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A Repeat Protein Links Rubisco to Form the Eukaryotic Carbon-Concentrating Organelle

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A Repeat Protein Links Rubisco to Form the Eukaryotic Carbon-Concentrating Organelle A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle Luke C. M. Mackindera, Moritz T. Meyerb, Tabea Mettler-Altmannc,1, Vivian K. Chena,d, Madeline C. Mitchellb,2, Oliver Casparib, Elizabeth S. Freeman Rosenzweiga,d, Leif Pallesena, Gregory Reevesa,3, Alan Itakuraa,d, Robyn Rothe, Frederik Sommerc,4, Stefan Geimerf, Timo Mühlhausc,4, Michael Schrodac,4, Ursula Goodenoughe, Mark Stittc, Howard Griffithsb, and Martin C. Jonikasa,d,5 aDepartment of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305; bDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom; cMax Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; dDepartment of Biology, Stanford University, Stanford, CA 94305; eDepartment of Biology, Washington University in Saint Louis, St. Louis, MO 63130; and fInstitute of Cell Biology, University of Bayreuth, 95440 Bayreuth, Germany Edited by Paul G. Falkowski, Rutgers, The State University of New Jersey, New Brunswick, NJ, and approved April 7, 2016 (received for review November 20, 2015) Biological carbon fixation is a key step in the global carbon cycle that traversed by membrane tubules continuous with the photosynthetic regulates the atmosphere’s composition while producing the food we thylakoid membranes (18). This matrix is thought to consist primarily eat and the fuels we burn. Approximately one-third of global carbon of tightly packed Rubisco and its chaperone, Rubisco activase (19). fixation occurs in an overlooked algal organelle called the pyrenoid. In higher plants and non–pyrenoid-containing photosynthetic eu- The pyrenoid contains the CO2-fixing enzyme Rubisco and enhances karyotes, Rubisco is instead soluble throughout the chloroplast stroma. carbon fixation by supplying Rubisco with a high concentration of The molecular mechanism by which Rubisco aggregates to form the CO2. Since the discovery of the pyrenoid more that 130 y ago, the pyrenoid matrix remains enigmatic. molecular structure and biogenesis of this ecologically fundamental Two mechanisms for Rubisco accumulation in the pyrenoid have organelle have remained enigmatic. Here we use the model green been proposed: (i) Rubisco holoenzymes could bind each other alga Chlamydomonas reinhardtii to discover that a low-complexity directly through hydrophobic residues (20), or (ii) a linker protein repeat protein, Essential Pyrenoid Component 1 (EPYC1), links Rubisco may link Rubisco holoenzymes together (18, 20). The second model CELL BIOLOGY to form the pyrenoid. We find that EPYC1 is of comparable abun- is based on analogy to the well-characterized prokaryotic carbon dance to Rubisco and colocalizes with Rubisco throughout the pyre- concentrating organelle, the β-carboxysome, where Rubisco aggre- noid. We show that EPYC1 is essential for normal pyrenoid size, gation is mediated by a linker protein consisting of repeats of a number, morphology, Rubisco content, and efficient carbon fixation at low CO2. We explain the central role of EPYC1 in pyrenoid bio- Significance genesis by the finding that EPYC1 binds Rubisco to form the pyrenoid matrix. We propose two models in which EPYC1’s four repeats could Eukaryotic algae, which play a fundamental role in global CO produce the observed lattice arrangement of Rubisco in the Chlamy- 2 fixation, enhance the performance of the carbon-fixing enzyme domonas pyrenoid. Our results suggest a surprisingly simple molecu- Rubisco by placing it into an organelle called the pyrenoid. De- lar mechanism for how Rubisco can be packaged to form the pyrenoid spite the ubiquitous presence and biogeochemical importance of matrix, potentially explaining how Rubisco packaging into a pyrenoid this organelle, how Rubisco assembles to form the pyrenoid could have evolved across a broad range of photosynthetic eukary- remains a long-standing mystery. Our discovery of an abundant otes through convergent evolution. In addition, our findings repre- repeat protein that binds Rubisco in the pyrenoid represents a sent a key step toward engineering a pyrenoid into crops to enhance critical advance in our understanding of pyrenoid biogenesis. their carbon fixation efficiency. The repeat sequence of this protein suggests elegant models to explain the structural arrangement of Rubisco enzymes in the pyrenoid | Rubisco | carbon fixation | Chlamydomonas reinhardtii | pyrenoid. Beyond advances in basic understanding, our findings CO -concentrating mechanism 2 open doors to the engineering of algal pyrenoids into crops to enhance yields. ubisco, the most abundant enzyme in the biosphere (1), fixes RCO2 into organic carbon that supports nearly all life on Earth Author contributions: L.C.M.M., M.T.M., T.M.-A., M. Schroda, M. Stitt, H.G., and M.C.J. (2, 3). Over the past 3 billion y, the enzyme became a victim of its designed research; L.C.M.M., M.T.M., T.M.