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Integrated flux and pool size analysis in plant central metabolism reveals unique roles of glycine and serine during photorespiration

Nature Plants volume 9, pages 169–178 (2023)Cite this article

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Abstract

Photorespiration is an essential process juxtaposed between plant carbon and nitrogen metabolism that responds to dynamic environments. Photorespiration recycles inhibitory intermediates arising from oxygenation reactions catalysed by Rubisco back into the C3 cycle, but it is unclear what proportions of its nitrogen-containing intermediates (glycine and serine) are exported into other metabolisms in vivo and how these pool sizes affect net CO2 gas exchange during photorespiratory transients. Here, to address this uncertainty, we measured rates of amino acid export from photorespiration using isotopically non-stationary metabolic flux analysis. This analysis revealed that ~23–41% of the photorespiratory carbon was exported from the pathway as serine under various photorespiratory conditions. Furthermore, we determined that the build-up and relaxation of glycine pools constrained a large portion of photosynthetic acclimation during photorespiratory transients. These results reveal the unique and important roles of glycine and serine in successfully maintaining various photorespiratory fluxes that occur under environmental fluctuations in nature and providing carbon and nitrogen for metabolism.

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Fig. 1: Central carbon assimilatory metabolic fluxes in tobacco leaves exposed to varying O2 conditions.
Fig. 2: The response of A to the chloroplastic CO2 concentration (Cc) in tobacco leaves exposed to 21% O2 under high light (1,000 μmol m−2 s−1).
Fig. 3: Metabolic pool size alterations in response to photorespiratory conditions.
Fig. 4: Active and inactive pools of glycine at varying O2 levels.
Fig. 5: Carbon lag of net assimilation during oxygen transients.

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Data availability

All data used in this study are provided as Supplementary Information of the article or available upon request. Gas exchange data for modelling the photosynthetic responses to carbon dioxide concentration and photosynthetic responses during oxygen transients can be found on GitHub at https://github.com/codexf/Modeling_Photosynthesis.

Code availability

Custom scripts for modelling the photosynthetic responses to carbon dioxide concentration and photosynthetic responses during oxygen transients can be found on GitHub at https://github.com/codexf/Modeling_Photosynthesis. A cloud-based workflow to run the Monte Carlo simulations for computing confidence intervals of metabolic fluxes can be found on GitHub at https://github.com/codexf/MFA_Cloud_Computing.

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Acknowledgements

We thank A. Ryce at Michigan State University (MSU) for experimental assistance; T. D. Sharkey (MSU) for providing lab space and guidance for performing the 14CO2 labelling experiments; Y. Xu and Y. Shachar-Hill (MSU) for helpful discussions on INST-MFA; J. Klug and C. Keilen (MSU Growth Chamber Facility) for plant maintenance; A. D. Jones, L. Chen and C. Johnny (MSU Mass Spectrometry and Metabolomics Core Facility) for advising metabolomics analyses; P. Bills (MSU IT Services), X. Wang and M. Parvizi (MSU Institute for Cyber-Enabled Research) for consulting on cloud computing and high-performance computing. The computational work was supported in part through the high-performance computing cluster and services provided by the Institute for Cyber-Enabled Research at MSU. The computational work was also supported in part through MSU’s Institute for Cyber-Enabled Research Cloud Computing Fellowship, with computational resources and services provided by Information Technology Services and the Office of Research and Innovation at MSU. We also thank J. Young for making INCA accessible and H. Stewart Williams for help establishing the online isotope analysis system. This work was supported by the US Department of Energy Office of Science, Basic Energy Sciences under Award DE- FG02-91ER20021 (B.J.W., X.F. and S.E.W.). This material is also based upon work supported in part by the Great Lakes Bioenergy Research Center, US Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-SC0018409 (B.J.W.) and the National Science Foundation under grant number 2030337 (B.J.W. and L.M.G.). We also thank the constructive feedback from three anonymous reviewers, which greatly increased the quality and strength of this work.

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Authors and Affiliations

  1. Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA

    Xinyu Fu, Luke M. Gregory, Sean E. Weise & Berkley J. Walker

  2. Department of Plant Biology, Michigan State University, East Lansing, MI, USA

    Luke M. Gregory & Berkley J. Walker

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  1. Xinyu Fu
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Contributions

B.J.W. and X.F. designed the experiments. X.F. carried out the bulk of the experiments and analysed the results. S.E.W. advised and assisted the 14CO2 experiments to measure starch and sucrose partitioning. L.M.G. performed the isotope analysis to measure gas exchange parameters. X.F. wrote the manuscript with contributions from all the authors. B.J.W. serves as the author responsible for contact and ensures communication.

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Correspondence to Berkley J. Walker.

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Nature Plants thanks Mark Stitt, Stefan Timm and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary Information

Supplementary Figs. 1–7, Tables 1 and 2 and Methods 1–4.

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Supplementary Data 1–7

Supplementary Figs. 1–7, Tables 1 and 2 and Methods 1–4.

Supplementary Data 8

INCA model files in MATLAB readable format.

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Fu, X., Gregory, L.M., Weise, S.E. et al. Integrated flux and pool size analysis in plant central metabolism reveals unique roles of glycine and serine during photorespiration. Nat. Plants 9, 169–178 (2023). https://doi.org/10.1038/s41477-022-01294-9

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