Team:ETH Zurich/Modeling/Genome-Scale Model
From 2008.igem.org
Genome Scale AnalysisIn the Restriction Enzymes Analysis modeling section we deal with the analysis of restriction enzymes effects on the genome from the simple point of view of nucleotide sequences and cutting patterns. This is not informative enough when we try to understand if the key principles of reduction and selection at the base of our minimal genome approach are valid in the context of the whole cell response. It is evident that our selection method for smaller genome size strains is based on the assumption that is possible to control growth rate as a function of its genome size. As explained in the Project Overview, we put a selective pressure on the genome size by combining two effects together: the random reduction of the genome size by restriction enzymes cutting and the feeding of a limited amount of thymidine nucleotides on the background of a thymidine auxotrophic strain. In this context, one should also consider the effects that the lost of chromosomal coding regions may have on the physiology of the cell. This scenario needs to be validate using modeling techniques that relate genome content and substrates avaiability with cell physiology, on a system level fashion. Fortunately, in the last ten year huge progress have been achieved in coding our understanding of biological networks into whole cell comprehensive stochiometric models. This model typology is called genome scale modeling and we use the most update genome scale model for our working strain (E.Coli K12 MG1655) in order to answer the following questions:
These questions are answered below, in the respective sections. As first we introduce the genome scale model concepts, the Flux Balance Analysis theory and in particular the iAF1260 E.Coli Genome Scale Model developed by [http://gcrg.ucsd.edu/|the Palsson's Group at UCSD], that we modified and used. In the following sections we show the results of simulations for the different questions to be answered. Genome Scale Models, FBA and E.Coli K12 MG1655Genome scale models are biological network reconstructions that effectively represent genome annotations defining the metabolic network that is specific to a particular organism. They are also called stoichiometric models because encode calculation of quantitative relationships of the reactants and products in the balanced biochemical reactions in the organism. For this reason the models that are enough informative to cover a huge part of the known organism functions are called in-silico organisms.
For example, the E. coli in silico metabolic genotype included the genes involved in central metabolism, amino acid metabolism, nucleotide metabolism, fatty acid and lipid metabolism, carbohydrate assimilation, vitamin and cofactor biosynthesis, energy and redox generation, and macromolecule production (i.e. peptidoglycan, glycogen, RNA, and DNA) Thymidine limitation effects on growth ratesGenome size effects on growth ratesDifferent mediumsGrowth rates as output of whole cell system behaviourComparing different approaches to minimal genomeReferences(1) "Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli" ,Jennifer L. Reed and Bernhard Ø. Palsson, Journal of Bacteriology, May 2003, p. 2692-2699, Vol. 185, No. 9 |