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Table 1 Differential expression pattern at pH 9 in comparison to pH 7.5

From: Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

Genes induced at pH 9   Transcriptome4 Proteome5 Regulators6
         cytoplasma envelope membrane  
No gene ID1 op2 gene function TMH3 pH 6 pH 9 6 7.5 9 6 7.5 9 6 7.5 9  
1 cg0077    Hypothetical protein 0 n.d. 1.04 -0.6 - - - - - -0.9 - -  
2 cg0105    Hypothetical protein Cgl0077 0 -0.83 1.65 - - - -0.4 - - - - -  
3 cg0310   katA Catalase 0 -0.62 1.73 4.2 5.1 6.4 - - 0.0 - - -0.6 RipA
4 cg0444   ramB Regulator of acetate metabolism 0 0.76 1.11 - - -0.8 - 0.7 3.5 - - - RamA, RamB
5 cg0445 c sdhCD Succinate dehydrogenase component CD 5 -1.31 1.31 - - - 1.8 1.4 2.4 3.2 4.0 5.0 RipA, DtxR, RamA*, RamB*
6 cg0446 c sdhA Succinate dehydrogenase A 0 -1.08 1.47 1.0 2.7 1.7 6.7 7.0 9.0 8.5 9.0 9.9 RipA, DtxR, RamA*, RamB*
7 cg0447 c sdhB Succinate dehydrogenase B 0 -1.43 1.14 - -0.4 - 4.6 5.0 6.7 3.5 3.4 5.3 RipA, DtxR, RamA*, RamB*
8 cg0448 c   Conserved hypothetical membrane protein 2 -0.98 1.18 - - - -0.4 0.8 1.7 - - - RipA*, DtxR, RamB*
9 cg0778   fecC putative iron or siderophore ABC-type transporter, permease component 8 -0.05 1.07 - - - - - - - - -  
10 cg0825    Dehydrogenases with different specificities 0 -0.19 1.07 4.1 4.6 5.0 -0.4 -0.3 1.8 -0.7 - -0.4  
11 cg0858    putative gamma subunit of the nitrate reductase 1 -0.28 1.22 - - - - - - - - -  
12 cg1095    Hypothetical protein 0 0.32 1.28 - - - - - - - - -  
13 cg1136    Hypothetical protein 0 0.15 1.02 1.6 0.5 2.2 - - - - - -  
14 cg1206    PEP phosphonomutase or related enzyme 0 0.38 1.05 2.6 2.8 2.7 - - - - - -  
15 cg1292 r   Flavin-containing monoxygenase 3 0 n.d. 3.87 - - 2.4 - - 4.4 - - -0.6  
16 cg1293 r   Hypothetical membrane protein 3 n.d. 1.71 - - - - - - - - -  
17 cg1312    Hypothetical membrane protein 4 n.d. 1.32 - - -0.2 1.9 2.1 4.7 5.3 4.4 6.3  
18 cg1344 s narG Nitrate dehydrogenases 2 (Fe4S4 containing) 0 1.36 1.94 - - -0.6 - - - - - -0.4 RipA, GlxR*
19 cg1345 s narK putative nitrate/nitrite transporter 12 n.d. 1.66 - - - -0.4 - 3.0 1.5 -0.6 3.0 RipA, GlxR*
20 cg1695    SAM dependent methyltransferase 0 n.d. 1.72 - - - - - - - - -  
21 cg1737   acn Aconitase A 0 -0.58 1.66 4.4 5.3 6.2 4.4 5.0 4.9 2.2 2.6 2.5 RipA, RamA*, RamB*
22 cg1759 x sufX Predicted metal-sulfur cluster biosynthetic enzyme 0 0.94 1.34 - - -0.8 -0.4 - - - - - SufR, SigM
23 cg1761 x nifS2 Cysteine desulfhydrase, Selenocysteine lyase 0 0.44 1.47 2.3 2.0 3.2 -0.4 - - - - - SufR, SigM
24 cg1762 x sufC Suf related ABC-type transporter, ATPase component 0 0.81 1.51 3.7 3.4 4.6 3.4 4.4 4.1 0.1 2.9 2.1 SufR, SigM
25 cg1764 x sufB Suf related ABC-type transporter SufB, permease component 0 0.93 1.81 2.8 3.4 5.0 3.4 3.4 3.8 0.1 0.4 1.6 SufR, SigM
26 cg1765 x sufR transcriptional regulator SufR 0 0.76 1.53 - - - - - - - - - SufR, SigM
27 cg1790   pgk Phosphoglycerate kinase 0 0.15 1.07 4.8 4.2 5.0 5.0 4.8 5.0 2.5 2.7 3.3 SigB*
28 cg1884    putative copper export protein CopC 2 -0.39 1.12 - - - - - - - - - LexA
29 cg1904    ABC-type transporter, permease component 6 0.09 1.12 - - - - - - - -0.6 1.2  
30 cg2191    putative 3-demethylubiquinone-9 3-methyltransferase 0 n.d. 1.02 - - - - - - - - -  
31 cg2274 ab   Hypothetical protein 0 -0.17 1.15 -0.6 0.4 1.8 - - - - - -  
