Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

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.

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.

References

  1. Walker, B. J., Kramer, D. M., Fisher, N. & Fu, X. Flexibility in the energy balancing network of photosynthesis enables safe operation under changing environmental conditions. Plants 9, 301 (2020).

    Article  CAS  Google Scholar 

  2. Bauwe, H., Hagemann, M. & Fernie, A. R. Photorespiration: players, partners and origin. Trends Plant Sci. 15, 330–336 (2010).

    Article  CAS  Google Scholar 

  3. Bauwe, H., Hagemann, M., Kern, R. & Timm, S. Photorespiration has a dual origin and manifold links to central metabolism. Curr. Opin. Plant Biol. 15, 269–275 (2012).

    Article  CAS  Google Scholar 

  4. Hanson, A. D. & Roje, S. One-carbon metabolism in higher plants. Annu. Rev. Plant Biol. 52, 119–137 (2001).

    Article  CAS  Google Scholar 

  5. Bloom, A. J. Photorespiration and nitrate assimilation: a major intersection between plant carbon and nitrogen. Photosynth. Res. 123, 117–128 (2015).

    Article  CAS  Google Scholar 

  6. Tcherkez, G. et al. Respiratory metabolism of illuminated leaves depends on CO2 and O2 conditions. Proc. Natl Acad. Sci. USA 105, 797–802 (2008).

    Article  CAS  Google Scholar 

  7. Rachmilevitch, S., Cousins, A. B. & Bloom, A. J. Nitrate assimilation in plant shoots depends on photorespiration. Proc. Natl Acad. Sci. USA 101, 11506–11510 (2004).

    Article  CAS  Google Scholar 

  8. Bloom, A. J., Burger, M., Asensio, J. S. R. & Cousins, A. B. Carbon dioxide enrichment inhibits nitrate assimilation in wheat and arabidopsis. Science 328, 899–903 (2010).

    Article  CAS  Google Scholar 

  9. Cotrufo, M. F., Ineson, P. & Scott, A. Elevated CO2 reduces the nitrogen concentration of plant tissues. Glob. Chang. Biol. 4, 43–54 (1998).

    Article  Google Scholar 

  10. Abadie, C., Blanchet, S., Carroll, A. & Tcherkez, G. Metabolomics analysis of postphotosynthetic effects of gaseous O2 on primary metabolism in illuminated leaves. Funct. Plant Biol. 44, 929–940 (2017).

    Article  CAS  Google Scholar 

  11. Tcherkez, G. et al. Short-term effects of CO2 and O2 on citrate metabolism in illuminated leaves. Plant Cell Environ. 35, 2208–2220 (2012).

    Article  CAS  Google Scholar 

  12. Hodges, M. et al. Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network. J. Exp. Bot. 67, 3015–3026 (2016). vol.

    Article  CAS  Google Scholar 

  13. Harley, P. C. & Sharkey, T. D. An improved model of C3 photosynthesis at high CO2: reversed O2 sensitivity explained by lack of glycerate reentry into the chloroplast. Photosynth. Res. 27, 169–178 (1991).

    Article  CAS  Google Scholar 

  14. Busch, F. A. & Sage, R. F. The sensitivity of photosynthesis to O2 and CO2 concentration identifies strong Rubisco control above the thermal optimum. N. Phytol. 213, 1036–1051 (2017).

    Article  CAS  Google Scholar 

  15. Busch, F. A., Sage, R. F. & Farquhar, G. D. Plants increase CO2 uptake by assimilating nitrogen via the photorespiratory pathway. Nat. Plants 4, 46–54 (2018).

    Article  CAS  Google Scholar 

  16. McClain, A. M. & Sharkey, T. D. Triose phosphate utilization and beyond: from photosynthesis to end product synthesis. J. Exp. Bot. 70, 1755–1766 (2019).

    Article  CAS  Google Scholar 

  17. Eisenhut, M. et al. Photorespiration is crucial for dynamic response of photosynthetic metabolism and stomatal movement to altered CO2 availability. Mol. Plant 10, 47–61 (2017).

    Article  CAS  Google Scholar 

  18. Timm, S. et al. High-to-low CO2 acclimation reveals plasticity of the photorespiratory pathway and indicates regulatory links to cellular metabolism of Arabidopsis. PLoS ONE 7, e42809 (2012).

