Table 1.
Candidate promoters with different strengths selected based on omics datasets
| Gene ID | Gene name | Operon | Gene function | Array | RNA-Seq | Proteomics | EGFP/opmCherry (log phase) | EGFP/opmCherry (sta phase) |
|---|---|---|---|---|---|---|---|---|
| Candidate promoters with strong strength | ||||||||
| ZMO0177 | gap | Glyceraldehyde-3-phosphate dehydrogenase, type I | 15.06 | 11.2 | 9.23 | 0.38 ± 0.0202 | 0.47 ± 0.0191 | |
| ZMO1360 | pdc | Thiamine pyrophosphate protein TPP binding domain-containing protein | 14.52 | 11.78 | 8.59 | 0.24 ± 0.0220 | 0.22 ± 0.0086 | |
| ZMO0516 | Tuf | ND | Elongation factor Tu | 15.33 | 11.58 | 8.08 | 0.24 ± 0.0162 | 0.30 ± 0.0148 |
| ZMO1608 | eno | Phosphopyruvate hydratase | 15.22 | 13.2 | 8.97 | 0.23 ± 0.0145 | 0.34 ± 0.0093 | |
| ZMO0997 | eda | Yes | 2-Dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase | 14.97 | 14.6 | 8.46 | 0.18 ± 0.0178 | 0.15 ± 0.0167 |
| ZMO0367 | zwf | Glucose-6-phosphate 1-dehydrogenase | 14.92 | 11.19 | 7.38 | 0.16 ± 0.0057 | 0.14 ± 0.0124 | |
| ZMO1719 | frk | ROK family protein | 15.06 | 12.2 | 6.85 | 0.12 ± 0.0038 | 0.17 ± 0.0098 | |
| ZMO1609 | Hypothetical protein | 15.26 | 12.77 | 5.78 | 0.12 ± 0.0061 | 0.14 ± 0.0038 | ||
| ZMO0689 | gfo | Oxidoreductase domain-containing protein | 14.49 | 11.68 | 6.38 | 0.10 ± 0.0075 | 0.13 ± 0.0130 | |
| ZMO1721 | gloA3 | ND | Glyoxalase/bleomycin resistance protein/dioxygenase | 14.35 | 12.66 | 5.97 | 0.09 ± 0.0044 | 0.11 ± 0.0022 |
| ZMO0514 | rpsG | Yes | 30S ribosomal protein S7 | 15.31 | 10.79 | 5.54 | 0.07 ± 0.0062 | 0.07 ± 0.0015 |
| ZMO0515 | Yes | Elongation factor G | 15.07 | 11.14 | 5.83 | 0.07 ± 0.0062 | 0.07 ± 0.0015 | |
| ZMO1596 | adhB | Iron-containing alcohol dehydrogenase | 15.32 | 10.98 | 7.07 | 0.07 ± 0.0084 | 0.07 ± 0.0030 | |
| ZMO1141 | ilvC | Yes | Ketol-acid reductoisomerase | 15.41 | 12.39 | 6.76 | 0.05 ± 0.0012 | 0.04 ± 0.0006 |
| ZMO0241 | atpD | Yes | F0F1 ATP synthase subunit beta | 15.09 | 11.73 | 7.77 | 0.05 ± 0.0030 | 0.04 ± 0.0029 |
| ZMO0244 | Histone family protein DNA-binding protein | 14.79 | 12.98 | 6.1 | 0.04 ± 0.0013 | 0.04 ± 0.0007 | ||
| Po1721 | 0.04 ± 0.0020 | 0.03 ± 0.0007 | ||||||
| ZMO0493 | glnA | Yes | Glutamine synthetase, type I | 14.53 | 10.02 | 6.17 | 0.03 ± 0.0023 | 0.03 ± 0.0005 |
| ZMO1779 | Yes | Antibiotic biosynthesis monooxygenase | 15.08 | 11.24 | 7.52 | 0.02 ± 0.0005 | 0.02 ± 0.0008 | |
