RBA for eukaryotic cells: foundations and theoretical developments

Abstract

Resource allocation models were recently identified as new ways to investigate cell design principles. In particular, the Resource Balance Analysis (RBA) framework is the first constraint-based modelling method capable of accurate quantitative predictions of the genome-wide resource allocation. Initially developed and validated on bacteria, the objective of this paper is to provide the mathematical fundations of the extension of the RBA framework to eukaryotic cells. We especially investigate the way to handle the cellular compartments in order to formalize eventually the functioning of organelles. It turns out that the final RBA problem for eukaryotic cells is close to the one of prokaryotic cells from a theoretical point of view. The mathematical properties that were already identified on the prokaryotic RBA framework can be easily transposed to eukaryotic cells. In particular, the eukaryotic RBA problem can be solved easily at the cell scale by Linear Programming. This paves the way to future developments of RBA models for eukaryotic cells.