TABLE 2.
Genes codifferentially regulated upon antibiotic treatmenta
| Gene | Gene ID | Fold change |
Product name | Annotated function | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TET | MMC | IPM | CAZ | KAN | CIP | PME | ERY | CHL | ||||
| Upregulation | ||||||||||||
| b0721 | sdhC | 20.99 | 6.54 | 10.11 | 8.95 | 6.15 | 5.89 | 4.18 | 9.81 | 6.89 | Succinate dehydrogenase | Respiration |
| b1530 | marR | 2.99 | 4.65 | 9.36 | 6.98 | 43.75 | 125.87 | 5.23 | 6.12 | 3.16 | DNA-binding transcriptional repressor | Antibiotic resistance |
| b1558 | cspF | 26.55 | 10.75 | 6.23 | 9.30 | 5.45 | 13.73 | 5.09 | 8.45 | 5.03 | Cold shock-like protein | Cold stress response |
| b1915 | yecF | 3.38 | 4.55 | 2.54 | 4.29 | 3.26 | 4.34 | 2.94 | 2.32 | 4.52 | DUF2594 domain-containing protein | Unknown |
| b2533 | suhB | 2.48 | 9.52 | 6.48 | 7.37 | 4.78 | 8.04 | 2.45 | 3.16 | 1.92 | Nus factor | rRNA maturation |
| b2667 | ygaV | 8.57 | 7.34 | 32.22 | 26.21 | 51.66 | 20.28 | 16.32 | 41.66 | 11.80 | Putative DNA-binding transcriptional regulator | Transcription regulation |
| b2668 | ygaP | 8.89 | 9.77 | 36.46 | 31.32 | 25.78 | 13.63 | 12.52 | 12.49 | 7.68 | Thiosulfate sulfurtransferase | Sulfur metabolism |
| b3704 | rnpA | 3.45 | 4.39 | 4.35 | 2.95 | 4.18 | 7.43 | 2.74 | 9.75 | 7.82 | RNase P protein component | tRNA processing |
| Downregulation | ||||||||||||
| b0019 | nhaA | 4.05 | 1.87 | 2.06 | 1.78 | 2.45 | 3.23 | 2.36 | 4.66 | 5.32 | Na+:H+ antiporter | Sodium ion homeostasis |
| b0207 | dkgB | 3.07 | 2.27 | 3.38 | 3.92 | 2.20 | 2.08 | 3.95 | 6.92 | 3.02 | Methylglyoxal reductase | Detoxification |
| b0486 | ybaT | 175.04 | 15.06 | 4.98 | 15.49 | 49.96 | 21.34 | 2.77 | 2.49 | 4.34 | Putative copper transporter | Copper resistance response |
| b0605 | ahpC | 8.14 | 4.61 | 2.67 | 4.24 | 15.62 | 5.01 | 3.69 | 7.07 | 5.19 | Peroxidase component of alkyl hydroperoxide reductase | Oxidative stress response |
| b0606 | ahpF | 2.44 | 4.51 | 2.81 | 4.41 | 4.60 | 3.53 | 3.11 | 3.05 | 4.05 | Peroxiredoxin reductase component of alkyl hydroperoxide reductase | Oxidative stress response |
| b0828 | iaaA | 3.39 | 6.49 | 4.05 | 4.13 | 4.11 | 4.29 | 2.89 | 3.26 | 2.33 | Isoaspartyl dipeptidase proenzyme | Amino acid biosynthesis |
| b0953 | rmf | 35.74 | 5.48 | 3.41 | 4.10 | 35.20 | 44.40 | 5.92 | 17.44 | 6.48 | Ribosome modulation factor | Ribosome protection |
| b1287 | yciW | 8.76 | 7.19 | 12.28 | 9.72 | 6.18 | 8.94 | 17.57 | 17.79 | 10.55 | Putative peroxidase | Cysteine tolerance |
| b1729 | tcyP | 2.05 | 4.28 | 7.81 | 3.79 | 1.99 | 3.79 | 9.41 | 2.42 | 3.03 | Cystine/sulfocysteine:cation symporter | Sulfur metabolism |
| b2013 | tsuA | 4.97 | 10.21 | 49.13 | 8.45 | 11.81 | 7.87 | 51.64 | 5.63 | 4.76 | Thiosulfate transporter | Sulfur metabolism |
| b2135 | yohC | 9.91 | 5.04 | 4.95 | 5.19 | 37.95 | 15.41 | 2.01 | 4.93 | 8.82 | Putative inner membrane protein | Unknown |
