Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts
- Max Planck Institute of Molecular Plant Physiology, Germany
- University of Potsdam, Germany
- Carnegie Institution for Science, United States
- University of Bayreuth, Germany
- Heinrich-Heine University, Germany
Figures
Figure 1
Simplified scheme of CBC cycle with and without carbon-concentrating mechanism (CCM) in Chlamydomonas reinhardtii.
Under high CO2 conditions, no CCM is established (A). After exposure to ambient CO2, CCM is induced (B). As most of Rubisco and the other CBC enzymes are in the stroma under high CO2, most CBC flux …
Figure 2 with 1 supplement
Experimental data for protein distributions (outer yellow circle) and metabolite concentrations (inner blue circle) in CCM-supressed (white bars, HC) and CCM-induced (grey bars, LC for proteins and LC* for metabolites) conditions.
Chlamydomonas reinhardtii CC1690 cells were grown under high CO2 (HC for proteins and metabolites; white bars), ambient CO2 (LC for proteins; grey bars) and ambient CO2 bubbled for 15 min with high …
Figure 2—figure supplement 1
Induction of carbon concentrating mechanism (CCM).
Chlamydomonas reinhardtii CC1690 were grown at 46 μmol photons*m−2*s−1, 24°C and bubbled with 5% CO2 (HC) for two days at constant turbidity in a bioreactor. CO2 in the outlet air of the bioreactor …
Figure 3
Localisation of CBC enzymes.
Chlamydomonas reinhardtii CC-4533 cells expressing Venus-fusion constructs (green) were grown under ambient CO2, imaged by fluorescence microscopy and two pictures per constructs are shown. On the …
Figure 4 with 1 supplement
Graphical representation of the model for carbon fixation in Chlamydomonas reinhardtii.
The model includes a copy of the Calvin-Benson cycle (CBC) in the chloroplast stroma and in the pyrenoid. In addition, the model considers reversible transport between the stroma and the pyrenoid …
Figure 4—figure supplement 1
Distribution of Chi-square statistic for 5000 sampled steady-state flux distributions under three different assumptions.
Model predictions under non-CCM (HC, (A) and CCM-induced (LC*; B) conditions were validated using the Chi-square statistic between predicted and measured total concentration for 11 metabolites over …
Figure 5 with 1 supplement
Comparison of metabolite data determined experimentally (Experiment) and by mathematical modelling (Model) under HC (A) and LC* (B) conditions.
(A + B) Modelled data is shown as white bars (n = 1,000 ± SD) and the SD-values are too small to be seen. Experimentally, metabolites were measured by HPLC-MS/MS as already shown in Figure 2 (n = 4 ±…
Figure 5—figure supplement 1
Distribution of estimated values for CBC metabolites over 1000 sampled steady-state flux distributions under no-CCM (HC; A) and CCM-induced (LC*; B) conditions.
The estimated was negative for all enzymes except RPE and RPI for which . In addition, TRK was found to be the only enzyme operating in both directions.
Figure 6 with 1 supplement
Changes in estimated reaction fluxes and metabolite concentrations for HC and LC* Chlamydomonas reinhardtii cells.
(A) Fold changes of model predicted average net flux (represented by arrows) and total metabolite concentrations (represented by circles) between LC* and HC cells indicated by a colour code (see …
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Figure 6—source data 1
Summary of the most important concentrations and fluxes.
- https://doi.org/10.7554/eLife.37960.012
Figure 6—figure supplement 1
Reaction flux estimated for Chlamydomonas reinhardtii cells grown under non-CCM (HC; A) and CCM-induced (LC*; B) conditions.
The average values of the flux and total metabolite concentration are indicated by a colour code (see legend) and size of the arrows (denoting the reactions). The actual values are provided in Supple…
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Chlamydomonas reinhardtii) | CC1690 wild-type strain | Chlamydomonas Resource Center | RRID:SCR_014960 | |
| Strain, strain background (Chlamydomonas reinhardtii) | CC-4533 wild-type strain | Chlamydomonas Resource Center | RRID:SCR_014960 | - |
| Antibody | rabbit Anti- Beta-CA1 | AgriSera | Cat# AS11 1737; RRID:AB_10752086 | (1:7500) |
| Antibody | rabbit Anti-AtpD | AgriSera | Cat# AS10 1590; RRID:AB_10754669 | (1:30000) |
| Software, algorithm | MaxQuant | MaxQuant (http://www.biochem.mpgde/5111795/maxquant) | RRID:SCR_014485 | version 1.5.2.8 |
| Software, algorithm | Codes used for modelling | The mathematical models can be accessed via https://github.com/ankueken/Chlamy_model (copy archived at https://github.com/elifesciences-publications/Chlamy_model). |
Additional files
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Supplementary file 1
Experimental data.
- https://doi.org/10.7554/eLife.37960.013
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Supplementary file 2
Protein information for Venus localization.
- https://doi.org/10.7554/eLife.37960.014
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Supplementary file 3
Model structure.
- https://doi.org/10.7554/eLife.37960.015
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Supplementary file 4
Predications of kcat-values compared to literature values.
- https://doi.org/10.7554/eLife.37960.016
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Supplementary file 5
Raw data of the model for HC conditions.
- https://doi.org/10.7554/eLife.37960.017
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Supplementary file 6
Raw data of the model for LC* conditions.
- https://doi.org/10.7554/eLife.37960.018
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Transparent reporting form
- https://doi.org/10.7554/eLife.37960.019
