Table 5.
Comparative RNAseq analysis of L-proline producing strain JJ004, its isogenic non-producing control strain JJ001, L-PA producing C. glutamicum strain GSL(pVWEx1-lysDH-proC) and its isogenic non-producing control strain GSL(pVWEx1).
| Log2 fold change of RNA level (P-value < 0.01) | |||
|---|---|---|---|
| Locus or gene | Product | JJ004/ control JJ001 | GSL(pVWEx1-lysDH-proC)/ control GSL(pVWEx1) |
| cg0018 | Conserved hypothetical membrane protein | 0.8 | -1.0 |
| cg0107 | Putative secreted protein | 0.3 | -1.0 |
| cg0175 | Putative secreted protein | -0.8 | -1.2 |
| cg0282 | CsbD family protein involved in stress response | -0.8 | -0.6 |
| ctpA | Putative Cu2+ transporting P-type ATPase | 1.1 | 0.2 |
| proC | Pyrroline-5-carboxylate reductase | 0.0 | 4.7 |
| glyR | Transcriptional activator of glyA, ArsR-family | 1.0 | -0.5 |
| cg0569 | Putative Cd2+ transporting P-type ATPase | 1.0 | 1.7 |
| whiB3 | Transcriptional regulator protein, WhiB-family | 2.6 | -0.5 |
| prpC2 | 2-Methylcitrate synthase | 0.9 | 0.7 |
| cg0770 | ABC-type putative iron-siderophore transporter, permease subunit | -1.9 | 0.3 |
| irp1 | ABC-type putative iron-siderophore transporter, substrate-binding lipoprotein | -2.3 | -0.3 |
| whcE | Transcriptional regulator, WhiB-family | 0.8 | -0.4 |
| pdxS | Pyridoxal 5’-phosphate (PLP) synthase subunit S | -0.8 | 0.0 |
| pdxT | Pyridoxal 5’-phosphate (PLP) synthase subunit T | -1.0 | 0.5 |
| cg0924 | ABC-type putative iron-siderophore transporter, substrate-binding lipoprotein | -1.7 | -0.5 |
| cg0926 | ABC-type putative iron-siderophore transporter, permease subunit | -1.3 | -0.2 |
| cg0935 | Conserved hypothetical protein | -0.4 | -1.3 |
| rpf1 | RPF-protein precursor | 0.9 | -0.4 |
| cg0952 | Putative integral membrane protein | -0.9 | -0.3 |
| betP | Na+/glutamate symporter | -1.2 | -0.7 |
| cg1091 | Hypothetical protein | -1.6 | -1.0 |
| cg1091 | Hypothetical protein | -1.6 | -1.0 |
| cg1109 | Hypothetical protein | -0.3 | -1.1 |
| cg1279 | Putative secreted protein | 0.8 | 0.6 |
| cg1291 | Putative membrane protein | 1.2 | -0.1 |
| cg1293 | Putative secreted protein | -0.8 | -0.4 |
| putP | Na+/proline symporter | -0.8 | -0.1 |
| cg1419 | Putative secondary Na+/bile acid symporter, bile acid:Na+ symporter (BASS) family | -1.7 | -0.2 |
| lysE | L-Lysine efflux permease | -5.4 | -0.5 |
| leuC | 3-Isopropylmalate dehydratase, large subunit | -0.8 | 0.0 |
| ptsG | Phosphotransferase system (PTS), glucose-specific enzyme IIBCA component | -0.9 | 0.1 |
| cg1604 | Secreted protein, putative channel protein | -0.9 | 0.1 |
| cg1665 | Putative secreted protein | -1.7 | -0.9 |
| cg1746 | Putative membrane protein | 0.8 | n.d. |
| cg1897 | Putative secreted protein | -3.1 | n.d. |
| cg1930 | Putative secreted hydrolase | -1.1 | n.d. |
| cg2068 | Hypothetical protein | -1.0 | n.d. |
| psp1 | Putative secreted protein | -1.6 | n.d. |
| int2’ | Putative phage Integrase (N-terminal fragment) | -1.6 | n.d. |
| cg2181 | ABC-type putative dipeptide/oligopeptide transporter, substrate-binding lipoprotein | -0.8 | 0.1 |
| xerC | Putative site-specific recombinase | -0.2 | -1.2 |
| cg2402 | Secreted protein NLP/P60 family | 0.8 | -0.1 |
| cg2425 | Putative permease | 0.7 | 0.3 |
| cg2477 | Conserved hypothetical protein | 0.0 | -0.8 |
| cg2564 | Conserved hypothetical protein | -1.7 | -0.5 |
| catA | Catechol 1,2-dioxygenase | 0.3 | 0.7 |
| cg2651 | Conserved hypothetical protein, pseudogene | -0.6 | -1.4 |
| cg2677 | ABC-type putative dipeptide/oligopeptide transporter, permease subunit | 0.0 | 0.9 |
| gntV | Gluconokinase | -0.5 | 1.8 |
| rpmJ | 50S ribosomal protein L36 | -0.3 | -1.0 |
| pstB | ABC-type phosphate transporter, ATPase subunit | 1.3 | 0.1 |
| pstA | ABC-type phosphate transporter, permease subunit | 1.2 | 0.5 |
| pstC | ABC-type phosphate transporter, permease subunit | 1.5 | 0.3 |
| pstS | ABC-type phosphate transporter, substrate-binding lipoprotein | 1.3 | 0.1 |
| cg2851 | Branched-chain amino acid aminotransferase, AT class III/4-amino-4-deoxychorismate lyase | 0.0 | -1.6 |
| cg2875 | Hypothetical protein | 0.8 | -0.3 |
| cg2908 | Putative membrane protein | -1.0 | 0.1 |
| pck | Phosphoenolpyruvate carboxykinase (GTP) | 0.8 | 0.0 |
| gntP | Gluconate:H+ symporter | -1.0 | 0.1 |
| cg3218 | Pyruvate kinase-like protein | 1.2 | 0.4 |
| ldh | L-Lactate dehydrogenase, NAD-dependent | 0.9 | 0.0 |
| cg3254 | Putative membrane protein | -0.8 | -0.9 |
| cg3271 | SAM-dependent methyltransferase | 0.3 | -1.1 |
| cg3281 | Putative Cu2+ transporting P-type ATPase | 1.2 | -0.4 |
| cg3282 | Putative Cu2+ transporting P-type ATPase | 1.4 | 0.0 |
| cg3326 | Hypothetical protein | 1.1 | 0.8 |
| mez | Malic enzyme | 0.9 | 0.3 |
| proP | Proline/betaine permease | -1.2 | -1.2 |
| cg3402 | Putative Hg2+ permease, MerTP-family | 1.2 | 0.0 |
| cg3404 | ABC-type putative iron(III) dicitrate transporter, substrate-binding lipoprotein | -2.1 | -0.4 |
| cg4014 | Conserved hypothetical protein, possibly involved in stress response | 0.3 | -1.0 |
| cg4019 | 0.8 | 0.1 | |
| cg4021 | -0.6 | -1.1 | |
Names of genes used for subsequent qRT-PCR analysis are given in bold. n.d., not detected.