
| cg3291 | Putative transcriptional regulator of Crp/FNR family | 95.66 | |
| cg3293 | Protein of unknown function | 3.17 | |
| cg3295 | Probable cation-transporting P-type ATPase | 4.19 | |
| cg3329 | Member of uncharacterized protein family UPF0027 (homolog of E. coli RtcB) | 2.06 | |
| cg3413 | azlC | Putative branched chain amino acid permease (azaleucine resistance) | 2.21 |
| cg3418 | Putative secreted protein | 3.21 | |