    Article  CAS  Google Scholar 

  19. Wingler, A. et al. The role of photorespiration during drought stress: an analysis utilizing barley mutants with reduced activities of photorespiratory enzymes. Plant Cell Environ. 22, 361–373 (1999).

    Article  CAS  Google Scholar 

  20. Abadie, C., Bathellier, C. & Tcherkez, G. Carbon allocation to major metabolites in illuminated leaves is not just proportional to photosynthesis when gaseous conditions (CO2 and O2) vary. N. Phytol. 218, 94–106 (2018).

    Article  CAS  Google Scholar 

  21. Abadie, C., Boex-Fontvieille, E. R. A., Carroll, A. J. & Tcherkez, G. In vivo stoichiometry of photorespiratory metabolism. Nat. Plants 2, 15220 (2016).

    Article  CAS  Google Scholar 

  22. Abadie, C. & Tcherkez, G. 13C isotope labelling to follow the flux of photorespiratory intermediates. Plants 10, 1–12 (2021).

    Article  Google Scholar 

  23. Bao, H. et al. Catalase protects against nonenzymatic decarboxylations during photorespiration in Arabidopsis thaliana. Plant Direct 5, e366 (2021).

    Article  CAS  Google Scholar 

  24. Tcherkez, G. et al. Leaf day respiration: low CO2 flux but high significance for metabolism and carbon balance. N. Phytol. 216, 986–1001 (2017).

    Article  CAS  Google Scholar 

  25. Szecowka, M. et al. Metabolic fluxes in an illuminated Arabidopsis rosette. Plant Cell 25, 694–714 (2013).

    Article  CAS  Google Scholar 

  26. Ma, F., Jazmin, L. J., Young, J. D. & Allen, D. K. Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation. Proc. Natl Acad. Sci. USA 111, 16967–16972 (2014).

    Article  CAS  Google Scholar 

  27. Abadie, C., Lalande, J., Limami, A. M. & Tcherkez, G. Non-targeted 13C metabolite analysis demonstrates broad re-orchestration of leaf metabolism when gas exchange conditions vary. Plant Cell Environ. 44, 445–457 (2021).

    Article  CAS  Google Scholar 

  28. Cegelski, L. & Schaefer, J. NMR determination of photorespiration in intact leaves using in vivo 13CO2 labeling. J. Magn. Reson. 178, 1–10 (2006).

    Article  CAS  Google Scholar 

  29. Dirks, R. C., Singh, M., Potter, G. S., Sobotka, L. G. & Schaefer, J. Carbon partitioning in soybean (Glycine max) leaves by combined 11C and 13C labeling. N. Phytol. 196, 1109–1121 (2012).

    Article  CAS  Google Scholar 

  30. Ratcliffe, R. G. & Shachar-Hill, Y. Measuring multiple fluxes through plant metabolic networks. Plant J. 45, 490–511 (2006).

    Article  CAS  Google Scholar 

  31. Chu, K. L. et al. Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves. Metab. Eng. 69, 231–248 (2022).

    Article  CAS  Google Scholar 

  32. Treves, H. et al. Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants. Nat. Plants 8, 78–91 (2022).

    Article  CAS  Google Scholar 

  33. Xu, Y., Fu, X., Sharkey, T. D., Shachar-Hill, Y. & Walker, B. J. The metabolic origins of non-photorespiratory CO2 release during photosynthesis: a metabolic flux analysis. Plant Physiol. 186, 297–314 (2021).

    Article  CAS  Google Scholar 

  34. Xu, Y., Wieloch, T., Kaste, J. A. M., Shachar-Hill, Y. & Sharkey, T. D. Reimport of carbon from cytosolic and vacuolar sugar pools into the Calvin–Benson cycle explains photosynthesis labeling anomalies. Proc. Natl. Acad. Sci. USA 119, 11 (2022).

    Google Scholar 

  35. Sharkey, T. D., Berry, J. A. & Raschke, K. Starch and sucrose synthesis in Phaseolus vulgaris as affected by light, CO2, and abscisic acid. Plant Physiol. 77, 617–620 (1985).

