| Ammonium assimilation model (AmtB
transporter and protein level regulation) |
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Modelling is an important methodology in systems biology research. In
this paper, we presented a kinetic model for the complex ammonium
assimilation regulation system of E. coli. Based on a previously
published model, the new model included the AmtB mediated ammonium
transport and its protein level regulation by GlnK. Protein
concentrations and several parameter values were determined or refined
based on new experimental data. Steady-state analysis of the model showed
that the expression of AmtB increased the ammonium assimilation rate by
4-5 fold at external ammonium concentrations as low as 5 µM. Model
analysis also suggested that AmtB and GS levels were coupled to maximize
the assimilation flux and to avoid a possible negative ammonia diffusion
flux. In addition, model simulation of the short term dynamic response to
increased external ammonium concentrations implied that the maximal rate
for GlnB/GlnK uridylylation/deuridylylation should be higher for a quick
response to environmental changes.
[ See
dx.doi.org/10.1016/j.jbiotec.2009.09.003 and
amtb-GS24.sbml]
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| Central carbon metabolic
models |
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A model of the
phosphotransferase system (PTS) was constructed by Rohwer et al. and a
model of glycolysis, pentose phosphate pathway and biosynthesis was
constructed by Chassagnole et al. The two models are available on JWS
online, a on-line repository. These two models were connected in a
large kinetic model. This model will be available on JWS online after
publication.
[ See link ]
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| Central nitrogen metabolic
models |
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A model of the central nitrogen
assimilation network was constructed by Bruggeman et al. and this model
is available on JWS online. The extended model of ammonium transport
and assimilation will be available on JWS online soon.
[ See link ]
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| Qualitative model of network of
global regulators in E. coli |
|
The adaptation of the bacterium Escherichia
coli to carbon starvation is controlled by a large network of
biochemical reactions involving genes, mRNAs, proteins, and signalling
molecules. The dynamics of these networks is difficult to analyze,
notably due to a lack of quantitative information on parameter values.
To overcome these limitations, model reduction approaches based on
quasi-steady-state (QSS) and piecewise-linear (PL) approximations have
been proposed, resulting in models that are easier to handle
mathematically and computationally. These approximations are not
supposed to affect the capability of the model to account for essential
dynamical properties of the system, but the validity of this assumption
has not been systematically tested. In this paper we carry out such a
study by evaluating a large and complex PL model of the carbon
starvation response in E. coli using an ensemble approach. The
results show that, in comparison with conventional nonlinear models,
the PL approximations generally preserve the dynamics of the carbon
starvation response network, although with some deviations concerning
notably the quantitative precision of the model predictions. This
encourages the application of PL models to the qualitative analysis of
bacterial regulatory networks, in situations where the reference
time-scale is that of protein synthesis and degradation.
[ See link1,
link2,
ecoli.sbml,
GNA basic and
GNA extended
]
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Models