Table 2. CGGR variables, parameters and constants.

Genetic Parameters		units
	Maximum transcription initiation rate of the i-th gene class	1/min
	Maximum translation initiation rate of the i-th gene class mRNA	1/min
Km,i	Binding affinity of RNAp holoenzyme to the i-th gene class promoter	1/(µm)3
Lm,i	Binding affinity of the 30S ribosome subunit to the i-th gene class mRNA RBS	1/(µm)3
tc,i	Average time to transcribe the i-th gene class ( = Li/ci)	min
tl,i	Average time to translate the mRNA of the i-th gene class ( = Li/3cp)	min
mi,j	Map location of the j-th gene in the i-th gene class	dimensionless
	Functional half-life for the i-th gene class mRNA in the absence of ribosomes	min
Vini	Initiation volume	(µm)3
Cell state variables
nRNAp	Concentration of total RNAp	1/(µm)3
nRNAp,free	Concentration of free functional RNAp	1/(µm)3
nribo	Concentration of total ribosomes	1/(µm)3
nribo,free	Concentration of free functional (30S) ribosomes	1/(µm)3
nbulk	Concentration of bulk protein	1/(µm)3
α	Specific growth rate (α = μ·ln(2), where μ is the doubling rate)	1/min
Parameters and constants for the unconstrained CGGR
cribo/load	Production cost of one ribosome or load protein	dimensionless
n0	Minimum cell density	1/(µm)3
Parameters and constants for the constrained CGGR
Mbulk	Bulk protein cutoff	1/(µm)3
	Maximal elongation rate	aa/min
h	Hill coefficient	dimensionless
Other parameters, variables and constants
cp	Peptide chain elongation rate	aa/min
ci	RNA chain elongation rate of the i-th gene class	bp/min
C	C period	min
di	Gene concentration of the i-th gene class	1/(µm)3
Li	Length of the i-th gene class	base pairs
vk	Volume of a macromolecule belonging to the k-th species	(µm)3
Φ	Macromolecule volume fraction = Vmacro/Vcell	dimensionless

Genetic parameters, cell state variables, and other variables and constants associated with the CGGR models. Gene classes labeled by index i include: rrn, r-protein, bulk protein and any load genes.