Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes

Sotiropoulos, Vassilios; Kaznessis, Yiannis N

doi:10.1186/1752-0509-1-7

BMC Systems Biology

Table 1 A Chemical kinetics representation of Network III

From: Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes

#	Reaction	k	Ref.	#	Reaction	k	Ref.
1	TcEx --> Tc	3.3E-4	[31]	48	TetOFF2 + OP2 --> TetOFF2:OP2	2.86E+06	[34]
2	2 TetR --> TetR2	1.00E+09	[32]	49	TetOFF2:OP2 --> TetOFF2 + OP2	5.11E-04	[34]
3	TetR2 --> 2 TetR	10	[32]	50	TetR2 + OP2 --> TetR2:OP2	2.86E+06	[34]
4	2 TetOFF --> TetOFF2	1.00E+09	[32]	51	TetR2:OP2 --> TetR2 + OP2	5.11E-04	[34]
5	TetOFF2 --> 2 TetOFF	10	[32]	52	TetOFF2:OP2 + Tc --> Tc:2TetOFF:OP2	2.0E+6	[4]
6	Tc + TetR2 -->Tc:2TetR	2.00E+06	[4]	53	Tc:2TetOFF:OP1 + Tc --> Tc:TetOFF2:OP2	1.0E+15	§
7	Tc + Tc:2TetR --> Tc:TetR2	1.0E+15	§	54	Tc:TetOFF2:OP2 --> Tc:TetOFF2 + OP2	5.8E-3	[35]
8	Tc:TetR2 --> TetR2 + 2Tc	0.001	[4]	55	TetR2:OP2 + Tc --> Tc:2TetR:OP2	2.0E+6	[4]
9	Tc + TetOFF2 --> Tc:2TetOFF	2.00E+06	[4]	56	Tc:2TetR:OP2 + Tc --> Tc:TetR2:OP2	1.0E+15	§
10	Tc + Tc:2TetOFF --> Tc:TetOFF2	1.0E+15	§	57	Tc:TetR2:OP2 --> Tc:TetR2 + OP2	5.8E-3	[35]
11	Tc:TetOFF2 --> TetOFF2 + 2Tc	0.001	[4]	58	RNAp + P2 + OP2 --> RNAp:P2:OP2	8.60E+6	[38]
12	TetOFF -->	0.0012	*	59	RNAp:P2:OP2 --> RNAp + P2 + OP2	0.01	[38]
13	TetOFF2 -->	0.0012	*	60	RNAp:P2:OP2 --> RNAp*:P2:OP2	0.013	[38]
14	TetR -->	0.0012	*	61	RNAp:P2:OP2 --> RNAp:DNA21 + P2 + OP2	30	[40]
15	TetR2 -->	0.0012	*	62	RNAp + P2 + OP2:TetR2 --> RNAp:P2:OP2:TetR2	8.60E+6	[38]
16	Tc:TetOFF2 --> Tc	0.0012	*	63	RNAp:P2:OP2:TetR2 --> RNAp + P2 + OP2:TetR2	0.01	[38]
17	Tc:TetR2 --> Tc	0.0012	*	64	RNAp:P2:OP2:TetR2 --> RNAp*:P2:OP2:TetR2	0.013	[38]
18	GFP-LAA -->	2.88E-04	[36]	65	RNAp:P2:OP2:TetR2 --> RNAp:DNA21 + P2 + OP2:TetR2	30	[40]
19	Tc -->	2.67E-06	[37]	66	RNAp + P2 + OP2:TetOFF2 --> RNAp:P2:OP2:TetOFF2	8.60E+6	[38]
20	TcEx -->	2.67E-06	[37]	67	RNAp:P2:OP2:TetOFF2 --> RNAp + P2 + OP2:TetOFF2	0.01	[38]
21	TetOFF2 + OP1 --> TetOFF2:OP1	2.86E+06	[34]	68	RNAp:P2:OP2:TetOFF2 --> RNAp*:P2:OP2:TetOFF2	0.13	¶
22	TetOFF2:OP1 --> TetOFF2 + OP1	5.11E-04	[34]	69	RNAp:P2:OP2:TetOFF2 --> RNAp:DNA21 + P2 + OP2:TetOFF2	30	[40]
23	TetR2 + OP1 --> TetR2:OP1	2.86E+06	[34]	70	RNAp*:DNA21 --> RNAp + mRNA2	30, 621	[40]
24	TetR2:OP1 --> TetR2 + OP1	5.11E-04	[34]	71	mRNA2 -->	0.002	$
25	TetOFF2:OP1 + Tc --> Tc:2TetOFF:OP1	2.0E+6	[4]	72	mRNA2 + Ribosome --> Rib:mRNA2	1.00E+05	$
26	Tc:2TetOFF:OP1 + Tc --> Tc:TetOFF2:OP1	1.0E+15	§	73	Rib:mRNA2 --> Rib:mRNA21 + mRNA2	100	[41]
27	Tc:TetOFF2:OP1 --> Tc:TetOFF2 + OP1	5.8E-3	[35]	74	Rib:mRNA21 --> Ribosome + TetR	100, 207	[41]
28	TetR2:OP1 + Tc --> Tc:2TetR:OP1	2.0E+6	[4]	75	TetOFF2 + OP3 --> TetOFF2:OP3	2.86E+06	[34]
