Plant genome-scale reconstruction: from single cell to multi-tissue modelling and omics analyses
Abstract
In this review, we present the latest developments in plant systems biology with particular emphasis on plant genome-scale reconstructions and multi-omics analyses. Understanding multicellular metabolism is far from trivial and 'omics' data are difficult to interpret in the absence of a systems framework. 'Omics' data appropriately integrated with genome-scale reconstructions and modelling facilitates our understanding of how individual components interact and influence overall cell, tissue or organisms function. Here we present examples of how plant metabolic reconstructions and modelling are used as a systems-based framework for improving our understanding of the plant metabolic processes in single cells and multiple tissues.
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Flux balance analysis is readily scaled to incorporate the entire metabolic system of a cell.
“In contrast, a second modeling approach, flux balance analysis (FBA), is readily scaled to incorporate the entire metabolic system of a cell (Sweetlove and Ratcliffe, 2011; Shi and Schwender, 2016; Gomes de Oliveira Dal’Molin and Nielsen, 2018).”
From Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light (2019) · cites this paper as Gomes de Oliveira Dal’Molin and Nielsen, 2018
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What is flux balance analysis?
Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903 · see citing works
Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism
Saha, R., Suthers, P. F., & Maranas, C. D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021784 · Cited by 201 · see citing works
Arnold, A., & Nikoloski, Z. (2014) · Plant Physiology · doi:10.1104/pp.114.235358 · Cited by 131 · see citing works
Nitrogen-use efficiency in maize (Zea mays L.): from ‘omics’ studies to metabolic modelling
Simons, M., Saha, R., Guillard, L., Clement, G., Armengaud, P., Canas, R., Maranas, C. D., Lea, P. J., & Hirel, B. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru227 · Cited by 87 · see citing works
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Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light
Shameer, S., Ratcliffe, R. G., & Sweetlove, L. J. (2019) · Plant Physiology · doi:10.1104/pp.19.00624 · Cited by 118 · see citing works
Insights into the spatial and temporal organisation of plant metabolism from network flux analysis
Moreira, T. B., Lima, J. M., Coca, G. C., & Williams, T. C. R. (2019) · Theoretical and Experimental Plant Physiology · doi:10.1007/s40626-018-0132-3 · Cited by 13 · see citing works
- Authors
- Gomes de Oliveira Dal’Molin, C., & Nielsen, L. K.
- Affiliations
- The University of Queensland (AU)
- Corresponding author
- Nielsen, Lars Keld
- ORCID
- Nielsen, Lars Keld
- Venue
- Current Opinion in Biotechnology
- Publisher
- Elsevier BV
- Published
- 2018-02
- Volume
- 49
- Pages
- 42-48
- ISSN
- 0958-1669 (ISSN-L)
- OpenAlex
- W2743271525
- Cited by
- 35
- References
- 4
- Citations by year
- 2025: 2 · 2024: 3 · 2023: 4 · 2022: 4 · 2021: 4 · 2020: 10 · 2019: 5 · 2018: 3
- FWCI
- 0.46
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Current Opinion in Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Australian Research Council
- Asian Office of Aerospace Research and Development
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- plant systems biology, multi-omics integration, plant metabolism, metabolic network reconstruction, plant metabolic engineering
- MeSH terms
- Models, Biological, Plants, Genome, Plant, Genomics, Systems Biology, Single-Cell Analysis
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