1
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Nguyen ND, Pulsford SB, Förster B, Rottet S, Rourke L, Long BM, Price GD. A carboxysome-based CO 2 concentrating mechanism for C 3 crop chloroplasts: advances and the road ahead. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:940-952. [PMID: 38321620 DOI: 10.1111/tpj.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
The introduction of the carboxysome-based CO2 concentrating mechanism (CCM) into crop plants has been modelled to significantly increase crop yields. This projection serves as motivation for pursuing this strategy to contribute to global food security. The successful implementation of this engineering challenge is reliant upon the transfer of a microcompartment that encapsulates cyanobacterial Rubisco, known as the carboxysome, alongside active bicarbonate transporters. To date, significant progress has been achieved with respect to understanding various aspects of the cyanobacterial CCM, and more recently, different components of the carboxysome have been successfully introduced into plant chloroplasts. In this Perspective piece, we summarise recent findings and offer new research avenues that will accelerate research in this field to ultimately and successfully introduce the carboxysome into crop plants for increased crop yields.
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Affiliation(s)
- Nghiem D Nguyen
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sacha B Pulsford
- Research School of Chemistry, Australian National University, 137 Sullivan's Ck Rd, Acton, Australian Capital Territory, 2601, Australia
| | - Britta Förster
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sarah Rottet
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Loraine Rourke
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Benedict M Long
- Discipline of Biological Sciences, School of Environmental and Life Sciences, ARC Centre of Excellence in Synthetic Biology, The University of Newcastle, University Drive, Callaghan, New South Wales, 2308, Australia
| | - G Dean Price
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
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2
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Plouviez M, Dubreucq E. Key Proteomics Tools for Fundamental and Applied Microalgal Research. Proteomes 2024; 12:13. [PMID: 38651372 PMCID: PMC11036299 DOI: 10.3390/proteomes12020013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.
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Affiliation(s)
- Maxence Plouviez
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
- The Cawthron Institute, Nelson 7010, New Zealand
| | - Eric Dubreucq
- Agropolymer Engineering and Emerging Technologies, L’Institut Agro Montpellier, 34060 Montpellier, France;
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3
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Moromizato R, Fukuda K, Suzuki S, Motomura T, Nagasato C, Hirakawa Y. Pyrenoid proteomics reveals independent evolution of the CO 2-concentrating organelle in chlorarachniophytes. Proc Natl Acad Sci U S A 2024; 121:e2318542121. [PMID: 38408230 PMCID: PMC10927497 DOI: 10.1073/pnas.2318542121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/25/2024] [Indexed: 02/28/2024] Open
Abstract
Pyrenoids are microcompartments that are universally found in the photosynthetic plastids of various eukaryotic algae. They contain ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and play a pivotal role in facilitating CO2 assimilation via CO2-concentrating mechanisms (CCMs). Recent investigations involving model algae have revealed that pyrenoid-associated proteins participate in pyrenoid biogenesis and CCMs. However, these organisms represent only a small part of algal lineages, which limits our comprehensive understanding of the diversity and evolution of pyrenoid-based CCMs. Here we report a pyrenoid proteome of the chlorarachniophyte alga Amorphochlora amoebiformis, which possesses complex plastids acquired through secondary endosymbiosis with green algae. Proteomic analysis using mass spectrometry resulted in the identification of 154 potential pyrenoid components. Subsequent localization experiments demonstrated the specific targeting of eight proteins to pyrenoids. These included a putative Rubisco-binding linker, carbonic anhydrase, membrane transporter, and uncharacterized GTPase proteins. Notably, most of these proteins were unique to this algal lineage. We suggest a plausible scenario in which pyrenoids in chlorarachniophytes have evolved independently, as their components are not inherited from green algal pyrenoids.