29	Tc:2TetR:OP1 + Tc --> Tc:TetR2:OP1	1.0E+15	§	76	TetOFF2:OP3 --> TetOFF2 + OP3	5.11E-04	[34]
30	Tc:TetR2:OP1 --> Tc:TetR2 + OP1	5.8E-3	[35]	77	TetR2 + OP3 --> TetR2:OP3	2.86E+06	[34]
31	RNAp + P1 + OP1 --> RNAp:P1:OP1	8.60E+06	[38]	78	TetR2:OP3 --> TetR2 + OP3	5.11E-04	[34]
32	RNAp:P1:OP1 --> RNAp + P1 + OP1	0.01	[38]	79	TetOFF2:OP3 + Tc --> Tc:2TetOFF:OP3	2.0E+6	[4]
33	RNAp:P1:OP1 --> RNAp*:P1:OP1	0.013	[38]	80	Tc:2TetOFF:OP1 + Tc --> Tc:TetOFF2:OP3	1.0E+15	§
34	RNAp:P1:OP1 --> RNAp:DNA11 + P1 + OP1	30	[40]	81	Tc:TetOFF2:OP3 --> Tc:TetOFF2 + OP3	5.8E-3	[35]
35	RNAp + P1 + OP1:TetR2 --> RNAp:P1:OP1:TetR2	8.60E+6	[38]	82	TetR2:OP3 + Tc --> Tc:2TetR:OP3	2.0E+6	[4]
36	RNAp:P1:OP1:TetR2 --> RNAp + P1 + OP1:TetR2	0.01	[38]	83	Tc:2TetR:OP3 + Tc --> Tc:TetR2:OP3	1.0E+15	§
37	RNAp:P1:OP1:TetR2 --> RNAp*:P1:OP1:TetR2	0.013	[38]	84	Tc:TetR2:OP3 --> Tc:TetR2 + OP3	5.8E-3	[35]
38	RNAp:P1:OP1:TetR2 --> RNAp:DNA11 + P1 + OP1:TetR2	30	[40]	85	RNAp + P3 + OP3 --> RNAp:P3:OP3	8.60E+6	[38]
39	RNAp + P1 + OP1:TetOFF2 --> RNAp:P1:OP1:TetOFF2	8.60E+6	[38]	86	RNAp:P3:OP3 --> RNAp + P3 + OP3	0.01	[38]
40	RNAp:P1:OP1:TetOFF2 --> RNAp + P1 + OP1:TetOFF2	0.01	[38]	87	RNAp:P3:OP3 --> RNAp*:P3:OP3	0.013	[38]
41	RNAp:P1:OP1:TetOFF2 --> RNAp*:P1:OP1:TetOFF2	0.13	¶	88	RNAp:P3:OP3 --> RNAp:DNA31 + P3 + OP3	30	[40]
42	RNAp:P1:OP1:TetOFF2 --> RNAp:DNA11 + P1 + OP1:TetOFF2	30	[40]	89	RNAp*:DNA31 --> RNAp + mRNA3	30, 723	[40]
43	RNAp*:DNA11 --> RNAp + mRNA1	30, 660	[40]	90	mRNA3 -->	0.002	$
44	mRNA1 -->	0.002	$	91	mRNA3 + Ribosome --> Rib:mRNA3	1.00E+05	$
45	mRNA1 + Ribosome --> Rib:mRNA1	1.00E+05	$	92	Rib:mRNA3 --> Rib:mRNA31 + mRNA3	100	[41]
46	Rib:mRNA1 --> Rib:mRNA11 + mRNA1	100	[41]	93	Rib:mRNA31 --> Ribosome + GFP-LAA	100, 248	[41]
47	Rib:mRNA11 --> Ribosome + TetOFF	100, 220	[41]

Reactions and kinetic rates for the chemical kinetics representation of network III. Units on k: 1^st order reaction: sec^-1, 2^nd order: (M sec)^-1, power law kinetics M^-2 sec^-1. Reactions with two kinetic constants are γ - distributed events, where the first number is the rate of each step and the second is the number of steps. References are noted next to each reaction. §: rate adjusted for fast reacting intermediates. *: rates adjusted for 10 min half-life. ¶: rate adjusted from the function of activator. $: rates adjusted to give 20 protein molecules per mRNA transcript. Numbering of the genes starts from top to bottom as they are shown in Figure 1. For example, P1: promoter of gene 1, OP1: operator of gene 1.

Back to article page

ISSN: 1752-0509

Contact us

General enquiries: ORSupport@springernature.com