Genome concentration limits cell growth and modulates proteome composition in Escherichia coli

The RNA slopes are also compared with the average protein slopes.

The abbreviations kan, cat, and spec refer to gene cassette insertions conferring resistance to kanamycin, chloramphenicol, and spectinomycin, respectively. These insertions are flanked by Flp site-specific recombination sites (frt) that allow the removal of the insertion using Flp recombinase from plasmid pCP20 (Cherepanov and Wackernagel, 1995).

This table describes how kinetic constants were estimated from the literature. Parameters $X_{ini}$, $Y_{ini}$, $r_1{,r}_2$ were used in ordinary differential equation (ODE) simulations. We assumed exponential growth and used the relation $M_{ini}=M/\left(2log2\right)$, where $M_{ini}$ is the biomass of a newborn cell and $M$ is the average cellular biomass in the population (Koch and Schaechter, 1962). The bulk transcription rate $r_1$ was defined as $r_1=\frac{mRNAsynthesisrate}{ofproteins\in thecell}$ , and the bulk translation rate $r_2$ was defined as $r_2=\frac{proteinsynthesisrate}{ofproteins\in thecell}$ . Values were estimated from a previous study (Bremer and Dennis, 2008). For our estimations, we assumed that the average protein length is 310 amino acids and that the average mRNA length is about 1 kb (Ishihama et al., 2008).

The active fraction of RNA polymerases (RNAPs) and ribosomes, ${\alpha }_{RNAP}$ and ${\alpha }_{ribo}$, are given by the formulae ${\alpha }_{RNAP}=\frac{\left[Z\right]}{K_1+\left[Z\right]}$ and ${\alpha }_{ribo}=\frac{\left[X\right]}{K_2+\left[X\right]}$, where [$Z$] and [$X$] are the DNA concentration and the mRNA concentration in the cells, respectively.

To infer the parameters $K_1$, $K_2$, we used the values of ${\alpha }_{RNAP}$, ${\alpha }_{ribo}$, [$Z$], and $\left[X\right]$ of wild-type cells determined in our study and back-calculated the values of $K_1$, $K_2$.

The mRNA degradation data were obtained from an experimental study (Balakrishnan et al., 2022).