Use of genome-scale metabolic models for plant metabolism

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademic

Abstract

Genome-scale metabolic models (GSMM) have been extensively applied for a wide variety of organisms. However, for plants genome-scale modeling is still in its infancy. It has been successfully developed for Arabidopsis in the last few years. In this study we appraise the existing GSMM for Arabidopsis by computing biomass accumulation using flux balance analysis (FBA) and attempt to outline potential applications for horticultural crops in the future. The predicted growth rates for the Poolman et al. (2009) and Dal’Molin et al. (2010) model were quite similar, despite different carbon sources were provided (glucose and sucrose,100 mmol/g*h DW). The exchange fluxes for respiration in nonphotosynthetic cells confirmed that plants prefer NH3 in the process of nitrogen assimilation. When carbohydrates were used as substrate for respiration the Respiratory quotient (RQ) of Poolman’s model approached 1, which is consistent with experimental data. For the Dal’Molin’s model the RQ is less than 1. H2S is utilized in the Dal’Molin model as sulfur source, whereas sulfate (SO42-) is consumed in the Poolman’s model. The Poolman’s model seems to reflect biological reality more closely than the Dal’Molin model. This could be due to the subcellular compartmentation included in the Dal’Molin model, adding subcellular compartmentation of reactions was done manually. In conclusion, to apply constraints-based reconstruction and analysis (COBRA) methods, including FBA, to plant metabolism requires careful analysis and possibly curation of existing GSMM’s.
LanguageEnglish
Title of host publicationThe Metabolic Pathway Analysis Conference(MPAC) 16-20th September 2013, Oxford, UK.
StatePublished - 2013
Eventconference; Metabolic Pathway Analysis Conference,Corpus Christi College, Oxford,UK; 2013-09-16; 2013-09-20 -
Duration: 16 Sep 201320 Sep 2013

Conference

Conferenceconference; Metabolic Pathway Analysis Conference,Corpus Christi College, Oxford,UK; 2013-09-16; 2013-09-20
Period16/09/1320/09/13
OtherMetabolic Pathway Analysis Conference,Corpus Christi College, Oxford,UK

Fingerprint

genome
metabolism
respiration
sucrose
carbohydrate
glucose
sulfur
sulfate
substrate
crop
analysis
nitrogen
carbon
biomass
modeling

Cite this

Yuan, H., Wijnen, B., Zhou, G., Hilbers, P. A. J., & Riel, van, N. A. W. (2013). Use of genome-scale metabolic models for plant metabolism. In The Metabolic Pathway Analysis Conference(MPAC) 16-20th September 2013, Oxford, UK.
Yuan, H. ; Wijnen, B. ; Zhou, G. ; Hilbers, P.A.J. ; Riel, van, N.A.W./ Use of genome-scale metabolic models for plant metabolism. The Metabolic Pathway Analysis Conference(MPAC) 16-20th September 2013, Oxford, UK.. 2013.
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title = "Use of genome-scale metabolic models for plant metabolism",
abstract = "Genome-scale metabolic models (GSMM) have been extensively applied for a wide variety of organisms. However, for plants genome-scale modeling is still in its infancy. It has been successfully developed for Arabidopsis in the last few years. In this study we appraise the existing GSMM for Arabidopsis by computing biomass accumulation using flux balance analysis (FBA) and attempt to outline potential applications for horticultural crops in the future. The predicted growth rates for the Poolman et al. (2009) and Dal’Molin et al. (2010) model were quite similar, despite different carbon sources were provided (glucose and sucrose,100 mmol/g*h DW). The exchange fluxes for respiration in nonphotosynthetic cells confirmed that plants prefer NH3 in the process of nitrogen assimilation. When carbohydrates were used as substrate for respiration the Respiratory quotient (RQ) of Poolman’s model approached 1, which is consistent with experimental data. For the Dal’Molin’s model the RQ is less than 1. H2S is utilized in the Dal’Molin model as sulfur source, whereas sulfate (SO42-) is consumed in the Poolman’s model. The Poolman’s model seems to reflect biological reality more closely than the Dal’Molin model. This could be due to the subcellular compartmentation included in the Dal’Molin model, adding subcellular compartmentation of reactions was done manually. In conclusion, to apply constraints-based reconstruction and analysis (COBRA) methods, including FBA, to plant metabolism requires careful analysis and possibly curation of existing GSMM’s.",
author = "H. Yuan and B. Wijnen and G. Zhou and P.A.J. Hilbers and {Riel, van}, N.A.W.",
year = "2013",
language = "English",
booktitle = "The Metabolic Pathway Analysis Conference(MPAC) 16-20th September 2013, Oxford, UK.",

}

Yuan, H, Wijnen, B, Zhou, G, Hilbers, PAJ & Riel, van, NAW 2013, Use of genome-scale metabolic models for plant metabolism. in The Metabolic Pathway Analysis Conference(MPAC) 16-20th September 2013, Oxford, UK.. conference; Metabolic Pathway Analysis Conference,Corpus Christi College, Oxford,UK; 2013-09-16; 2013-09-20, 16/09/13.