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Affiliation(s)
- Rena Moromizato
- Degree Programs in Life and Earth Sciences, University of Tsukuba, Tsukuba305-8572, Japan
| | - Kodai Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba305-8572, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba305-8506, Japan
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran051-0013, Japan
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran051-0013, Japan
| | - Yoshihisa Hirakawa
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba305-8572, Japan
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4
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Atkinson N, Stringer R, Mitchell SR, Seung D, McCormick AJ. SAGA1 and SAGA2 promote starch formation around proto-pyrenoids in Arabidopsis chloroplasts. Proc Natl Acad Sci U S A 2024; 121:e2311013121. [PMID: 38241434 PMCID: PMC10823261 DOI: 10.1073/pnas.2311013121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024] Open
Abstract
The pyrenoid is a chloroplastic microcompartment in which most algae and some terrestrial plants condense the primary carboxylase, Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) as part of a CO2-concentrating mechanism that improves the efficiency of CO2 capture. Engineering a pyrenoid-based CO2-concentrating mechanism (pCCM) into C3 crop plants is a promising strategy to enhance yield capacities and resilience to the changing climate. Many pyrenoids are characterized by a sheath of starch plates that is proposed to act as a barrier to limit CO2 diffusion. Recently, we have reconstituted a phase-separated "proto-pyrenoid" Rubisco matrix in the model C3 plant Arabidopsis thaliana using proteins from the alga with the most well-studied pyrenoid, Chlamydomonas reinhardtii [N. Atkinson, Y. Mao, K. X. Chan, A. J. McCormick, Nat. Commun. 11, 6303 (2020)]. Here, we describe the impact of introducing the Chlamydomonas proteins StArch Granules Abnormal 1 (SAGA1) and SAGA2, which are associated with the regulation of pyrenoid starch biogenesis and morphology. We show that SAGA1 localizes to the proto-pyrenoid in engineered Arabidopsis plants, which results in the formation of atypical spherical starch granules enclosed within the proto-pyrenoid condensate and adjacent plate-like granules that partially cover the condensate, but without modifying the total amount of chloroplastic starch accrued. Additional expression of SAGA2 further increases the proportion of starch synthesized as adjacent plate-like granules that fully encircle the proto-pyrenoid. Our findings pave the way to assembling a diffusion barrier as part of a functional pCCM in vascular plants, while also advancing our understanding of the roles of SAGA1 and SAGA2 in starch sheath formation and broadening the avenues for engineering starch morphology.
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Affiliation(s)
- Nicky Atkinson
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
- Centre of Engineering Biology, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
| | - Rhea Stringer
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, NorwichNR4 7UH, United Kingdom
| | - Stephen R. Mitchell
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
| | - David Seung
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, NorwichNR4 7UH, United Kingdom
| | - Alistair J. McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
- Centre of Engineering Biology, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
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5
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He S, Crans VL, Jonikas MC. The pyrenoid: the eukaryotic CO2-concentrating organelle. THE PLANT CELL 2023; 35:3236-3259. [PMID: 37279536 PMCID: PMC10473226 DOI: 10.1093/plcell/koad157] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023]
Abstract
The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.
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Affiliation(s)
- Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| | - Victoria L Crans
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
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6
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An Y, Wang D, Du J, Wang X, Xiao J. Pyrenoid: Organelle with efficient CO 2-Concentrating mechanism in algae. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154044. [PMID: 37392525 DOI: 10.1016/j.jplph.2023.154044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/18/2023] [Indexed: 07/03/2023]
Abstract
The carbon dioxide emitted by human accounts for only a small fraction of global photosynthesis consumption, half of which is due to microalgae. The high efficiency of algae photosynthesis is attributed to the pyrenoid-based CO2-concentrating mechanism (CCM). The formation of pyrenoid which has a variety of Rubisco-binding proteins mainly depends on liquid-liquid phase separation (LLPS) of Rubisco, a CO2 fixing enzyme. At present, our understanding of pyrenoid at the molecular level mainly stems from studies of the model algae Chlamydomonas reinhardtii. In this article, we summarize the current research on the structure, assembly and application of Chlamydomonas reinhardtii pyrenoids, providing new ideas for improving crop photosynthetic performance and yield.
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Affiliation(s)
- Yaqi An
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Dong Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Jingxia Du
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Xinwei Wang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, China.
| | - Jianwei Xiao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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7
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Findinier J, Grossman AR. Chlamydomonas: Fast tracking from genomics. JOURNAL OF PHYCOLOGY 2023; 59:644-652. [PMID: 37417760 DOI: 10.1111/jpy.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.
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Affiliation(s)
- Justin Findinier
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| | - Arthur R Grossman
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
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8
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Ang WSL, How JA, How JB, Mueller-Cajar O. The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:612-626. [PMID: 35903998 DOI: 10.1093/jxb/erac321] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme's active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid-liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid-liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure-function relationship of phase separation in biology.
