Kierzek2001_LacZ

  public model
Short description
An approximation to the <a href = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11062240 ">Kierzek AM. et al. J Biol Chem. (2001) 276(11):8165-72</a> model of LacZ gene expression in E. coli. They use stochastic simulation and model cell growth. Despite these discrepancies, the continuous fixed size model is within a factor of 3 of their results. Parameter values identical.

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Format
SBML (L2V1)
Related Publication
  • The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression.
  • Kierzek AM, Zaim J, Zielenkiewicz P
  • The Journal of biological chemistry , 3/ 2001 , Volume 276 , pages: 8165-8172
  • Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland. andrzejk@ibbrain.ibb.waw.pl
  • The kinetics of prokaryotic gene expression has been modelled by the Monte Carlo computer simulation algorithm of Gillespie, which allowed the study of random fluctuations in the number of protein molecules during gene expression. The model, when applied to the simulation of LacZ gene expression, is in good agreement with experimental data. The influence of the frequencies of transcription and translation initiation on random fluctuations in gene expression has been studied in a number of simulations in which promoter and ribosome binding site effectiveness has been changed in the range of values reported for various prokaryotic genes. We show that the genes expressed from strong promoters produce the protein evenly, with a rate that does not vary significantly among cells. The genes with very weak promoters express the protein in "bursts" occurring at random time intervals. Therefore, if the low level of gene expression results from the low frequency of transcription initiation, huge fluctuations arise. In contrast, the protein can be produced with a low and uniform rate if the gene has a strong promoter and a slow rate of ribosome binding (a weak ribosome binding site). The implications of these findings for the expression of regulatory proteins are discussed.
Contributors
Sharat Vayttaden

Metadata information

is
BioModels Database MODEL4821294342
isDescribedBy
PubMed 11062240
hasTaxon
isVersionOf
hasProperty
Mathematical Modelling Ontology Ordinary differential equation model
Curation status
Non-curated
Original model(s)
http://doqcs.ncbs.res.in/~doqcs/template.php?&y=accessiondetails&an=29
  • Model originally submitted by : Sharat Vayttaden
  • Submitted: 11-Dec-2006 16:54:00
  • Last Modified: 15-Jul-2007 15:38:10
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 15-Jul-2007 15:38:10
    • Submitted by: Sharat Vayttaden
    • With comment: Current version of Kierzek2001_LacZ
  • Version: 1 public model Download this version
    • Submitted on: 11-Dec-2006 16:54:00
    • Submitted by: Sharat Vayttaden
    • With comment: Original import of Kierzek_LacZ