Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration

Table 1 Parameters and data in simulations

Parameter/Data	Symbol	Distribution	Value(mode)	cv	Unit
RK2 abundance	D ₀	lognormal	4.5	0.5	nM
KorA abundance	A_tot	lognormal	1600 [18]	0. 5	nM
KorB abundance	B_tot	lognormal	400 [28]	0. 5	nM
KorB abundance (mutant)	BM_tot	lognormal	920	0. 5	nM
Scaling parameter for KorA synthesis	π _X	uniform	[0,1]	-	-
Scaling parameter for KorB synthesis	π _Y	uniform	[0,1]	-	-
KorA synthesis	k _A	-	-	-	s^-1
KorB synthesis	k _B	-	-	-	s^-1
KorA affinity to DNA	k ₁	lognormal	12.9 [18]	0. 5	nM
KorB affinity to DNA	k ₂	lognormal	9.3 [22]	0. 5	nM
KorA affinity to KorB-DNA	k ₃	lognormal	3.1	0. 5	nM
KorB affinity to KorA-DNA	k ₄	lognormal	3.1 [22]	0. 5	nM
KorA monomerization	σ _A	-	-	-	s^-1
KorB monomerization	σ _B	-	-	-	s^-1
KorA dimerization	λ _A	lognormal	0.001	0.05	nM^-1s^-1
KorB dimerization	λ _B	lognormal	0.001	0.05	nM^-1s^-1
Protein degradation	γ _P	lognormal	0.0003875	0.05	s^-1

cv - coefficient of variation; RK2 abundance (D₀) and protein degradation (γ_P) are calculated for bacteria with the population doubling time of 43 minutes; KorB abundance for plasmid mutant (BM_tot) is unpublished data from C. Thomas et al.; affinity of KorA to the KorB-DNA complex (k₃) were assumed to be three fold higher as it is in the case of affinity of KorB to the KorA-DNA complex (k₄); dimerization rates were defined by diffusion properties.

ISSN: 1752-0509