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Affiliation(s)
- Warren Shou Leong Ang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Ann How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Boon How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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9
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Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. The small subunit of Rubisco and its potential as an engineering target. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:543-561. [PMID: 35849331 PMCID: PMC9833052 DOI: 10.1093/jxb/erac309] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 05/06/2023]
Abstract
Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
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Affiliation(s)
| | | | - Aranzazú Díaz-Ramos
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - George R L Greiff
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stavros Azinas
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Laura Gunn
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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10
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He G, GrandPre T, Wilson H, Zhang Y, Jonikas MC, Wingreen NS, Wang Q. Phase-separating pyrenoid proteins form complexes in the dilute phase. Commun Biol 2023; 6:19. [PMID: 36611062 PMCID: PMC9825591 DOI: 10.1038/s42003-022-04373-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
While most studies of biomolecular phase separation have focused on the condensed phase, relatively little is known about the dilute phase. Theory suggests that stable complexes form in the dilute phase of two-component phase-separating systems, impacting phase separation; however, these complexes have not been interrogated experimentally. We show that such complexes indeed exist, using an in vitro reconstitution system of a phase-separated organelle, the algal pyrenoid, consisting of purified proteins Rubisco and EPYC1. Applying fluorescence correlation spectroscopy (FCS) to measure diffusion coefficients, we found that complexes form in the dilute phase with or without condensates present. The majority of these complexes contain exactly one Rubisco molecule. Additionally, we developed a simple analytical model which recapitulates experimental findings and provides molecular insights into the dilute phase organization. Thus, our results demonstrate the existence of protein complexes in the dilute phase, which could play important roles in the stability, dynamics, and regulation of condensates.
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Affiliation(s)
- Guanhua He
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Trevor GrandPre
- grid.16750.350000 0001 2097 5006Department of Physics, Princeton University, Princeton, NJ 08544 USA ,grid.16750.350000 0001 2097 5006Center for the Physics of Biological Function, Princeton University, Princeton, NJ USA
| | - Hugh Wilson
- grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA
| | - Yaojun Zhang
- grid.16750.350000 0001 2097 5006Center for the Physics of Biological Function, Princeton University, Princeton, NJ USA ,grid.21107.350000 0001 2171 9311Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Biophysics, Johns Hopkins University, Baltimore, MD USA
| | - Martin C. Jonikas
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA ,grid.16750.350000 0001 2097 5006Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544 USA
| | - Ned S. Wingreen
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA
| | - Quan Wang
- grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA ,grid.419635.c0000 0001 2203 7304Present Address: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MA 20892 USA
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11
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Adler L, Díaz-Ramos A, Mao Y, Pukacz KR, Fei C, McCormick AJ. New horizons for building pyrenoid-based CO2-concentrating mechanisms in plants to improve yields. PLANT PHYSIOLOGY 2022; 190:1609-1627. [PMID: 35961043 PMCID: PMC9614477 DOI: 10.1093/plphys/kiac373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/06/2022] [Indexed: 05/06/2023]
Abstract
Many photosynthetic species have evolved CO2-concentrating mechanisms (CCMs) to improve the efficiency of CO2 assimilation by Rubisco and reduce the negative impacts of photorespiration. However, the majority of plants (i.e. C3 plants) lack an active CCM. Thus, engineering a functional heterologous CCM into important C3 crops, such as rice (Oryza sativa) and wheat (Triticum aestivum), has become a key strategic ambition to enhance yield potential. Here, we review recent advances in our understanding of the pyrenoid-based CCM in the model green alga Chlamydomonas reinhardtii and engineering progress in C3 plants. We also discuss recent modeling work that has provided insights into the potential advantages of Rubisco condensation within the pyrenoid and the energetic costs of the Chlamydomonas CCM, which, together, will help to better guide future engineering approaches. Key findings include the potential benefits of Rubisco condensation for carboxylation efficiency and the need for a diffusional barrier around the pyrenoid matrix. We discuss a minimal set of components for the CCM to function and that active bicarbonate import into the chloroplast stroma may not be necessary for a functional pyrenoid-based CCM in planta. Thus, the roadmap for building a pyrenoid-based CCM into plant chloroplasts to enhance the efficiency of photosynthesis now appears clearer with new challenges and opportunities.
