Table 1. Model parameters: definitions and estimated values.

Parameter	Meaning	Value	Reference
βR	Basal transcription rate of xylR-mRNA	240 molecules per houra	(Vogel and Jensen, 1994) (and adjusted)
		80 molecules per hourb	(Proshkin et al., 2010)
fR, fR3	Fold changes for negative autoregulation by XylR	3	(Fraile et al., 2001)
fIHF	Fold change for Pr repression by IHF	5	(Silva-Rocha and de Lorenzo, 2011)
θR,θR3	Thresholds for negative autoregulation by XylR	15 molecules	Adjusted to levels of XylR in (Fraile et al., 2001)
θIHF	Threshold for Pr repression by IHF	4000 molecules	Adjusted to levels of IHF in (Valls et al., 2002)
μ	Crc-xylR mRNA association	1 per molecule per hour	(Levine et al., 2007).
mxyl/θm	m-Xylene above threshold after induction	10	Saturating conditions
fm	Fold change in Ra due to m-xylene activation	0.018	Adjusted
kR	Basal Ra formation in non-inducing conditions	10−5 per molecule2 per hour	Adjusted to give negligible Ra
KRoff	Ra dissociation	10 per hour	Adjusted
θu	Threshold for IHF activation of Pu promoter	4000 molecules	Adjusted to levels of IHF in (Valls et al., 2002)
fu	Fold change in Pu activity by IHF	0.1	(Valls et al., 2002)
ku	Basal Pu activation in the absence of IHF	0.08 per molecule per hour	Adjusted from induction time of GFP distributions
Kuoff	Dissociation of Ra from Pu promoter	0.5 per hour	Adjusted
βu	Transcription rate from the active Pu promoter	200 molecules per houra	(Vogel and Jensen, 1994) and adjusted
		60 molecules per hourb	(Proshkin et al., 2010)
ρR	Ri translation rate	20 per houra	(Proshkin et al., 2010) and adjusted
		7 per hourb
ρu	Pu-GFP translation rate	20 per houra	(Proshkin et al., 2010)
		7 per hourb
δmR,δmu	xylR/Pu-GFP mRNAs degradation rates	10 per houra	(Bernstein et al., 2002)
		5 per hourb
δR,δGFP	Ri, Pu-GFP degradation rates	1 per houra	Stable proteins
		0.5 per hourb
IHF	IHF levels	2000 moleculesa	(Valls et al., 2002)
		14 000 moleculesb
Crc	Crc levels	200 moleculesa	(Ruiz-Manzano et al., 2005) and adjusted
		50 moleculesb
γR	Basal transcription from lacI-Ptrc promoter	2400 molecules per hour	(de Lorenzo et al., 1993; Silva-Rocha and de Lorenzo, 2011)
a	Ratio of total LacI and lacI repression threshold	10	Arbitrary value >>1 (Ozbudak et al., 2004)
fL	Fold change in lacI-Ptrc-xylR expression due to LacI repression	3.8	Adjusted (see Materials and methods)
θIPTG	Threshold for LacI inactivation by IPTG	22.6	Adjusted (see Materials and methods)

^aExponential phase.

^bStationary phase. Except stated otherwise, the parameters were taken/adjusted in exponential phase conditions and the same values used in stationary phase.