Team:ETH Zurich/Modeling/Genome-Scale Model

Genome Scale Analysis

In 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:

• Is it possible to slow the growth of a strain by using a thymidine auxotrophyc strain and limiting thymidine feeding? How are thymidine uptake rates (concentration in the medium) quantitatively related to the growth rate in the auxotrophyc strain background?
• What is the quantitative effect on growth rate when reducing the genome size of wild type strain (under the assumption of not losing any functionality)?
• What is the combined effect of thymidine limitation and genome reduction on growth rate? It is possible to identify the best initial and running settings?
• What are the best restriction enzymes to be used in order to maximize genome reduction and at the same time vitality (growth rate) of thymidine auxotrophyc strains?
• What is the predicted genome reduction difference if the cell are grown in minimal or very rich medium (in term of nutrients)?
• What are the differencies if we were to use alternative approaches to our reduction and selection methods such as complete random search or methodical knockout strategy?

These questions are answered below, in the respective sections. As first we introduce the genome scale model concepts and 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 and E.Coli K12 MG1655

Thymidine limitation effects on growth rates

Genome size effects on growth rates

Different mediums

Growth rates as output of whole cell system behaviour

References