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Affiliation(s)
| | | | - Yuwei Mao
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Krzysztof Robin Pukacz
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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12
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Iñiguez C, Aguiló-Nicolau P, Galmés J. Improving photosynthesis through the enhancement of Rubisco carboxylation capacity. Biochem Soc Trans 2021; 49:2007-2019. [PMID: 34623388 DOI: 10.1042/bst20201056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022]
Abstract
Rising human population, along with the reduction in arable land and the impacts of global change, sets out the need for continuously improving agricultural resource use efficiency and crop yield (CY). Bioengineering approaches for photosynthesis optimization have largely demonstrated the potential for enhancing CY. This review is focused on the improvement of Rubisco functioning, which catalyzes the rate-limiting step of CO2 fixation required for plant growth, but also catalyzes the ribulose-bisphosphate oxygenation initiating the carbon and energy wasteful photorespiration pathway. Rubisco carboxylation capacity can be enhanced by engineering the Rubisco large and/or small subunit genes to improve its catalytic traits, or by engineering the mechanisms that provide enhanced Rubisco expression, activation and/or elevated [CO2] around the active sites to favor carboxylation over oxygenation. Recent advances have been made in the expression, assembly and activation of foreign (either natural or mutant) faster and/or more CO2-specific Rubisco versions. Some components of CO2 concentrating mechanisms (CCMs) from bacteria, algae and C4 plants has been successfully expressed in tobacco and rice. Still, none of the transformed plant lines expressing foreign Rubisco versions and/or simplified CCM components were able to grow faster than wild type plants under present atmospheric [CO2] and optimum conditions. However, the results obtained up to date suggest that it might be achievable in the near future. In addition, photosynthetic and yield improvements have already been observed when manipulating Rubisco quantity and activation degree in crops. Therefore, engineering Rubisco carboxylation capacity continues being a promising target for the improvement in photosynthesis and yield.
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Affiliation(s)
- Concepción Iñiguez
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
- Department of Ecology, Faculty of Sciences, University of Málaga, Málaga, Spain
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
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13
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Barrett J, Girr P, Mackinder LCM. Pyrenoids: CO 2-fixing phase separated liquid organelles. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118949. [PMID: 33421532 DOI: 10.1016/j.bbamcr.2021.118949] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 02/06/2023]
Abstract
Pyrenoids are non-membrane bound organelles found in chloroplasts of algae and hornwort plants that can be seen by light-microscopy. Pyrenoids are formed by liquid-liquid phase separation (LLPS) of Rubisco, the primary CO2 fixing enzyme, with an intrinsically disordered multivalent Rubisco-binding protein. Pyrenoids are the heart of algal and hornwort biophysical CO2 concentrating mechanisms, which accelerate photosynthesis and mediate about 30% of global carbon fixation. Even though LLPS may underlie the apparent convergent evolution of pyrenoids, our current molecular understanding of pyrenoid formation comes from a single example, the model alga Chlamydomonas reinhardtii. In this review, we summarise current knowledge about pyrenoid assembly, regulation and structural organization in Chlamydomonas and highlight evidence that LLPS is the general principle underlying pyrenoid formation across algal lineages and hornworts. Detailed understanding of the principles behind pyrenoid assembly, regulation and structural organization within diverse lineages will provide a fundamental understanding of this biogeochemically important organelle and help guide ongoing efforts to engineer pyrenoids into crops to increase photosynthetic performance and yields.2.
