title: Development of principles and methods of ab initio Cell Design
reg no: ETF5188
project type: Estonian Science Foundation research grant
subject: 1.6-1.9. Chemistry and Molecular Biology
2.7. Biotechnology, Food and Drink Technology
status: completed
institution: Tallinn Technical University
head of project: Raivo Vilu
duration: 01.01.2002 - 31.12.2005
description: The main hypothesis of the project is that enzyme composition of the bacterial (and probably also unicellular eukaryotic cells like yeast, fungi etc.) is optimised for the maximum growth rate conditions. In these conditions functioning of the enzymes is balanced and the enzymes are functioning with full capacity, close to kcat. This allows to further develop the flux model of the cellular metabolism and link catalytic properties of the enzymes (kcat and KM, concentration of the enzymes, their amino acid composition etc.) with growth characteristics of the cells (µmax, KS values). Calculating enzyme content of the cells and comparing it with the data available in the proteomic databases and obtained in the result of the experiments carried out in the framework of the project will be the first step in validation of the model. The second hypothesis is that the polymerisation fluxes (protein synthesis, RNA, DNA synthesis, synthesis of lipids and polysaccharides etc.) are balanced and optimised for the maximum growth rate conditions. This hypothesis would allow us to calculate using the flux model of cell metabolism (MFA, see above) the enzyme and macromolecular and monomer compositions of the cells, and also the µmax value from the molecular and catalytic properties of the enzymes (kcat and KM, concentration of the enzymes, their amino acid composition etc.). The calculated enzyme contents of the cells growing with maximum growth rate using monomer composition of the cells and principles of balancing (optimising) polymerisation fluxes will be verified experimentally using experimental data obtained in batch and A-stat cultivations, and 2D SDS-electrophoresis. The third hypothesis is that the cell size (a very important parameter in the cell design) is determined by the diffusion limits either at high growth rate (intracellular diffusion) or at low growth substrate concentration (extracellular diffusion). This hypothesis will be verified through comparison of the calculated cell sizes with the data available in the literature, and experimentally studying change of the cell sizes in the very well controlled cultivation conditions using the A-stat technology, Coulter counter and flow cytometry. The fourth hypothesis is that certain modifications and additional constraints for the optimisation of the intracellular flux patterns and enzyme composition are imposed by the timing of the cell cycle events. Helmstetter-Cooper model of the prokaryotic cell cycle will be used. Model calculations will be verified by the data available in the literature.

project group
no name institution position  
1.Kaarel AdambergTallinn Technical UniversityPh.D student 
2.Kaja KasemetsTallinn Technical UniversityPh.D student 
3.Marina KrapivinaTallinn Technical UniversityPh.D student 
4.Anne MenertTallinn Technical UniversityScientist 
5.Toomas PaalmeTallinn Technical UniversityProf. 
6.Raivo ViluTallinn Technical UniversitySen. res, scientist