Revision as of 03:04, 29 October 2011

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In-Silico - Comparative Growth Analysis of Wild type vs PR Transformed cells

(Metabolic Modeling using Constraint Based Reconstruction and Analysis)

Hypothesis

Increase in cell growth rate due to the proton efflux generated by Proteorhodopsin in minimal carbon media

Model Design

Reconstruction and Mathematical Modeling of E.coli K12-MG1655 pathway with Proteorhodopsin. Literature data:

Genome scale metabolic model thermodynamic data for genome scale E.coli K-12 MG1655 was derived. This was done by alignment with genomic annotation and the metabolic content of EcoCyc, characterization and quantification of biomass components and maintenance requirements of cell required for growth of the cell and thermodynamic data for reactions ^[1].

Reconstruction of the pathway was carried out to suit our project, hence involving the effects due to Proteorhodpsin pumping activity. Data for pH gradient ^[2], the delta [H+] ^[3] was taken from literature and hence flux was calculated to formulate a comprehensive model.

Model Construction

Protocol for Metabolic Modeling

Click here to download SBML file for the genome scale e.coli (K-12 MG1665) model including Proteorhodopsin

Validation of Model

Simulations for Proof of Concept

References

"A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information" Adam M Feist, Christopher S Henry, Jennifer L Reed, Markus Krummenacker, Andrew R Joyce, Peter D Karp,Linda J Broadbelt, Vassily Hatzimanikatis and Bernhard Ø Palsson,Molecular Systems Biology-2007

"Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host" A. Martinez, A. S. Bradley†, J. R. Waldbauer, R. E. Summons and E. F. DeLong,PNAS-2007

"Light-powering Escherichia coli with proteorhodopsin" Jessica M. Walter, Derek Greenfield, Carlos Bustamante and Jan Liphardt,PNAS-2007

@@ Line 32: / Line 32: @@
 Literature data:<br/>
 <ol>
-<li>Genome scale metabolic model thermodynamic data for genome scale <b>E.coli K-12 MG1655</b> was derived. This was done by alignment with genomic annotation and the metabolic content of EcoCyc, characterization and quantification of biomass components and maintenance requirements of cell required for growth of the cell and thermodynamic data for reactions[1].</li> <br/>
+<li>Genome scale metabolic model thermodynamic data for genome scale <b>E.coli K-12 MG1655</b> was derived. This was done by alignment with genomic annotation and the metabolic content of EcoCyc, characterization and quantification of biomass components and maintenance requirements of cell required for growth of the cell and thermodynamic data for reactions <sup>[1]</sup>.</li> <br/>
-<li>Reconstruction of the pathway was carried out to suit our project, hence involving the effects due to Proteorhodpsin pumping activity. Data for pH gradient [2], the delta [H+] [3] was taken from literature and hence flux was calculated to formulate a comprehensive model.</li> <br/><br/><br/><br/><br/>
+<li>Reconstruction of the pathway was carried out to suit our project, hence involving the effects due to Proteorhodpsin pumping activity. Data for pH gradient <sup>[2]</sup>, the delta [H+] <sup>[3]</sup> was taken from literature and hence flux was calculated to formulate a comprehensive model.</li> <br/><br/><br/><br/><br/>
 </ol>
 <br/> <br/>
@@ Line 55: / Line 55: @@
 A. Martinez, A. S. Bradley†, J. R. Waldbauer, R. E. Summons and E. F. DeLong,PNAS-2007</li>
 <li>"Light-powering Escherichia coli with proteorhodopsin"
-Jessica M. Walter, Derek Greenfield, Carlos Bustamante, and Jan Liphardt,PNAS-2007</li></b></p>
+Jessica M. Walter, Derek Greenfield, Carlos Bustamante and Jan Liphardt,PNAS-2007</li></b></p>
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Team:IIT Madras/Dry lab/Modelling

From 2011.igem.org