Caulobacter Cell Cycle Control

Parameters

Basal parameter values for the wild-type (WT) cell cycle. All parameters that start with 'k' are rate constants (min-1) and all other parameters are dimensionless.


Basal parameter values for the wild-type stalked-cell division cycle.
A. Rate constants, units = min-1

ks,CtrA-P1 = 0.0083, ks,CtrA-P2 = 0.073

(Domian et al., 1999; Grunenfelder et al., 2001; Holtzendorff et al., 2004)

kd,CtrA1 = 0.002

(Hung and Shapiro, 2002)

kd,CtrA2 = 0.15

(Domian et al., 1997)

ks,GcrA = 0.045

(Holtzendorff et al., 2004)

kd,GcrA = 0.022

(Collier et al., 2006; Holtzendorff et al., 2004)

ks,DnaA = 0.0165

(Zweiger and Shapiro, 1994)

kd,DnaA = 0.007

(Gorbatyuk and Marczynski, 2005)

ks,Fts = 0.063, kd,Fts = 0.035

(Martin et al., 2004; Sackett et al., 1998)

kzring,open = 0.8

(Judd et al., 2003)

kzring,closed1 = 0.0001, kzring,closed2 = 0.6

(Judd et al., 2003)

ks,DivK = 0.0054

(Grunenfelder et al., 2001)

kd,DivK = 0.002, kd,DivK~P = 0.002

(Jacobs et al., 2001)

ktrans,DivK = 0.5, ktrans,DivK~P = 0.0295

(Jacobs et al., 2001)

ks,I = 0.08, kd,I = 0.04

(Grunenfelder et al., 2001)

ks,CcrM = 0.072

(Grunenfelder et al., 2001)

kd,CcrM = 0.07

(Stephens et al., 1996)

km,cori = 0.4, km,ctrA = 0.4

(Stephens et al., 1996)

km,ccrM = 0.4, km,fts = 0.4

(Stephens et al., 1996)

ka,Ini = 0.01

(Quon et al., 1998)

kelong = 0.006

(Dingwall and Shapiro, 1989)

B. Binding constants and thresholds (dimensionless)

Ji,CtrA-CtrA = 0.4

Ja,CtrA-CtrA = 0.45

Jd,CtrA-DivK~P = 0.55

Ji,GcrA-CtrA = 0.2

Ji,DnaA-GcrA = 0.5

Ja,DnaA-CtrA = 0.3

Ja,open = 0.01

Ja,closed = 0.1

JZring-Fts = 0.78

Jm,cori = 0.95

Jm,ctrA = 0.95

Jm,ccrM = 0.95

Jm,fts = 0.95

θCtrA = 0.2

θGcrA = 0.45

θDnaA = 0.6

θcori = 0.0002

C. Gene positions on the chromosome (from http://ecocyc.org)

*Pelong = 0.05

PccrM = 0.2

PctrA = 0.375

Pfts = 0.625

*Pelong is assumed as the end point of replication initiation and the starting point of chromosome elongation.
D. Initial values of model variables, for a newborn, wild-type stalked cell

[CtrA] = 0.11

[GcrA] = 0.78

[DnaA] = 0.6

[Fts] = 0.29

[Zring] = 1

[DivK] = 0.66

[DivK~P] = 0.34

[I] = 0.11

[CcrM] = 0.5

[hctrA] = 0

[hccrM] = 0

[hfts] = 0

[hcori] = 1

[Ini] = 0.0

[Elong] = 0.05

[DNA] = 1.05