-A., V.K.C., M.C.M., O.C., E.S.F.R., L.P., G.R., A.I., own success as it drew down the atmospheric CO concentration to R.R., F.S., S.G., and T.M. performed research; L.C.M.M., M.T.M., T.M.-A., L.P., M. Schroda, 2 and U.G. contributed new reagents/analytic tools; L.C.M.M., M.T.M., T.M.-A., M.C.M., F.S., trace levels (4) and as the oxygen-producing reactions of photo- S.G., T.M., and M.C.J. analyzed data; and L.C.M.M., M.T.M., T.M.-A., U.G., M. Stitt, H.G., synthesis filled our atmosphere with O2 (4). In today’s atmosphere, and M.C.J. wrote the paper. O2 competes with CO2 at Rubisco’s catalytic site, producing the Conflict of interest statement: The authors wish to note that the Carnegie Institution for toxic compound phosphoglycolate (5). Phosphoglycolate must be Science has submitted a provisional patent application on aspects of the findings. metabolized at the expense of energy and loss of fixed carbon and This article is a PNAS Direct Submission. nitrogen (6). To overcome Rubisco’s limitations, many photosyn- Freely available online through the PNAS open access option. thetic organisms have evolved carbon-concentrating mechanisms 1Present address: Cluster of Excellence in Plant Sciences and Institute of Plant Biochemis- try, Heinrich-Heine University, 40225 Düsseldorf, Germany. (CCMs) (7, 8). CCMs increase the CO2 concentration around 2Present address: Agriculture, Commonwealth Scientific and Industrial Research Organi- Rubisco, decreasing O2 competition and enhancing carbon fixation. At the heart of the CCM of eukaryotic algae is an organelle zation, Canberra, ACT 2601, Australia. 3Present address: Department of Plant Sciences, University of Cambridge, Cambridge CB2 known as the pyrenoid (9). The pyrenoid is a spherical structure in 3EA, United Kingdom. the chloroplast stroma, discovered more than 130 y ago (10–12). 4Present address: Institute of Molecular Biotechnology and Systems Biology, Technical Pyrenoids have been found in nearly all of the major oceanic University of Kaiserslautern, 67663 Kaiserslautern, Germany. ∼ – eukaryotic primary producers and mediate 28 44% of global 5To whom correspondence should be addressed. Email: [email protected]. SI Appendix – carbon fixation ( ,TableS1)(3,1317). A pyrenoid This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. typically consists of a matrix surrounded by a starch sheath and 1073/pnas.1522866113/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1522866113 PNAS Early Edition | 1of6 Downloaded by guest on September 26, 2021 pyrenoid fraction was increased by ∼12-fold after the shift from high ABLow CO 9 2 to low CO (Fig. 1B and SI Appendix,Fig.S1D and Dataset S1), an rbcL 2 8 increase similar to that of rbcL (7-fold), RBCS (7-fold), and RCA1 RBCS EPYC1 (19-fold). To confirm the pyrenoid localization of EPYC1, we 7 coexpressed fluorescently tagged EPYC1 and RBCS. Venus-tagged RCA1 EPYC1 showed clear colocalization with mCherry-tagged RBCS in Whole cell 6 the pyrenoid (Fig. 1C and SI Appendix,Fig.S1E). pyrenoid fraction 2 5 protein abundance in EPYC1 Is Essential for a Functional CCM. The high abundance of 10 4 EPYC1 in the pyrenoid led us to ask whether EPYC1 is required low CO Log for the CCM. We isolated a mutant in the 5′ UTR of the EPYC1 3 Pellet gene (SI Appendix,Fig.S2A and Table S2), which contains mark- -4 -3 -2 -1 0 1 2 3 4 5 EPYC1 SI Appendix B Log protein abundance change (low CO edly reduced levels of mRNA ( ,Fig.S2 and 2 2 Table S3) and EPYC1 protein (Fig. 2A), and lacks transcriptional pyrenoid fraction / high CO2 pyrenoid fraction) regulation in response to CO2 (SI Appendix,Fig.S2B). Similar to C Venus mCherry Chlorophyll previously described mutants in other components of the CCM, the epyc1 mutant showed defective photoautotrophic growth in low CO2, which was rescued by high CO2 and by reintroducing the EPYC1 gene (Fig. 2B and SI Appendix,Fig.S2C–E). We further tested the CCM activity in the epyc1 mutant by measuring whole-cell affinity for inorganic carbon, inferred from photosynthetic O2 evolution. When grown under low CO2,the epyc1 mutant showed a reduced affinity for inorganic carbon (in- Fig. 1. EPYC1 is an abundant pyrenoid protein. (A) TEM images of Chlamy- creased K0.5)relativetoWT(P = 0.0055, Student’s t test; n = 5) domonas whole cells and pyrenoid-enriched pellet fraction from cells grown at C SI Appendix F low CO . The yellow arrow indicates the pyrenoid, and green arrows indicate (Fig. 2 and ,Fig.S2 and Table S4). The affinity of the 2 epyc1 pyrenoid-like structures. (Scale bar: 2 μm.) (B) Mass spectrometry analysis of 366 mutant under low CO2 was slightly greater than that of WT at proteins in pyrenoid-enriched pellet fractions from low- and high-CO2–grown high CO2, indicating a residual level of CCM activity. This activity cells (mean of four biological replicates; raw data are provided in SI Appendix may be due to trace levels of EPYC1 in the epyc1 mutant (SI Ap- and Dataset S1).
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