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.

  • Article
  • Published:

The structural basis of Rubisco phase separation in the pyrenoid

Nature Plants volume 6, pages 1480–1490 (2020)Cite this article

Subjects

Abstract

Approximately one-third of global CO2 fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO2-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Fig. 1: EPYC1 consists of five tandem sequence repeats, each of which contains a Rubisco-binding region.
Fig. 2: EPYC1 binds to Rubisco small subunits.
Fig. 3: EPYC1 binds to Rubisco small subunit α-helices via salt bridges and a hydrophobic pocket.
Fig. 4: Interface residues on EPYC1 are required for the binding and phase separation of EPYC1 and Rubisco in vitro.
Fig. 5: Interface residues on Rubisco are required for yeast two-hybrid interactions between EPYC1 and Rubisco and for pyrenoid matrix formation in vivo.
Fig. 6: A model for matrix structure consistent with in situ Rubisco positions and orientations.

Similar content being viewed by others

Data availability

All data generated or analysed during this study are included in this Article, the extended data and the supplementary tables. The single-particle cryo-electron microscopy maps have been deposited in the Electron Microscopy Data Bank with accession codes EMDB-22401, EMDB-22308 and EMDB-22462. The atomic models have been deposited in the Protein Data Bank under accession codes PDB 7JN4, PDB 7JFO and PDB 7JSX. The raw datasets have been deposited in the Electron Microscopy Public Image Archive with accession codes EMPIAR-10503, EMPIAR-10502 and EMPIAR-10501. The subtomogram average of Rubisco has been deposited in the Electron Microscopy Data Bank with accession code EMD-3694.

References

  1. Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240 (1998).

    Article  CAS  PubMed  Google Scholar 

  2. Hessler, A. M., Lowe, D. R., Jones, R. L. & Bird, D. K. A lower limit for atmospheric carbon dioxide levels 3.2 billion years ago. Nature 428, 736–738 (2004).

    Article  CAS  PubMed  Google Scholar 

  3. Ainsworth, E. A. & Long, S. P. What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2. N. Phytol. 165, 351–371 (2005).

    Article  Google Scholar 

  4. Raven, J. A., Cockell, C. S. & De La Rocha, C. L. The evolution of inorganic carbon concentrating mechanisms in photosynthesis. Phil. Trans. R. Soc. B 363, 2641–2650 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Freeman Rosenzweig, E. S. et al. The eukaryotic CO2-concentrating organelle is liquid-like and exhibits dynamic reorganization. Cell 171, 148–162 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Badger, M. R. et al. The diversity and coevolution of Rubisco, plastids, pyrenoids, and chloroplast-based CO2-concentrating mechanisms in algae. Can. J. Bot. 76, 1052–1071 (1998).

    CAS  Google Scholar 

  7. Villarreal, J. C. & Renner, S. S. Hornwort pyrenoids, carbon-concentrating structures, evolved and were lost at least five times during the last 100 million years. Proc. Natl Acad. Sci. USA 109, 18873–18878 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Wang, Y., Stessman, D. J. & Spalding, M. H. The CO2 concentrating mechanism and photosynthetic carbon assimilation in limiting CO2: how Chlamydomonas works against the gradient. Plant J. Cell Mol. Biol. 82, 429–448 (2015).

    Article  CAS  Google Scholar 

  9. Raven, J. A. CO2-concentrating mechanisms: a direct role for thylakoid lumen acidification? Plant Cell Environ. 20, 147–154 (1997).

    Article  CAS  Google Scholar 

  10. Mackinder, L. C. et al. A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle. Proc. Natl Acad. Sci. USA 113, 5958–5963 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Wunder, T., Cheng, S. L. H., Lai, S. K., Li, H. Y. & Mueller-Cajar, O. The phase separation underlying the pyrenoid-based microalgal Rubisco supercharger. Nat. Commun. 9, 5076 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. Atkinson, N. et al. The pyrenoidal linker protein EPYC1 phase separates with hybrid Arabidopsis–Chlamydomonas Rubisco through interactions with the algal Rubisco small subunit. J. Exp. Bot. 70, 5271–5285 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Taylor, T. C., Backlund, A., Bjorhall, K., Spreitzer, R. J. & Andersson, I. First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii. J. Biol. Chem. 276, 48159–48164 (2001).