| Candidate promoters with medium strength | ||||||||
| ZMO1351 | clcD1 | Yes | Carboxymethylenebutenolidase | 12.93 | 6.81 | 3.14 | 0.14 ± 0.0064 | 0.16 ± 0.0036 |
| ZMO0056 | glmS | Glucosamine–fructose-6-phosphate aminotransferase | 12.93 | 6.91 | 2.45 | 0.12 ± 0.0021 | 0.11 ± 0.0024 | |
| ZMO0559 | Hypothetical protein | 12.68 | 6.75 | 3.1 | 0.11 ± 0.0064 | 0.08 ± 0.0039 | ||
| ZMO1385 | Toxic anion resistance family protein | 12.83 | 6.93 | 2.55 | 0.06 ± 0.0012 | 0.05 ± 0.0018 | ||
| ZMO0127 | Yes | S1/P1 nuclease | 12.84 | 7.11 | 3.13 | 0.05 ± 0.0015 | 0.05 ± 0.0014 | |
| ZMO1100 | Yes | Nucleotidyl transferase | 12.58 | 7.18 | 2.82 | 0.05 ± 0.0012 | 0.05 ± 0.0023 | |
| ZMO1392 | Hypothetical protein | 12.46 | 7.43 | 2.45 | 0.04 ± 0.0012 | 0.04 ± 0.0012 | ||
| ZMO0326 | 7-cyano-7-deazaguanine reductase | 12.65 | 7.41 | 2.7 | 0.03 ± 0.0018 | 0.04 ± 0.0012 | ||
| ZMO0570 | prmA | Ribosomal L11 methyltransferase | 12.38 | 7.32 | 2.45 | 0.03 ± 0.0030 | 0.04 ± 0.0013 | |
| Candidate promoters with weak strength | ||||||||
| ZMO1231 | recJ | Single-stranded-DNA-specific exonuclease RecJ | 11.03 | 5.7 | 0.07 | 0.08 ± 0.0023 | 0.07 ± 0.0029 | |
| ZMO1980 | gidB | Yes | Methyltransferase GidB | 10.59 | 5.27 | 0.07 | 0.05 ± 0.0025 | 0.05 ± 0.0029 |
| ZMO1484 | UvrD/REP helicase | 10.93 | 5.4 | 0.07 | 0.05 ± 0.0013 | 0.05 ± 0.0026 | ||
| ZMO0145 | Yes | Peptidase M28 | 11.37 | 4.98 | 0.07 | 0.04 ± 0.0018 | 0.04 ± 0.0006 | |
| ZMO0101 | NAD-dependent epimerase/dehydratase | 10.61 | 5.05 | 0.07 | 0.04 ± 0.0013 | 0.04 ± 0.0014 | ||
| ZMO1194 | dprA | Yes | DNA protecting protein DprA | 10.7 | 4.77 | 0.07 | 0.04 ± 0.0011 | 0.03 ± 0.0006 |
| ZMO1644 | DEAD/DEAH box helicase domain-containing protein | 10.61 | 4.98 | 0.07 | 0.03 ± 0.0013 | 0.03 ± 0.0007 | ||
| ZMO1582 | Uracil-DNA glycosylase superfamily protein | 10.33 | 4.63 | 0.07 | 0.03 ± 0.0004 | 0.03 ± 0.0003 | ||
| ZMO0005 | cysD | Yes | Sulfate adenylyltransferase subunit 2 | 11.5 | 5.28 | 0.07 | 0.03 ± 0.0012 | 0.03 ± 0.0009 |
| ZMO0300 | xseA | Exodeoxyribonuclease VII large subunit | 11.6 | 4.71 | 0.07 | 0.03 ± 0.0010 | 0.03 ± 0.0013 | |
The operon information is predicted by DOOR2 prediction server. The values of array, RNA-Seq and proteomics of each gene are the average log2-transformed values under different growth conditions
ND non-determined, Log phase exponential phase, Sta phase stationary phase