| b2241 | glpA | 10.13 | 10.14 | 28.37 | 22.93 | 4.99 | 4.83 | 35.01 | 4.24 | 23.38 | Anaerobic glycerol-3-phosphate dehydrogenase subunit A | Respiration |
| b2414 | cysK | 2.72 | 8.25 | 12.56 | 6.50 | 20.56 | 10.22 | 9.73 | 6.19 | 4.77 | Cysteine synthase A | Sulfur metabolism |
| b2421 | cysM | 2.57 | 4.57 | 4.37 | 4.20 | 3.91 | 4.26 | 5.51 | 3.81 | 3.82 | Cysteine synthase B | Sulfur metabolism |
| b2422 | cysA | 13.77 | 27.91 | 34.32 | 15.51 | 16.44 | 39.86 | 67.64 | 23.07 | 7.29 | Sulfate/thiosulfate ABC transporter ATP binding subunit | Sulfur metabolism |
| b2423 | cysW | 17.90 | 27.37 | 22.88 | 13.64 | 12.07 | 40.12 | 85.87 | 23.99 | 10.81 | Sulfate/thiosulfate ABC transporter inner membrane subunit CysW | Sulfur metabolism |
| b2424 | cysU | 18.47 | 21.31 | 20.92 | 13.64 | 13.79 | 46.49 | 72.58 | 23.26 | 12.74 | Sulfate/thiosulfate ABC transporter inner membrane subunit CysU | Sulfur metabolism |
| b2425 | cysP | 21.85 | 29.53 | 29.08 | 16.11 | 25.79 | 44.15 | 71.89 | 30.03 | 16.93 | Thiosulfate/sulfate ABC transporter periplasmic binding protein CysP | Sulfur metabolism |
| b2750 | cysC | 6.62 | 12.11 | 20.88 | 11.62 | 5.31 | 14.38 | 13.37 | 18.23 | 6.20 | Adenylyl-sulfate kinase | Sulfur metabolism |
| b2751 | cysN | 9.37 | 13.65 | 10.53 | 12.43 | 5.65 | 13.61 | 11.04 | 8.13 | 5.13 | Sulfate adenylyltransferase subunit 1 | Sulfur metabolism |
| b2752 | cysD | 11.02 | 20.49 | 39.05 | 17.08 | 10.65 | 21.38 | 41.75 | 24.31 | 16.82 | Sulfate adenylyltransferase subunit 2 | Sulfur metabolism |
| b2762 | cysH | 11.52 | 11.45 | 23.94 | 6.03 | 36.37 | 37.69 | 36.47 | 19.21 | 10.43 | Phosphoadenosine phosphosulfate reductase | Sulfur metabolism |
| b2763 | cysI | 13.60 | 16.99 | 23.33 | 9.71 | 30.77 | 50.28 | 79.25 | 29.45 | 9.34 | Sulfite reductase, hemoprotein subunit | Sulfur metabolism |
| b2764 | cysJ | 14.06 | 15.34 | 16.53 | 9.79 | 76.36 | 40.98 | 74.41 | 26.08 | 10.07 | Sulfite reductase, flavoprotein subunit complex | Sulfur metabolism |
| b3491 | yhiM | 242.66 | 18.38 | 18.48 | 64.46 | 67.48 | 33.71 | 3.04 | 9.90 | 38.44 | Inner membrane protein | Acid stress response |
| b3990 | thiH | 10.10 | 8.77 | 4.85 | 4.22 | 12.70 | 1.93 | 3.10 | 9.28 | 11.33 | 2-Iminoacetate synthase | Sulfur metabolism |
| b3991 | thiG | 10.16 | 8.62 | 4.87 | 4.37 | 8.92 | 1.92 | 2.99 | 6.17 | 8.21 | 1-Deoxy-d-xylulose 5-phosphate:thiol sulfurtransferase | Sulfur metabolism |
| b3992 | thiF | 9.47 | 6.95 | 5.12 | 4.32 | 8.25 | 1.63 | 3.07 | 11.80 | 11.96 | Sulfur carrier protein, ThiS adenylyltransferase | Sulfur metabolism |
| b4452 | gadY | 5.50 | 3.22 | 4.14 | 6.97 | 7.14 | 2.14 | 3.55 | 4.25 | 14.11 | Small regulatory RNA | Acid stress response |
| b4704 | arrS | 264.70 | 10.50 | 9.46 | 14.81 | 438.25 | 18.50 | 2.73 | 5.55 | 27.53 | Small regulatory RNA | Acid stress response |
a
Upregulated fold change indicates the FPKMs of the antibiotic-treated group in relation to the control group. Downregulation fold change indicates the FPKMs of the control group in relation to the antibiotic-treated group. ID, identifier.