32 cg2275 ab   Hypothetical protein 0 -0.28 1.03 1.0 2.4 1.3 - - - -0.9 - -  
33 cg2320    ArsR type transcriptional regulator 0 -0.26 1.25 - - - - - - - - -  
34 cg2572    Hypothetical protein 0 0.45 1.44 - - - - - - - - -  
35 cg2636   catA1 Protocatechuate 3,4-dioxygenase beta subunit 0 n.d. 3.09 - - 1.6 - - - - - - RipA, GlxR*
36 cg2736   bcp putative 3-demethylubiquinone-9 3-methyltransferase 0 0.12 1.12 0.5 -0.5 0.4 - - - - - -  
37 cg2782   ftn Ferritin-like protein 0 0.56 1.29 - - 0.8 - - - - - - DtxR
38 cg2853    Hypothetical protein 0 0.41 1.4 0.6 -0.5 1.8 - - - - - -  
39 cg3117 ai cysX Hypothetical protein 0 3.5 1.08 - - - - - - - - - DtxR, McbR*, CysR*
40 cg3118 ai cysI Sulfite reductase hemoprotein beta-component 0 3.5 1.06 0.6 1.5 2.4 3.5 2.1 -0.3 - - - DtxR, McbR, CysR*
41 cg3236    MFS-type transporter 0 1.27 1.01 - - -0.8 - - - - - -  
42 cg3331   ogt Methylated DNA-protein cysteine methyltransferase 0 0.2 1.34 - -0.8 - -0.1 - 1.3 - - -  
Genes repressed at pH 9
1 cg0071    Metallo-beta-lactamase superfamily 0 n.d. -1.01 - - - - - - - - -  
2 cg0133   abgT P-aminobenzoyl-glutamate transporter 13 -0.86 -1.02 - - - - - - 0.3 3.7 2.1  
3 cg0202   iolD Putative acetolactate synthase 0 n.d. -1.13 - - - - - - - - -  
4 cg0265    putative ABC-type molybdate transporter, ATPase component 0 -0.22 -1.08 - - - - - - - - -  
5 cg0303   leuA 2-isopropylmalate synthase 0 -0.97 -1.06 4.3 4.7 4.5 - -0.3 - - - -  
6 cg0404 b   putative nitroreductase 0 1.77 -1.50 3.4 2.5 0.9 0.9 - - -0.9 - -  
7 cg0467    ABC-type cobalamin/Fe3+-siderophores transporter, periplasmic component 0 -0.50 -1.10 - 0.2 - - 0.7 - 0.2 1.0 -0.4 DtxR
8 cg0527    ArsR type transcriptional regulator 0 -0.32 -1.13 - - - - - - - - - DtxR
9 cg0589    ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component 0 -0.15 -1.01 - - - 1.2 - - 0.1 - - DtxR
10 cg0623    putative ABC-type cobalt transporter, permease components 8 -1.05 -1.35 - - - - - - - - -  
11 cg0624 h   Hypothetical membrane protein 2 -1.09 -1.09 - - - - - - 1.3 1.6 -0.4  
12 cg0625 h   putative terpenoide cylase 1 -1.28 -1.04 - 2.2 0.0 2.8 3.6 2.2 - -0.6 -0.4  
13 cg0723   crtE Geranylgeranyl-pyrophosphate sythase 0 0.66 -1.01 - - - - -0.2 - - - -  
14 cg0748    ABC-type Fe3+-siderophores transporter, periplasmic components 0 -1.07 -2.14 -0.3 1.3 - 1.2 0.7 - 0.1 -0.6 - DtxR
15 cg0756   cstA putative carbon starvation protein A 16 -0.83 -1.56 - - - 1.9 2.1 1.0 2.1 2.8 -0.6  
16 cg0767 m   Siderophore-interacting protein 0 -0.34 -2.99 0.5 -0.8 - - - - - - - DtxR, RamB*
17 cg0768 m   ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component 0 -0.17 -2.03 - - - 1.7 1.7 - - -0.6 - DtxR, RamB*
18 cg0924 n   ABC-type cobalamin/Fe3+-siderophores transporter, periplasmic component 0 -0.60 -2.91 4.8 5.2 2.7 3.6 4.1 0.7 5.1 4.5 3.4 DtxR
19 cg0927 n   ABC-type cobalamin/Fe3+-siderophores transporter, permease component 9 -0.10 -2.08 - - - 1.2 -0.2 0.0 3.0 3.3 - DtxR
20 cg0928 n   ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component 0 -0.14 -2.35 - -0.8 - 3.3 4.0 - 1.8 1.0 - DtxR
21 cg0952 o mctB putative monocarboxylate transporter subunit 2 -2.55 -1.32 - 0.5 - 2.4 4.7 4.1 - 2.1 -0.6 RamA, RamB
22 cg0953 o mctC monocarboxylate transporter 13 -2.44 -1.01 - 3.0 -0.2 1.9 4.7 4.7 3.2 4.5 3.2 RamA, RamB
