Team:IIT Madras/Dry lab/Modelling

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MODELING

Hypothesis

  1. Increase in growth rate due to Proteorhodopsin proton efflux in minimal carbon media
  2. Proton efflux generated by Proteorhodopsin increases ATP production

Model Design


Reconstruction and Mathematical Modeling of E.coli K12-MG1655 pathway with Proteorhodopsin. Literature data:
  1. 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].

  2. 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


A Systems Biology Markup Language (SBML) file was created for the E.Coli transformed with PR (model_PR) and Wildtype(model_WT). The flux balance studies were done by constraint based reconstruction and analysis FBA computations, which fall into the category of constraint-based reconstruction and analysis (COBRA) methods using the COBRA toolbox. The COBRA Toolbox is a freely available Matlab toolbox that can be used to perform a variety of COBRA methods, including many FBA-based methods. In Matlab, the models are structures with fields, such as 'rxns' (a list of all reaction names), 'mets' (a list of all metabolite names) and 'S' (the stoichiometric matrix). The function 'optimizeCbModel' is used to perform FBA. Also, gene deletion analysis and their effect on growth rates can also be modeled using COBRA toolbox.

Procedure for setting the model



Simulation Design for Validation


The model was validated using literature for oxidative phosphorylation like azide[]






Reference

  1. "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information" Adam M Feist[1], Christopher S Henry[2], Jennifer L Reed[1], Markus Krummenacker[3], Andrew R Joyce[1], Peter D Karp[3],Linda J Broadbelt[2], Vassily Hatzimanikatis[4] and Bernhard Ø Palsson[1],*
  2. "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*§
  3. "Light-powering Escherichia coli with proteorhodopsin" Jessica M. Walter*†, Derek Greenfield*‡, Carlos Bustamante*†‡§¶_, and Jan Liphardt*†‡**
    4.