Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling

Abstract Motivation The accurate prediction of complex phenotypes such as metabolic fluxes in living systems is a grand challenge for systems biology and central to efficiently identifying biotechnological interventions that can address pressing industrial needs. The application of gene expression d...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2023-05, Vol.39 (5)
Main Authors: Kaste, Joshua A M, Shachar-Hill, Yair
Format: Article
Language:English
Subjects:
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Computer Science
Gene Expression Profiling
Mathematical & Computational Biology
Mathematics
Metabolic Flux Analysis - methods
Metabolic Networks and Pathways
Models, Biological
Original Paper
Proteomics
Systems Biology
Transcriptome
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Summary:Abstract Motivation The accurate prediction of complex phenotypes such as metabolic fluxes in living systems is a grand challenge for systems biology and central to efficiently identifying biotechnological interventions that can address pressing industrial needs. The application of gene expression data to improve the accuracy of metabolic flux predictions using mechanistic modeling methods such as flux balance analysis (FBA) has not been previously demonstrated in multi-tissue systems, despite their biotechnological importance. We hypothesized that a method for generating metabolic flux predictions informed by relative expression levels between tissues would improve prediction accuracy. Results Relative gene expression levels derived from multiple transcriptomic and proteomic datasets were integrated into FBA predictions of a multi-tissue, diel model of Arabidopsis thaliana’s central metabolism. This integration dramatically improved the agreement of flux predictions with experimentally based flux maps from 13C metabolic flux analysis compared with a standard parsimonious FBA approach. Disagreement between FBA predictions and MFA flux maps was measured using weighted averaged percent error values, and for parsimonious FBA this was169%–180% for high light conditions and 94%–103% for low light conditions, depending on the gene expression dataset used. This fell to 10%-13% and 9%-11% upon incorporating expression data into the modeling process, which also substantially altered the predicted carbon and energy economy of the plant. Availability and implementation Code and data generated as part of this study are available from https://github.com/Gibberella/ArabidopsisGeneExpressionWeights.
ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btad186