    Article  CAS  PubMed  Google Scholar 

  14. Duff, A. P., Andrews, T. J. & Curmi, P. M. The transition between the open and closed states of Rubisco is triggered by the inter-phosphate distance of the bound bisphosphate. J. Mol. Biol. 298, 903–916 (2000).

    Article  CAS  PubMed  Google Scholar 

  15. Meyer, M. T. et al. Rubisco small-subunit α-helices control pyrenoid formation in Chlamydomonas. Proc. Natl Acad. Sci. USA 109, 19474–19479 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Engel, B. D. et al. Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography. eLife 4, e04889 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Goodenough, U. W. & Levine, R. P. Chloroplast structure and function in ac-20, a mutant strain of Chlamydomonas reinhardi. 3. Chloroplast ribosomes and membrane organization. J. Cell Biol. 44, 547–562 (1970).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ma, Y., Pollock, S. V., Xiao, Y., Cunnusamy, K. & Moroney, J. V. Identification of a novel gene, CIA6, required for normal pyrenoid formation in Chlamydomonas reinhardtii. Plant Physiol. 156, 884–896 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Caspari, O. D. et al. Pyrenoid loss in Chlamydomonas reinhardtii causes limitations in CO2 supply, but not thylakoid operating efficiency. J. Exp. Bot. 68, 3903–3913 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Li, P. et al. Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336–340 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Borkhsenious, O. N., Mason, C. B. & Moroney, J. V. The intracellular localization of ribulose-1,5-bisphosphate carboxylase/oxygenase in Chlamydomonas reinhardtii. Plant Physiol. 116, 1585–1591 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Turkina, M. V., Blanco-Rivero, A., Vainonen, J. P., Vener, A. V. & Villarejo, A. CO2 limitation induces specific redox-dependent protein phosphorylation in Chlamydomonas reinhardtii. Proteomics 6, 2693–2704 (2006).

    Article  CAS  PubMed  Google Scholar 

  23. Meyer, M. T. et al. Assembly of the algal CO2-fixing organelle, the pyrenoid, is guided by a Rubisco-binding motif. Sci. Adv. https://doi.org/10.1126/sciadv.abd2408 (in the press).

  24. Cai, F. et al. Advances in understanding carboxysome assembly in Prochlorococcus and Synechococcus implicate CsoS2 as a critical component. Life (Basel) 5, 1141–1171 (2015).

    CAS  Google Scholar 

  25. Oltrogge, L. M. et al. Multivalent interactions between CsoS2 and Rubisco mediate alpha-carboxysome formation. Nat. Struct. Mol. Biol. 27, 281–287 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Long, B. M., Badger, M. R., Whitney, S. M. & Price, G. D. Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple Rubisco complexes with carboxysomal proteins CcmM and CcaA. J. Biol. Chem. 282, 29323–29335 (2007).

    Article  CAS  PubMed  Google Scholar 

  27. Wang, H. et al. Rubisco condensate formation by CcmM in beta-carboxysome biogenesis. Nature 566, 131–135 (2019).

    Article  CAS  PubMed  Google Scholar 

  28. Hennacy, J. H. & Jonikas, M. C. Prospects for engineering biophysical CO2 concentrating mechanisms into land plants to enhance yields. Annu. Rev. Plant Biol. https://doi.org/10.1146/annurev-arplant-081519-040100 (2020).

  29. Long, B. M. et al. Carboxysome encapsulation of the CO2-fixing enzyme Rubisco in tobacco chloroplasts. Nat. Commun. 9, 3570 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Lin, M. T., Occhialini, A., Andralojc, P. J., Parry, M. A. & Hanson, M. R. A faster Rubisco with potential to increase photosynthesis in crops. Nature 513, 547–550 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Atkinson, N. et al. Introducing an algal carbon-concentrating mechanism into higher plants: location and incorporation of key components. Plant Biotechnol. J. 14, 1302–1315 (2016).

    Article  CAS  PubMed  Google Scholar 

  32. Hanson, M. R., Gray, B. N. & Ahner, B. A. Chloroplast transformation for engineering of photosynthesis. J. Exp. Bot. 64, 731–742 (2013).

    Article  CAS  PubMed  Google Scholar 

  33. Raven, J. A., Beardall, J. & Sanchez-Baracaldo, P. The possible evolution and future of CO2-concentrating mechanisms. J. Exp. Bot. 68, 3701–3716 (2017).

    Article  CAS  PubMed  Google Scholar 

  34. Kropat, J. et al. A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. Plant J. Cell Mol. Biol. 66, 770–780 (2011).

    Article  CAS  Google Scholar 

  35. Khrebtukova, I. & Spreitzer, R. J. Elimination of the Chlamydomonas gene family that encodes the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Proc. Natl Acad. Sci. USA 93, 13689–13693 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Zhang, R. et al. High-throughput genotyping of green algal mutants reveals random distribution of mutagenic insertion sites and endonucleolytic cleavage of transforming DNA. Plant Cell 26, 1398–1409 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. BIAevaluation 4.1.1 (Biacore AB, 2020).

  38. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. eLife 7, e35383 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  42. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article  CAS  PubMed  Google Scholar 

  43. Punjani, A., Brubaker, M. A. & Fleet, D. J. Building proteins in a day: efficient 3D molecular structure estimation with electron cryomicroscopy. IEEE Trans. Pattern Anal. Mach. Intell. 39, 706–718 (2017).

    Article  PubMed  Google Scholar 

  44. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  PubMed  Google Scholar 

  45. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of COOT. Acta Crystallogr. D 66, 486–501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Drozdetskiy, A., Cole, C., Procter, J. & Barton, G. J. JPred4: a protein secondary structure prediction server. Nucleic Acids Res. 43, W389–W394 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

    Article  CAS  PubMed  Google Scholar 

  49. Sueoka, N. Mitotic replication of deoxyribonucleic acid in Chlamydomonas reinhardi. Proc. Natl Acad. Sci. USA 46, 83–91 (1960).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Catanzariti, A. M., Soboleva, T. A., Jans, D. A., Board, P. G. & Baker, R. T. An efficient system for high-level expression and easy purification of authentic recombinant proteins. Protein Sci. 13, 1331–1339 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Ewalt, K. L., Hendrick, J. P., Houry, W. A. & Hartl, F. U. In vivo observation of polypeptide flux through the bacterial chaperonin system. Cell 90, 491–500 (1997).

    Article  CAS  PubMed  Google Scholar 

  52. Baker, R. T. et al. in Ubiquitin and Protein Degradation, Part A: Methods in Enzymology (eds Deshaies, R. J.) 540–554 (Academic Press, 2005).

  53. Genkov, T., Meyer, M., Griffiths, H. & Spreitzer, R. J. Functional hybrid Rubisco enzymes with plant small subunits and algal large subunits: engineered rbcS cDNA for expression in Chlamydomonas. J. Biol. Chem. 285, 19833–19841 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).

    Article  CAS  PubMed  Google Scholar 

  55. Li, X. et al. A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. Nat. Genet. 51, 627–635 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Martinez-Sanchez, A. et al. Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms. Nat Methods https://doi.org/10.1038/s41592-019-0675-5 (2020).

  57. Cheng, S., Cetinkaya, M. & Grater, F. How sequence determines elasticity of disordered proteins. Biophys. J. 99, 3863–3869 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank J. Wu, N. Yan, L. Mackinder, C. Brangwynne and members of the Jonikas laboratory for helpful discussions; N. Wingreen, S. Ramundo, J. Hennacy, E. Franklin and A. Wilson for constructive feedback on the manuscript; W. Baumeister and J. Plitzko for providing support and cryo-electron tomography instrumentation; and M. Schaffer for help with acquiring the cryo-electron tomography data, previously published in ref. 5. This project was funded by National Science Foundation (nos IOS-1359682 and MCB-1935444), National Institutes of Health (no. DP2-GM-119137), and Simons Foundation and Howard Hughes Medical Institute (no. 55108535) grants to M.C.J.; a Deutsche Forschungsgemeinschaft grant (EN 1194/1-1 as part of FOR2092) to B.D.E.; a Ministry of Education (MOE Singapore) Tier 2 grant (no. MOE2018-T2-2-059) to O.M.-C.; UK Biotechnology and Biological Sciences Research Council (no. BB/S015531/1) and Leverhulme Trust (no. RPG-2017-402) grants to A.J.M. and N.A.; NIH grant no. R01GM071574 to F.M.H.; a Deutsche Forschungsgemeinschaft fellowship (no. PO2195/1-1) to S.A.P.; and a National Institute of General Medical Sciences of the National Institutes of Health (no. T32GM007276) training grant to V.K.C. The content is solely the responsibility of the authors and does not necessarily represent the official view of the National Institutes of Health.