    Article  CAS  Google Scholar 

  36. Cegelski, L. & Schaefer, J. Glycine metabolism in intact leaves by in vivo 13C and 15N labeling. J. Biol. Chem. 280, 39238–39245 (2005).

    Article  CAS  Google Scholar 

  37. Heinemann, B., Künzler, P., Eubel, H., Braun, H. P. & Hildebrandt, T. M. Estimating the number of protein molecules in a plant cell: protein and amino acid homeostasis during drought. Plant Physiol. 185, 385–404 (2021).

    CAS  Google Scholar 

  38. Madore, M. & Grodzinski, B. Effect of oxygen concentration on 14C-photoassimilate transport from leaves of Salvia splendens L. Plant Physiol. 76, 782–786 (1984).

    Article  CAS  Google Scholar 

  39. Takahashi, H., Kopriva, S., Giordano, M., Saito, K. & Hell, R. Sulfur assimilation in photosynthetic organisms: molecular functions and regulations of transporters and assimilatory enzymes. Annu. Rev. Plant Biol. 62, 157–184 (2011).

    Article  CAS  Google Scholar 

  40. Radwanski, E. R. & Last, R. L. Tryptophan biosynthesis and metabolism: biochemical and molecular genetics. Plant Cell 7, 921–934 (1995).

    CAS  Google Scholar 

  41. Ros, R., Muñoz-Bertomeu, J. & Krueger, S. Serine in plants: biosynthesis, metabolism, and functions. Trends Plant Sci. 19, 564–569 (2014).

    Article  CAS  Google Scholar 

  42. Noctor, G., Arisi, A. C. M., Jouanin, L. & Foyer, C. H. Photorespiratory glycine enhances glutathione accumulation in both the chloroplastic and cytosolic compartments. J. Exp. Bot. 50, 1157–1167 (1999).

    Article  CAS  Google Scholar 

  43. Foyer, C. H., Bloom, A. J., Queval, G. & Noctor, G. Photorespiratory metabolism: genes, mutants, energetics, and redox signaling. Annu. Rev. Plant Biol. 60, 455–484 (2009).

    Article  CAS  Google Scholar 

  44. Gauthier, P. P. G. et al. In folio isotopic tracing demonstrates that nitrogen assimilation into glutamate is mostly independent from current CO2 assimilation in illuminated leaves of Brassica napus. N. Phytol. 185, 988–999 (2010).

    Article  CAS  Google Scholar 

  45. Zelitch, I., Schultes, N. P., Peterson, R. B., Brown, P. & Brutnell, T. P. High glycolate oxidase activity is required for survival of maize in normal air. Plant Physiol. 149, 195–204 (2009).

    Article  CAS  Google Scholar 

  46. Fu, X. & Walker, B. J. Dynamic response of photorespiration in fluctuating light environments. J. Exp. Bot. https://doi.org/10.1093/jxb/erac335 (2022).

  47. Hitz, W. D. & Stewart, C. R. Oxygen and carbon dioxide effects on the pool size of some photosynthetic and photorespiratory intermediates in soybean (Glycine max [L.] Merr.). Plant Physiol. 65, 442–446 (1980).

    Article  CAS  Google Scholar 

  48. Flügel, F. et al. The photorespiratory metabolite 2-phosphoglycolate regulates photosynthesis and starch accumulation in Arabidopsis. Plant Cell 29, 2537–2551 (2017).

    Article  Google Scholar 

  49. Anderson, L. E. Chloroplast and cytoplasmic enzymes II. Pea leaf triose phosphate isomerases. Biochim. Biophys. Acta 235, 237–244 (1971).

    Article  CAS  Google Scholar 

  50. Campbell, W. J. & Ogren, W. L. Glyoxylate inhibition of ribulosebisphosphate carboxylase/oxygenase activation in intact, lysed, and reconstituted chloroplasts. Photosynth. Res. 23, 257–268 (1990).

    Article  CAS  Google Scholar 

  51. Gonzalez-Moro, B., Lacuesta, M., Becerril, J. M., Gonzalez-Murua, C. & Munoz-Rueda, A. Glycolate accumulation causes a decrease of photosynthesis by inhibiting RUBISCO activity in maize. J. Plant Physiol. 150, 388–394 (1997).