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Affiliation(s)
- James Barrett
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Department of Biology, University of York, York YO10 5DD, UK
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14
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Matsuzaki R, Suzuki S, Yamaguchi H, Kawachi M, Kanesaki Y, Yoshikawa H, Mori T, Nozaki H. The Rubisco small subunits in the green algal genus Chloromonas provide insights into evolutionary loss of the eukaryotic carbon-concentrating organelle, the pyrenoid. BMC Ecol Evol 2021; 21:11. [PMID: 33514317 PMCID: PMC7853309 DOI: 10.1186/s12862-020-01733-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/10/2020] [Indexed: 12/14/2022] Open
Abstract
Background Pyrenoids are protein microcompartments composed mainly of Rubisco that are localized in the chloroplasts of many photosynthetic organisms. Pyrenoids contribute to the CO2-concentrating mechanism. This organelle has been lost many times during algal/plant evolution, including with the origin of land plants. The molecular basis of the evolutionary loss of pyrenoids is a major topic in evolutionary biology. Recently, it was hypothesized that pyrenoid formation is controlled by the hydrophobicity of the two helices on the surface of the Rubisco small subunit (RBCS), but the relationship between hydrophobicity and pyrenoid loss during the evolution of closely related algal/plant lineages has not been examined. Here, we focused on, the Reticulata group of the unicellular green algal genus Chloromonas, within which pyrenoids are present in some species, although they are absent in the closely related species. Results Based on de novo transcriptome analysis and Sanger sequencing of cloned reverse transcription-polymerase chain reaction products, rbcS sequences were determined from 11 strains of two pyrenoid-lacking and three pyrenoid-containing species of the Reticulata group. We found that the hydrophobicity of the RBCS helices was roughly correlated with the presence or absence of pyrenoids within the Reticulata group and that a decrease in the hydrophobicity of the RBCS helices may have primarily caused pyrenoid loss during the evolution of this group. Conclusions Although we suggest that the observed correlation may only exist for the Reticulata group, this is still an interesting study that provides novel insight into a potential mechanism determining initial evolutionary steps of gain and loss of the pyrenoid.
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Affiliation(s)
- Ryo Matsuzaki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.,NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Toshiyuki Mori
- Department of Tropical Medicine and Parasitology, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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15
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Donovan S, Mao Y, Orr DJ, Carmo-Silva E, McCormick AJ. CRISPR-Cas9-Mediated Mutagenesis of the Rubisco Small Subunit Family in Nicotiana tabacum. Front Genome Ed 2020; 2:605614. [PMID: 34713229 PMCID: PMC8525408 DOI: 10.3389/fgeed.2020.605614] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
Engineering the small subunit of the key CO2-fixing enzyme Rubisco (SSU, encoded by rbcS) in plants currently poses a significant challenge, as many plants have polyploid genomes and SSUs are encoded by large multigene families. Here, we used CRISPR-Cas9-mediated genome editing approach to simultaneously knock-out multiple rbcS homologs in the model tetraploid crop tobacco (Nicotiana tabacum cv. Petit Havana). The three rbcS homologs rbcS_S1a, rbcS_S1b and rbcS_T1 account for at least 80% of total rbcS expression in tobacco. In this study, two multiplexing guide RNAs (gRNAs) were designed to target homologous regions in these three genes. We generated tobacco mutant lines with indel mutations in all three genes, including one line with a 670 bp deletion in rbcS-T1. The Rubisco content of three selected mutant lines in the T1 generation was reduced by ca. 93% and mutant plants accumulated only 10% of the total biomass of wild-type plants. As a second goal, we developed a proof-of-principle approach to simultaneously introduce a non-native rbcS gene while generating the triple SSU knockout by co-transformation into a wild-type tobacco background. Our results show that CRISPR-Cas9 is a viable tool for the targeted mutagenesis of rbcS families in polyploid species and will contribute to efforts aimed at improving photosynthetic efficiency through expression of superior non-native Rubisco enzymes in plants.
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Affiliation(s)
- Sophie Donovan
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yuwei Mao
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Douglas J. Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | | | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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16
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Atkinson N, Mao Y, Chan KX, McCormick AJ. Condensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts. Nat Commun 2020; 11:6303. [PMID: 33298923 PMCID: PMC7726157 DOI: 10.1038/s41467-020-20132-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022] Open
Abstract
Photosynthetic CO2 fixation in plants is limited by the inefficiency of the CO2-assimilating enzyme Rubisco. In most eukaryotic algae, Rubisco aggregates within a microcompartment known as the pyrenoid, in association with a CO2-concentrating mechanism that improves photosynthetic operating efficiency under conditions of low inorganic carbon. Recent work has shown that the pyrenoid matrix is a phase-separated, liquid-like condensate. In the alga Chlamydomonas reinhardtii, condensation is mediated by two components: Rubisco and the linker protein EPYC1 (Essential Pyrenoid Component 1). Here, we show that expression of mature EPYC1 and a plant-algal hybrid Rubisco leads to spontaneous condensation of Rubisco into a single phase-separated compartment in Arabidopsis chloroplasts, with liquid-like properties similar to a pyrenoid matrix. This work represents a significant initial step towards enhancing photosynthesis in higher plants by introducing an algal CO2-concentrating mechanism, which is predicted to significantly increase the efficiency of photosynthetic CO2 uptake.