Author information

Authors and Affiliations

  1. Department of Molecular Biology, Princeton University, Princeton, NJ, USA

    Shan He, Moritz T. Meyer, Philip D. Jeffrey, Sarah A. Port, Weronika Patena, Guanhua He, Frederick M. Hughson & Martin C. Jonikas

  2. Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA

    Hui-Ting Chou, Doreen Matthies & Zhiheng Yu

  3. Department of Therapeutic Discovery, Amgen Discovery Research, Amgen Inc., South San Francisco, CA, USA

    Hui-Ting Chou

  4. School of Biological Sciences, Nanyang Technological University, Singapore, Singapore

    Tobias Wunder & Oliver Mueller-Cajar

  5. SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK

    Nicky Atkinson & Alistair J. McCormick

  6. Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany

    Antonio Martinez-Sanchez & Benjamin D. Engel

  7. Institute of Neuropathology, University of Göttingen Medical Center, Göttingen, Germany

    Antonio Martinez-Sanchez

  8. Department of Biology, Stanford University, Stanford, CA, USA

    Vivian K. Chen

  9. Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany

    Benjamin D. Engel

  10. Department of Chemistry, Technical University of Munich, Garching, Germany

    Benjamin D. Engel

Authors
  1. Shan He
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hui-Ting Chou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Doreen Matthies
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tobias Wunder
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Moritz T. Meyer
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Nicky Atkinson
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Antonio Martinez-Sanchez
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Philip D. Jeffrey
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Sarah A. Port
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Weronika Patena
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Guanhua He
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Vivian K. Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Frederick M. Hughson
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Alistair J. McCormick
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Oliver Mueller-Cajar
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Benjamin D. Engel
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Zhiheng Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Martin C. Jonikas
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

S.H., P.D.J., V.K.C., F.M.H., T.W., O.M.-C., B.D.E. and M.C.J. designed the experiments. S.H. identified EPYC1’s Rubisco-binding regions by peptide tiling array and surface plasmon resonance. S.H. and S.A.P. prepared the Rubisco and EPYC1 peptide samples for single-particle cryo-electron microscopy. S.H., S.A.P. and G.H. prepared the Rubisco samples for peptide tiling array and surface plasmon resonance experiments. H.-T.C., D.M. and Z.Y. performed the cryo-electron microscopy grid preparation, sample screening, data acquisition, image processing, reconstruction and map generation. D.M. and P.D.J. carried out the single-particle model building and fitting and refinement. S.H., H.-T.C., D.M., P.D.J., F.M.H. and M.C.J. analysed the structures. S.H. and W.P. analysed EPYC1 binding to Rubisco by peptide substitution array and surface plasmon resonance experiments. T.W. performed the in vitro reconstitution phase separation experiments. N.A. and A.J.M. performed the yeast two-hybrid experiments. S.H. and M.T.M. made the Rubisco small subunit point mutants. S.H. performed the spot test experiments. M.T.M. performed the transmission electron microscopy. A.M.-S. performed the cryo-electron tomography data analysis and modelling. S.H. and M.C.J. wrote the manuscript. All authors read and commented on the manuscript.

Corresponding author

Correspondence to Martin C. Jonikas.

Ethics declarations

Competing interests

Princeton University and HHMI have submitted a provisional patent application on aspects of the findings.

Additional information

Peer review information Nature Plants thanks Jean-David Rochaix and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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

Extended data

Extended Data Fig. 1 The EPYC1 peptides with the highest binding affinities to Rubisco were chosen for structural studies.

a, Diagram indicating the differences between the previously defined sequence repeats10 and the newly defined sequence repeats on full-length EPYC1. b, To verify the Rubisco-binding regions on EPYC1, surface plasmon resonance (SPR) was used to measure the binding of EPYC1 peptides to Rubisco. Purified Rubisco was immobilized on a sensor surface, and the EPYC1 peptides in solution were injected over the surface. The binding activity was recorded in real time in a sensorgram. c, The peptides used in SPR experiments are shown aligned to the sequence as shown in Fig. 1. The Rubisco-binding signal from the SPR experiment of each peptide is shown after normalization to the peptide’s molecular weight. EPYC149-72 (boxed in red) and EPYC1106-135 (boxed in pink) were chosen for structural studies based on their reproducible high Rubisco binding signal. d, The Rubisco-binding response of the EPYC149-72 peptide at different concentrations was measured by SPR. e, The binding responses shown in (d) were fitted to estimate the KD of EPYC149-72 peptide binding to Rubisco.