    Article  CAS  Google Scholar 

  52. Kelly, G. J. & Latzko, E. Inhibition of spinach-leaf phosphofructokinase by 2-phosphoglycollate. FEBS Lett. 68, 55–58 (1976).

    Article  CAS  Google Scholar 

  53. South, P. F., Cavanagh, A. P., Liu, H. W. & Ort, D. R. Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field. Science 363, 45 (2019).

    Article  Google Scholar 

  54. Timm, S. et al. Serine acts as a metabolic signal for the transcriptional control of photorespiration-related genes in Arabidopsis. Plant Physiol. 162, 379–389 (2013).

    Article  CAS  Google Scholar 

  55. Schimkat, D., Heineke, D. & Heldt, H. W. Regulation of sedoheptulose-1,7-bisphosphatase by sedoheptulose-7-phosphate and glycerate, and of fructose-1,6-bisphosphatase by glycerate in spinach chloroplasts. Planta 181, 97–103 (1990).

    Article  CAS  Google Scholar 

  56. Heineke, D., Bykova, N., Gardeström, P. & Bauwe, H. Metabolic response of potato plants to an antisense reduction of the P-protein of glycine decarboxylase. Planta 212, 880–887 (2001).

    Article  CAS  Google Scholar 

  57. Timm, S. et al. Glycine decarboxylase controls photosynthesis and plant growth. FEBS Lett. 586, 3692–3697 (2012).

    Article  CAS  Google Scholar 

  58. López-Calcagno, P. E. et al. Overexpressing the H-protein of the glycine cleavage system increases biomass yield in glasshouse and field-grown transgenic tobacco plants. Plant Biotechnol. J. 17, 141–151 (2019).

    Article  Google Scholar 

  59. Bykova, N. V., Møller, I. M., Gardeström, P. & Igamberdiev, A. U. The function of glycine decarboxylase complex is optimized to maintain high photorespiratory flux via buffering of its reaction products. Mitochondrion 19, 357–364 (2014).

    Article  CAS  Google Scholar 

  60. da Fonseca-Pereira, P. et al. Thioredoxin h2 contributes to the redox regulation of mitochondrial photorespiratory metabolism. Plant Cell Environ. 43, 188–208 (2020).

    Article  Google Scholar 

  61. Reinholdt, O. et al. Redox-regulation of photorespiration through mitochondrial thioredoxin O1. Plant Physiol. 181, 442–457 (2019).

    Article  CAS  Google Scholar 

  62. Eisenhut, M., Pick, T. R., Bordych, C. & Weber, A. P. M. Towards closing the remaining gaps in photorespiration—the essential but unexplored role of transport proteins. Plant Biol. 15, 676–685 (2013).

    Article  CAS  Google Scholar 

  63. Young, J. D. INCA: a computational platform for isotopically non-stationary metabolic flux analysis. Bioinformatics 30, 1333–1335 (2014).

    Article  CAS  Google Scholar 

  64. Young, J. D., Walther, J. L., Antoniewicz, M. R., Yoo, H. & Stephanopoulos, G. An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis. Biotechnol. Bioeng. 99, 686–699 (2008).

    Article  CAS  Google Scholar 

  65. Antoniewicz, M. R., Kelleher, J. K. & Stephanopoulos, G. Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab. Eng. 8, 324–337 (2006).

    Article  CAS  Google Scholar 

  66. Farquhar, G. D., von Caemmerer, S. & Berry, J. A. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149, 78–90 (1980).

    Article  CAS  Google Scholar 

  67. Sharkey, T. D., Bernacchi, C. J., Farquhar, G. D. & Singsaas, E. L. Fitting photosynthetic carbon dioxide response curves for C3 leaves. Plant, Cell Environ. 30, 1035–1040 (2007).

    Article  CAS  Google Scholar 

Download references

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.

Author information

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

Authors
  1. Xinyu Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Luke M. Gregory
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sean E. Weise
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Berkley J. Walker
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Corresponding author

Correspondence to Berkley J. Walker.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

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

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

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

Reporting Summary

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.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-022-01294-9

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing