An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control.
NPJ Syst Biol Appl
; 8(1): 30, 2022 08 19.
Article
en En
| MEDLINE
| ID: mdl-35986058
ABSTRACT
Growth and environmental responses are essential for living organisms to survive and adapt to constantly changing environments. In order to simulate new conditions and capture dynamic responses to environmental shifts in a developing whole-cell model of E. coli, we incorporated additional regulation, including dynamics of the global regulator guanosine tetraphosphate (ppGpp), along with dynamics of amino acid biosynthesis and translation. With the model, we show that under perturbed ppGpp conditions, small molecule feedback inhibition pathways, in addition to regulation of expression, play a role in ppGpp regulation of growth. We also found that simulations with dysregulated amino acid synthesis pathways provide average amino acid concentration predictions that are comparable to experimental results but on the single-cell level, concentrations unexpectedly show regular fluctuations. Additionally, during both an upshift and downshift in nutrient availability, the simulated cell responds similarly with a transient increase in the mRNArRNA ratio. This additional simulation functionality should support a variety of new applications and expansions of the E. coli Whole-Cell Modeling Project.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Escherichia coli
/
Guanosina Tetrafosfato
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
NPJ Syst Biol Appl
Año:
2022
Tipo del documento:
Article
País de afiliación:
Estados Unidos