C4GEM, a genome-scale metabolic model to study C4 plant metabolism

Dal'Molin, Cristiana Gomes de, Quek, Lake-Ee, Palfreyman, Robin William, Brumbley, Stevens Michael and Nielsen, Lars Keld (2010) C4GEM, a genome-scale metabolic model to study C4 plant metabolism. Plant Physiology, 154 4: 1871-1885. doi:10.1104/pp.110.166488

Author Dal'Molin, Cristiana Gomes de
Quek, Lake-Ee
Palfreyman, Robin William
Brumbley, Stevens Michael
Nielsen, Lars Keld
Title C4GEM, a genome-scale metabolic model to study C4 plant metabolism
Formatted title
C4GEM, a genome-scale metabolic model to study C4 plant metabolism
Journal name Plant Physiology   Check publisher's open access policy
ISSN 0032-0889
Publication date 2010-12-01
Year available 2010
Sub-type Article (original research)
DOI 10.1104/pp.110.166488
Open Access Status DOI
Volume 154
Issue 4
Start page 1871
End page 1885
Total pages 15
Place of publication Rockville, MD, U.S.A.
Publisher American Society of Plant Biologists
Language eng
Abstract The human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.
Formatted abstract
Leaves of C4 grasses (such as maize [Zea mays], sugarcane [Saccharum officinarum], and sorghum [Sorghum bicolor]) form a classical Kranz leaf anatomy. Unlike C3 plants, where photosynthetic CO2 fixation proceeds in the mesophyll (M), the fixation process in C4 plants is distributed between two cell types, the M cell and the bundle sheath (BS) cell. Here, we develop a C4 genome-scale model (C4GEM) for the investigation of flux distribution in M and BS cells during C4 photosynthesis. C4GEM, to our knowledge, is the first large-scale metabolic model that encapsulates metabolic interactions between two different cell types. C4GEM is based on the Arabidopsis (Arabidopsis thaliana) model (AraGEM) but has been extended by adding reactions and transporters responsible to represent three different C4 subtypes (NADP-ME [for malic enzyme], NAD-ME, and phosphoenolpyruvate carboxykinase). C4GEM has been validated for its ability to synthesize 47 biomass components and consists of 1,588 unique reactions, 1,755 metabolites, 83 interorganelle transporters, and 29 external transporters (including transport through plasmodesmata). Reactions in the common C4 model have been associated with well-annotated C4 species (NADP-ME subtypes): 3,557 genes in sorghum, 11,623 genes in maize, and 3,881 genes in sugarcane. The number of essential reactions not assigned to genes is 131, 135, and 156 in sorghum, maize, and sugarcane, respectively. Flux balance analysis was used to assess the metabolic activity in M and BS cells during C4 photosynthesis. Our simulations were consistent with chloroplast proteomic studies, and C4GEM predicted the classical C4 photosynthesis pathway and its major effect in organelle function in M and BS. The model also highlights differences in metabolic activities around photosystem I and photosystem II for three different C4 subtypes. Effects of CO2 leakage were also explored. C4GEM is a viable framework for in silico analysis of cell cooperation between M and BS cells during photosynthesis and can be used to explore C4 plant metabolism.
© 2010 American Society of Plant Biologists.

Keyword Bundle-sheath-cells
Transgenic rice plants
Cyclic electron-transport
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID BB/M017702/1
R01 GM080219
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
Australian Institute for Bioengineering and Nanotechnology Publications
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Created: Sun, 19 Dec 2010, 10:04:05 EST