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. 2020 Feb 24;15(2):e0229408.
doi: 10.1371/journal.pone.0229408. eCollection 2020.

An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models

Gunvor Bjerkelund Røkke  1 , Martin Frank Hohmann-Marriott  1 , Eivind Almaas  1   2
Affiliations

An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models

Gunvor Bjerkelund Røkke et al. PLoS One. .

Abstract

The chloroplast is a central part of plant cells, as this is the organelle where the photosynthesis, fixation of inorganic carbon, and other key functions related to fatty acid synthesis and amino acid synthesis occur. Since this organelle should be an integral part of any genome-scale metabolic model for a microalgae or a higher plant, it is of great interest to generate a detailed and standardized chloroplast model. Additionally, we see the need for a novel type of sub-model template, or organelle model, which could be incorporated into a larger, less specific genome-scale metabolic model, while allowing for minor differences between chloroplast-containing organisms. The result of this work is the very first standardized chloroplast model, iGR774, consisting of 788 reactions, 764 metabolites, and 774 genes. The model is currently able to run in three different modes, mimicking the chloroplast metabolism of three photosynthetic microalgae-Nannochloropsis gaditana, Chlamydomonas reinhardtii and Phaeodactylum tricornutum. In addition to developing the chloroplast metabolic network reconstruction, we have developed multiple software tools for working with this novel type of sub-model in the COBRA Toolbox for MATLAB, including tools for connecting the chloroplast model to a genome-scale metabolic reconstruction in need of a chloroplast, for switching the model between running in different organism modes, and for expanding it by introducing more reactions either related to one of the current organisms included in the model, or to a new organism.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. The number of chloroplast reactions affiliated with each major subsystem group.
Fig 2
Fig 2. Representation of photosynthesis in the chloroplast model.
The areas marked PSII, b6f, PSI and ATP synthase shows where in the photosynthetic electron transport chain the different electron transfers and reactions are taking place. Light blue nodes represent metabolites, while purple nodes represent reactions.
Fig 3
Fig 3. Phenotype phase plane showing how the fluxes of carbon fixation (NanoG0589) and photon usage by PSII (PSII_photon) affect the flux of the chloroplast biomass function.
Fig 4
Fig 4. Phenotype phaseplane showing the dependency of lipid synthesis on photosynthesis (photon usage by PSII used as control reaction) and the Calvin-Benson cycle (CO2 fixation by RuBisCO used as control reaction).
See this image and copyright information in PMC

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Publication types

Grants and funding

The Faculty of Natural Sciences (priority programme NTNU Ocean) at the Norwegian University of Science and Technology (NTNU) founded the PhD position (GBR). Grant number is not available. This funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.