Table 1.
Fold change of genes which were detected as upregulated during cultivation with (A) gluconate plus TDP in comparison to gluconate, (B) gluconate plus DTDP in comparison to gluconate, (C) gluconate plus TDP in comparison to gluconate plus DTDP, and (D) gluconate plus DTDP in comparison to gluconate plus TDP
| ID | Gene name | Annotation | Fold change | |||
|---|---|---|---|---|---|---|
| 24 h | 48 h | 72 h | 96 h | |||
| A | ||||||
| Genes putatively involved in the uptake of TDP | ||||||
| H16_A3658 | ABC-type transporter, permease component | 6.28 | 3.66 | 3.64 | 3.60 | |
| H16_A3659 | ABC-type transporter, permease component | 6.90 | 3.34 | 6.58 | 3.44 | |
| H16_A3660 | ABC-type transporter, permease component | 6.90 | 4.48 | 7.86 | 9.37 | |
| Genes putatively involved in the catabolism of TDP | ||||||
| H16_B0782 | Acetyltransferase (GNAT) family | 8.16 | 80.25 | 30.38 | 34.75 | |
| H16_A0217 | Hypothetical membrane-associated protein | 3.16 | 3.11 | 40.29 | 30.94 | |
| H16_A1954 | Predicted acyltransferase | 4.09 | 2.04 | 2.61 | x | |
| H16_A2171 | phaB3 | Acetoacetyl-CoA reductase | 4.68 | 2.20 | 3.97 | x |
| H16_B1292 | phnT | Acetyltransferase (GNAT) family | 6.36 | 2.74 | 3.46 | x |
| H16_B2322 | frnE | Predicted dithiol-disulfide isomerase | 2.99 | 6.25 | 5.80 | 5.26 |
| Genes putatively involved in detoxification | ||||||
| H16_A0306 | bcp | Peroxiredoxin | 3.53 | 2.99 | 3.11 | 2.70 |
| H16_A1090 | Glutathione S-transferase | 2.89 | 6.15 | 3.82 | 3.77 | |
| H16_B0571 | Glutathione S-transferase | 2.78 | 5.00 | 3.56 | 2.94 | |
| B | ||||||
| Genes putatively involved in the uptake of DTDP | ||||||
| H16_A2779 | Probable extracytoplasmic solute receptor | 3.35 | 3.96 | 2.12 | x | |
| H16_A0337 | Probable extracytoplasmic solute receptor | 2.62 | 3.06 | 4.44 | x | |
| Genes putatively involved in the catabolism of DTDP | ||||||
| H16_A0180 | bioA | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 17.16 | 47.67 | 8.12 | 5.55 |
| H16_A0181 | bioF | 8-amino-7-oxononanoate synthase | 5.98 | 8.22 | 2.60 | 3.57 |
| H16_A0182 | bioD | Dethiobiotin synthetase | 5.16 | 6.49 | 4.68 | 2.15 |
| H16_A0183 | bioB | Biotin synthase | 8.02 | 5.86 | 6.73 | 3.39 |
| H16_A0333 | Rhodanese-related sulfurtransferase | 3.59 | 6.58 | 7.55 | 7.00 | |
| H16_A0161 | dsbA | Thiol:disulfide interchange protein | 3.78 | 3.34 | 4.53 | 3.25 |
| H16_A3455 | dsbD | Thiol:disulfide interchange protein | 8.19 | 5.70 | 8.79 | x |
| H16_B2322 | frnE | Predicted dithiol-disulfide isomerase | 6.58 | 14.50 | 10.00 | 6.60 |
| H16_A0179 | Enoyl-CoA hydratase/carnithine racemase | 3.25 | 4.35 | 5.07 | 2.98 | |
| H16_A0217 | Hypothetical membrane-associated protein | 5.77 | 13.37 | 46.08 | 21.53 | |
| H16_A0244 | ahcY | Adenosylhomocysteinase | 5.55 | 10.25 | 10.90 | 13.39 |