Extended Data Fig. 2 Single-particle cryo-EM data collection and image processing procedure.

a-c, Representative micrographs of the apo Rubisco sample (a), the Rubisco-EPYC149-72 complex (b) and the Rubisco-EPYC1106-135 complex (c). Scale bars = 100 nm. d-f, Representative 2D class averages of the apo Rubisco sample (d), the Rubisco-EPYC149-72 complexes (e) and the Rubisco-EPYC1106-135 complexes (f). g-i, Overview of the workflow for single-particle data processing for the apo Rubisco sample (g), the Rubisco-EPYC149-72 sample (h) and the Rubisco-EPYC1106-135 sample (i). j-l, Local resolution estimation of the final refined apo Rubisco map (j), the final refined Rubisco-EPYC149-72 complex map (k) and the final refined Rubisco-EPYC1106-135 complex map (l).

Extended Data Fig. 3 Cryo-EM analysis and resolution of apo Rubisco and Rubisco-EPYC1 peptide complexes in this study.

a-b, Representative cryo-EM density quality showing an α-helix of residues 214-232 in chain A (one of the Rubisco large subunits) (a) and a β-sheet of residues 36-43 in chain A (b) of the Rubisco-EPYC149-72 density map and structural model. The densities are shown as meshwork in gray. The backbones of the structural model are in ribbon representation, and side chains are shown in stick representation. c-d, Representative cryo-EM density quality showing water molecules as orange spheres. One water molecule between R312 and E136 on chain A is shown in panel c, and another water molecule between D137 and K316 on chain A is shown in panel d. e, Fourier shell correlation (FSC) curves of the final density maps of apo Rubisco and the Rubisco-EPYC1 peptide complexes.

Extended Data Fig. 4 Comparison of our EM structure of apo Rubisco and the published X-ray crystallography structure (1gk8) of Rubisco purified from Chlamydomonas reinhardtii13, and comparison of our EM structure of apo Rubisco and Rubisco bound with EPYC149-72 peptide.

a, Comparison of the structure of the small subunit of apo Rubisco obtained here by EM with 1gk8. The EM structure has additional C-terminus density past residue 126, circled by a red dashed line. b, Comparison of our two EM structures of the small subunit: from apo Rubisco and from EPYC149-72 peptide-bound Rubisco. c, Comparison of the structure of the large subunit of apo Rubisco obtained here by EM with 1gk8. The three major differences found between the X-ray structure and the EM structure of the large subunit are circled with red dashed lines. d, Comparison of our two EM structures of the large subunit: from apo Rubisco and from EPYC149-72 peptide-bound Rubisco. The major difference found between the EPYC149-72 peptide-bound structure and the apo EM structure was the loop between K175 and L180 of the large subunit, which is shown circled by a red dashed line.

Extended Data Fig. 5 Additional residues may contribute to the interaction between EPYC1 and Rubisco.

Our Rubisco-EPYC149-72 peptide structure suggests that R56 of the EPYC149-72 peptide may interact with D31 of the Rubisco small subunit and E433 of the Rubisco large subunit (the atoms of the backbone of E433 are also shown to display the possible interaction). R51 of the EPYC149-72 peptide may form a salt bridge with Y32 of the Rubisco small subunit. Residues S57 and V58 of the EPYC149-72 peptide are close to D31 in the structure, which may explain why replacing either of these residues with a negatively charged residue disrupts binding (Fig. 4a).