Use of genome-scale metabolic models for plant metabolism. / Yuan, H.; Wijnen, B.; Zhou, G.; Hilbers, P.A.J.; Riel, van, N.A.W.

The Metabolic Pathway Analysis Conference(MPAC) 16-20th September 2013, Oxford, UK.. 2013.

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademic

TY - GEN

T1 - Use of genome-scale metabolic models for plant metabolism

AU - Yuan,H.

AU - Wijnen,B.

AU - Zhou,G.

AU - Hilbers,P.A.J.

AU - Riel, van,N.A.W.

PY - 2013

Y1 - 2013

N2 - Genome-scale metabolic models (GSMM) have been extensively applied for a wide variety of organisms. However, for plants genome-scale modeling is still in its infancy. It has been successfully developed for Arabidopsis in the last few years. In this study we appraise the existing GSMM for Arabidopsis by computing biomass accumulation using flux balance analysis (FBA) and attempt to outline potential applications for horticultural crops in the future. The predicted growth rates for the Poolman et al. (2009) and Dal’Molin et al. (2010) model were quite similar, despite different carbon sources were provided (glucose and sucrose,100 mmol/g*h DW). The exchange fluxes for respiration in nonphotosynthetic cells confirmed that plants prefer NH3 in the process of nitrogen assimilation. When carbohydrates were used as substrate for respiration the Respiratory quotient (RQ) of Poolman’s model approached 1, which is consistent with experimental data. For the Dal’Molin’s model the RQ is less than 1. H2S is utilized in the Dal’Molin model as sulfur source, whereas sulfate (SO42-) is consumed in the Poolman’s model. The Poolman’s model seems to reflect biological reality more closely than the Dal’Molin model. This could be due to the subcellular compartmentation included in the Dal’Molin model, adding subcellular compartmentation of reactions was done manually. In conclusion, to apply constraints-based reconstruction and analysis (COBRA) methods, including FBA, to plant metabolism requires careful analysis and possibly curation of existing GSMM’s.

AB - Genome-scale metabolic models (GSMM) have been extensively applied for a wide variety of organisms. However, for plants genome-scale modeling is still in its infancy. It has been successfully developed for Arabidopsis in the last few years. In this study we appraise the existing GSMM for Arabidopsis by computing biomass accumulation using flux balance analysis (FBA) and attempt to outline potential applications for horticultural crops in the future. The predicted growth rates for the Poolman et al. (2009) and Dal’Molin et al. (2010) model were quite similar, despite different carbon sources were provided (glucose and sucrose,100 mmol/g*h DW). The exchange fluxes for respiration in nonphotosynthetic cells confirmed that plants prefer NH3 in the process of nitrogen assimilation. When carbohydrates were used as substrate for respiration the Respiratory quotient (RQ) of Poolman’s model approached 1, which is consistent with experimental data. For the Dal’Molin’s model the RQ is less than 1. H2S is utilized in the Dal’Molin model as sulfur source, whereas sulfate (SO42-) is consumed in the Poolman’s model. The Poolman’s model seems to reflect biological reality more closely than the Dal’Molin model. This could be due to the subcellular compartmentation included in the Dal’Molin model, adding subcellular compartmentation of reactions was done manually. In conclusion, to apply constraints-based reconstruction and analysis (COBRA) methods, including FBA, to plant metabolism requires careful analysis and possibly curation of existing GSMM’s.

M3 - Conference contribution

BT - The Metabolic Pathway Analysis Conference(MPAC) 16-20th September 2013, Oxford, UK.

ER -

Yuan H, Wijnen B, Zhou G, Hilbers PAJ, Riel, van NAW. Use of genome-scale metabolic models for plant metabolism. In The Metabolic Pathway Analysis Conference(MPAC) 16-20th September 2013, Oxford, UK.. 2013.