23 cg1091    Hypothetical protein 0 0.95 -1.18 - - - - - - - - - SigM*
24 cg1167   metS putative methionine transporter subunit 0 -1.04 -1.43 - - - - - - -0.9 - -0.6  
25 cg1290   metE 5-methyltetrahydropteroyltri-glutamate-homocystein-emethyltransferase 0 0.65 -1.06 8.2 6.8 6.4 8.0 8.0 6.5 6.2 6.4 4.2 McbR*
26 cg1365 t atpH F0F1 ATP synthase delta subunit 0 -1.26 -1.03 1.9 2.3 1.3 3.9 4.8 4.7 3.2 4.1 3.4 SigH*
27 cg1367 t atpG F0F1 ATP synthase gamma subunit 0 -1.71 -1.11 1.1 4.2 3.4 3.3 4.9 4.7 4.0 4.0 2.5 SigH*
28 cg1451   serA Phosphoglycerate dehydrogenase 0 -0.22 -1.10 6.5 5.4 6.1 7.7 7.5 7.2 5.3 5.3 4.2  
29 cg1537   ptsM PTS system mannose-specific EIIBCA component 10 -0.39 -1.06 2.6 3.5 1.8 5.9 5.6 6.0 6.6 6.4 6.1 RamB*, GlxR*
30 cg1859    Putative secreted protein 0 0.04 -1.34 - 1.7 - - 3.6 1.5 0.1 5.0 -0.4  
31 cg1930 z   Putative secreted hydrolase 0 -1.18 -3.26 - - - - - - - - - DtxR
32 cg1931 z   Hypothetical protein 0 -0.88 -2.55 - - - - - - -0.7 -0.6 - DtxR
33 cg2283    Hypothetical protein 0 0.00 -1.51 4.2 4.3 3.4 - -0.2 - - - -  
34 cg2336    Putative secreted protein 0 -0.09 -1.31 - - - - 2.1 - 3.6 3.9 1.9  
35 cg2445   hmuO putative heme oxygenase 0 -0.93 -1.19 -0.2 2.5 - - -0.2 - - -0.6 - DtxR
36 cg2560 ad aceA Isocitrate lyase 0 -2.73 -2.19 - 4.9 2.4 - -0.3 - - - - RamA, RamB
37 cg2962    Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides 0 0.45 -1.18 -0.3 0.2 - - - - - - -  
38 cg3156   htaA secreted protein implicated in iron acquisition and transport 0 -2.50 -2.76 - - - - - -0.3 2.7 5.7 - DtxR
39 cg3254    Hypothetical membrane protein 3 0.07 -1.29 - - - - - - -0.5 - -  
  1. Genes for which an increased or decreased mRNA level was found at pH 9 in comparison to pH 7.5. The gene locus tag, organisation in operons, the gene name, the (proposed) function of the protein as well as the predicted number of transmembrane helices are given. The results of the transcriptome analysis are given as induction factor at pH 6 and pH 9 in comparison to pH 7.5. Results of the proteome analysis are indicated for the soluble, membrane and envelope fraction. Regulators of particular genes are given based on the CoryneRegNet data base.
  2. 1 The geneID according to the accession number BX927147 was used.
  3. 2 Genes known to form an operon and closely adjacent, equally oriented genes that likely form an operon were indicated by equal Latin letters.
  4. 3 Prediction of transmembrane helices were performed by using the TMHMM 2.0 sever at http://www.cbs.dtu.dk/services/TMHMM/.
  5. 4 The induction factors are given as log2 values of the ration of mRNA levels at pH 6 and pH 9 in comparison to pH 7.5, respectively.
  6. 5 The determined relative peptide numbers are given as log2 values in order to allow calculation of ratios by simple subtraction of values. Peptide numbers found to be significantly altered at pH 6 and pH 9 in comparison to pH 7.5 are shown in bold and peptide numbers found to be significantly altered at pH 6 in comparison to pH 9 are shown in italic (see M&M section for the details of calculation).
  7. 6 Data whether a particular gene was experimentally proven or predicted (*) to be regulated by a transcription factor was obtained by using the data base CoryneRegNet http://coryneregnet.cebitec.uni-bielefeld.de/v4/.