Plant genome-scale modeling and implementation.
Considerable progress has been made in plant genome-scale metabolic reconstruction and modeling in recent years. Such reconstructions made it possible to explore metabolic phenotypes through appropriate model formulation and optimization methods. As a result, plant genome-scale modeling has increasingly attracted interest from the plant research community. In this chapter, the first generation of plant genome-scale metabolic reconstructions is presented, along with the important concepts behind model and constraint formulation. A brief protocol describing the use of constraint-based reconstruction and analysis (COBRA) Toolbox in flux simulation and model modification is provided. This is followed by a presentation of metabolic constraints required to generate fluxes in AraGEM using COBRA that describe photosynthesis, photorespiration, and respiration, respectively. Overall, plant genome-scale modeling is a powerful approach that is accessible and readily adopted.
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia.
Cristiana G O
CG
Dal'molin
Lake-Ee
LE
Quek
Robin W
RW
Palfreyman
Lars K
LK
Nielsen
D003198:Computer Simulation; D018745:Genome, Plant; D064688:Metabolic Flux Analysis; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008954:Models, Biological; D010944:Plants / Q000235:genetics / Q000378:metabolism; D012984:Software