Extended Data Fig. 6 The EPYC1106-135 peptide binds to Rubisco small subunit α-helices via salt bridges and a hydrophobic pocket in a similar manner to the EPYC149-72 peptide.

a, The EPYC1106-135 peptide represents the second, third and fourth Rubisco-binding regions of EPYC1 indicated by pink lines and dash line (the peptide is a perfect match to the second and fourth Rubisco-binding regions, and there is a one-amino acid difference between the peptide and the third repeat). b-c, Side view (b) and top view (c) of the density map of the EPYC1106-135 peptide-Rubisco complex. Dashes in panel b indicate regions shown in panels d-i. d-e, Front (d) and side (e) views of the EPYC1106-135 peptide (red) bound to the two α-helices of the Rubisco small subunit (blue). f-g, Three pairs of residues form salt bridges between the helix of the EPYC1106-135 peptide and the helices on the Rubisco small subunit. Shown are front (f) and side (g) views as in panel d and panel e. The distances from EPYC1 K127, R134 and E129 to Rubisco small subunit E24, D23 and R91 are 2.96 Å, 3.17 Å, and 2.68 Å, respectively. h-i, A hydrophobic pocket is formed by three residues of the EPYC1106-135 peptide and three residues of helix B of the Rubisco small subunit. Shown are front (h) and side (i) views as in panel d and panel e. j, Summary of the interactions observed between the EPYC1106-135 peptide and the two α-helices of the Rubisco small subunit. Helices are highlighted; the residues mediating interactions are bold; salt bridges are shown as dotted lines; residues contributing to the hydrophobic pocket are shown in black. k, Color keys used in this figure.

Extended Data Fig. 7 Surface plasmon resonance analysis of binding of point mutants of EPYC155-72 to Rubisco.

The wild-type (WT) peptide or peptides with the indicated mutations were synthesized, and their Rubisco-binding signal was measured by surface plasmon resonance.

Extended Data Fig. 8 Interface residues on EPYC1 identified by cryo-EM are important for binding and phase separation of EPYC1 and Rubisco.

a, SDS-PAGE analysis of purified proteins used for in vitro phase separation experiments. WT = wild-type EPYC1; R/K = EPYC1R64A/K127A/K187A/K248A/R314. b-c, A droplet sedimentation assay was used as a readout of phase separation complementary to the microscopy analyses shown in Fig. 4b. Proteins at indicated concentrations were mixed and incubated for 10 minutes, then condensates were pelleted by centrifugation. Supernatant (S) and pellet (P) fractions were run on a denaturing gel. The negative controls with no Rubisco or with no EPYC1 are shown in (b), and the wild-type Rubisco with wild-type EPYC1 or mutant EPYC1 are shown in (c). Data shown here are representative of two independent replicates.

Extended Data Fig. 9 Yeast two-hybrid assays of interactions between EPYC1 and wild-type or mutated Rubisco small subunit.

Colonies are shown after 3 days growth on plates. A subset of the data shown in this figure is shown in Fig. 5a.

Extended Data Fig. 10 Selection of the Rubisco small subunit mutant strains for phenotype analysis.

a, The Rubisco small subunit-less mutant T60 (Δrbcs) was transformed with DNA encoding wild-type and mutant Rubisco small subunits (RBCS) to produce candidate transformants with the genotypes Δrbcs;RBCSWT, Δrbcs;RBCSD23A/E24A, and Δrbcs;RBCSM87D/V94D. Total protein extracts for three strains from each transformation were separated on a polyacrylamide gel. b, The gel shown in panel a was probed by Western blot using a polyclonal antibody mixture that detects both large and small Rubisco subunits. The experiments shown in panel a and b were performed once for selecting the candidate transformants with the highest RBCS expression level from each genotype, in case any phenotype may be caused by low expression level of Rubisco. Selected strains are indicated by an arrow below the lanes and were used for the subsequent phenotypic analyses shown in Fig. 5 and panel c. c, Additional representative TEM images of whole cells of the strains expressing wild-type, D23A/E24A, and M87D/V94D Rubisco small subunit. Scale bar = 500 nm. For each strain, at least 25 images (one image for one cell) were taken and showing similar results.

Supplementary information

Supplementary Information

Supplementary Tables 1 and 2.

Reporting Summary

Supplementary Tables

Supplementary Tables 3–5.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

He, S., Chou, HT., Matthies, D. et al. The structural basis of Rubisco phase separation in the pyrenoid. Nat. Plants 6, 1480–1490 (2020). https://doi.org/10.1038/s41477-020-00811-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-020-00811-y

This article is cited by

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