Table 1. Definitions and starting values for the 10 variables in ODE model A (Fig 1A).
For variables measured as a concentration, the volume within which this is calculated is given in the “region” column. wtCell and cytVol starting values equate to 2,175 cells (assuming 2357528 GC bp in the E. coli genome (strain MG1655, EBI Accession U00096.3)) and cell volume of 1.03 × 10-12 ml [83]).
| Variable | Definition | Starting value | Units | Region |
|---|---|---|---|---|
| eGlc | External glucose | 3.1 × 10-4 to 6.2 × 10-3 (log spaced) | M | 1 ml culture |
| iGlc | Internal glucose | 0 | M | Cytoplasm |
| dGTP | Deoxyguanosine triphosphate | 0 | M | Cytoplasm |
| DNA | Guanine nucleotides in the newly synthesised strand | 0 | M | Cytoplasm |
| wtCell | Guanine nucleotides in the template strand | 8.5 × 10-12 | M | 1 ml culture |
| ROS | Reactive oxygen species (H2O2) | 0 | M | Cytoplasm |
| odGTP | 8-oxo-2′-deoxyguanosine triphosphate | 0 | M | Cytoplasm |
| mDNA | odGTP nucleotides in the newly synthesised DNA strand | 0 | M | Cytoplasm |
| mCell | odGTP nucleotides in the template DNA strand | 0 | M | 1 ml culture |
| cytVol | Total cytoplasmic volume | 2.25 × 10-9 | ml | NA |
ODE, ordinary differential equation; ROS reactive oxygen species.