Endy:Computational modeling of demand/Parameterization

Cytoplasmic nucleotide levels

It is hard to measure the cytoplasmic levels of free NTPs. Several groups have tried to make these measurements when studying the growth rate dependence of rRNA synthesis [1, 2]. Both of these groups calculated nucleotide levels per unit absorbance. Liang et al.[3] used this data to estimate that cytoplasmic ATP levels are in the range of 10mM. That corresponds to ~1e7 of each nucleotide per cell. For the moment, I'm going to use this value in my model.

References

1. Petersen C and Møller LB. Invariance of the nucleoside triphosphate pools of Escherichia coli with growth rate. J Biol Chem. 2000 Feb 11;275(6):3931-5. DOI:10.1074/jbc.275.6.3931 |
2. Gaal T, Bartlett MS, Ross W, Turnbough CL Jr, and Gourse RL. Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. Science. 1997 Dec 19;278(5346):2092-7. DOI:10.1126/science.278.5346.2092 |
3. Liang S, Bipatnath M, Xu Y, Chen S, Dennis P, Ehrenberg M, and Bremer H. Activities of constitutive promoters in Escherichia coli. J Mol Biol. 1999 Sep 10;292(1):19-37. DOI:10.1006/jmbi.1999.3056 |