| H16_A1070 | Acyl dehydratase | 4.44 | 4.70 | 2.79 | 2.59 | |
| H16_B0782 | Acetyltransferase, GNAT-family | 38.41 | 428.83 | 27.49 | 25.35 | |
| H16_B1784 | Signal transduction histidine kinase | 4.17 | 8.26 | 3.62 | 2.67 | |
| H16_B1785 | Response regulator, OmpR-family | 4.00 | 4.15 | 3.73 | 3.88 | |
| Genes putatively involved in detoxification | ||||||
| H16_A0705 | groES | Co-chaperonin (HSP10) | 23.51 | 9.41 | 3.03 | x |
| H16_A0706 | groEL | Chaperoning (HSP60 family) | 15.68 | 2.94 | 2.49 | x |
| H16_A1137 | grpE | Molecular chaperone | 6.84 | 9.17 | 6.51 | 5.46 |
| H16_A3089 | dnaK | Molecular chaperone (HSP70) | 4.26 | 4.34 | 8.64 | 5.66 |
| H16_B0451 | Glutathione S-transferase | 4.77 | 3.68 | 2.44 | x | |
| H16_A1090 | Glutathione S-transferase | 7.50 | 6.88 | 3.97 | 3.87 | |
| H16_A0306 | bcp | Peroxiredoxin | 3.45 | 5.02 | 3.60 | 4.47 |
| C | ||||||
| Genes putatively involved in the uptake of TDP | ||||||
| H16_A0357 | ABC-type transporter, ATPase component: NitT family | 79.34 | 13.73 | 17.89 | x | |
| H16_A0358 | ABC-type transporter, permease component: NitT family | 129.50 | 15.34 | 11.60 | x | |
| H16_A0359 | ABC-type transporter, periplasmic component: NitT family | 107.15 | 45.76 | 6.24 | x | |
| Genes putatively involved in the catabolism of TDP | ||||||
| H16_B1102 | Acetyl-CoA synthetase | 17.01 | 19.93 | 3.29 | 2.31 | |
| H16_A0234 | aidB | Acyl-CoA dehydrogenase, short-chain specific | 2.78 | 2.65 | 3.35 | x |
| H16_A0280 | sbml | Methylmalonyl-Coa mutase | 9.72 | 6.11 | 4.05 | x |
| H16_A1949 | sbm2 | Methylmalonyl-Coa mutase | 248.35 | 2.87 | 7.00 | x |
| H16_A2251 | phaY1 | d-(−)-3-hydroxybutyrate oligomer hydrolase | 3.07 | 3.79 | 9.93 | x |
| H16_B1192 | Acyl-CoA dehydrogenase | 25.89 | 77.24 | 2.92 | x | |
| D | ||||||
| Genes putatively involved in the uptake of DTDP | ||||||
| H16_A2779 | Probable extracytoplasmic solute receptor | 5.46 | 4.13 | 2.63 | x | |
| H16_A3718 | Probable extracytoplasmic solute receptor | 5.37 | 2.01 | 2.29 | x | |
| Genes putatively involved in the catabolism of DTDP | ||||||
| H16_A0333 | Rhodanese-related sulfurtransferase | 2.74 | 3.92 | 5.22 | 3.72 | |
| H16_A0161 | dsbA | Thiol:disulfide interchange protein | 3.51 | 3.88 | 2.70 | x |
| Genes putatively involved in detoxification | ||||||
| H16_A0705 | groES | Co-chaperonin (HSP10) | 54.77 | 8.00 | 2.85 | x |
| H16_A0706 | groEL | Chaperonin (HSP60 family) | 21.04 | 2.99 | 2.11 | x |
| H16_A1137 | grpE | Molecular chaperone | 9.46 | 9.24 | 7.60 | 2.79 |
| H16_A3089 | dnaK | Molecular chaperone (HSP70) | 7.40 | 4.03 | 6.14 | 6.34 |
| H16_A0183 | bioB | Biotin synthase | 7.45 | 3.32 | 4.70 | 2.59 |
x data were excluded from further analyses due to the adjusted software filter as outlined in the “Material and methods” section