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Affiliation(s)
- Nicky Atkinson
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Yuwei Mao
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Kher Xing Chan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 Gregory Drive, Urbana, IL, 61801, USA
| | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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17
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Yang X, Medford JI, Markel K, Shih PM, De Paoli HC, Trinh CT, McCormick AJ, Ployet R, Hussey SG, Myburg AA, Jensen PE, Hassan MM, Zhang J, Muchero W, Kalluri UC, Yin H, Zhuo R, Abraham PE, Chen JG, Weston DJ, Yang Y, Liu D, Li Y, Labbe J, Yang B, Lee JH, Cottingham RW, Martin S, Lu M, Tschaplinski TJ, Yuan G, Lu H, Ranjan P, Mitchell JC, Wullschleger SD, Tuskan GA. Plant Biosystems Design Research Roadmap 1.0. BIODESIGN RESEARCH 2020; 2020:8051764. [PMID: 37849899 PMCID: PMC10521729 DOI: 10.34133/2020/8051764] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/30/2020] [Indexed: 10/19/2023] Open
Abstract
Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - June I. Medford
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Henrique C. De Paoli
- Department of Biodesign, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cong T. Trinh
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1858, Frederiksberg, Copenhagen, Denmark
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology and the Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jessy Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jun Hyung Lee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Stanton Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Stan D. Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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18
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Wunder T, Mueller-Cajar O. Biomolecular condensates in photosynthesis and metabolism. CURRENT OPINION IN PLANT BIOLOGY 2020; 58:1-7. [PMID: 32966943 DOI: 10.1016/j.pbi.2020.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/29/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
The transient assembly or sequestration of enzymes into clusters permits the channeling of metabolites, but requires spatiotemporal control. Liquid liquid phase separation (LLPS) has recently emerged as a fundamental concept enabling formation of such assemblies into non-membrane bound organelles. The role of LLPS in the formation of condensates containing the CO2-fixing enzyme Rubisco has recently become appreciated. Both prokaryotic carboxysomes and eukaryotic pyrenoids enhance the carboxylation reaction by enabling the saturation of the enzyme with CO2 gas. Biochemical reconstitution and structural biology are revealing the mechanistic basis of these photosynthetic condensates. At the same time other enzyme clusters, such as purinosomes for de-novo purine biosynthesis and G-bodies containing glycolytic enzymes, are emerging to behave like phase-separated systems. In the near future we anticipate details of many more such metabolic condensates to be revealed, deeply informing our ability to influence metabolic fluxes.
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Affiliation(s)
- Tobias Wunder
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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19
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He S, Chou HT, Matthies D, Wunder T, Meyer MT, Atkinson N, Martinez-Sanchez A, Jeffrey PD, Port SA, Patena W, He G, Chen VK, Hughson FM, McCormick AJ, Mueller-Cajar O, Engel BD, Yu Z, Jonikas MC. The structural basis of Rubisco phase separation in the pyrenoid. NATURE PLANTS 2020; 6:1480-1490. [PMID: 33230314 PMCID: PMC7736253 DOI: 10.1038/s41477-020-00811-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/21/2020] [Indexed: 05/04/2023]
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.
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Affiliation(s)
- Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hui-Ting Chou
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Therapeutic Discovery, Amgen Discovery Research, Amgen Inc., South San Francisco, CA, USA
| | - Doreen Matthies
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Tobias Wunder
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nicky Atkinson
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Antonio Martinez-Sanchez
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Neuropathology, University of Göttingen Medical Center, Göttingen, Germany
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sarah A Port
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Guanhua He
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Vivian K Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Zhiheng Yu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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20
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Meyer MT, Itakura AK, Patena W, Wang L, He S, Emrich-Mills T, Lau CS, Yates G, Mackinder LCM, Jonikas MC. Assembly of the algal CO 2-fixing organelle, the pyrenoid, is guided by a Rubisco-binding motif. SCIENCE ADVANCES 2020; 6:eabd2408. [PMID: 33177094 PMCID: PMC7673724 DOI: 10.1126/sciadv.abd2408] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/25/2020] [Indexed: 05/05/2023]
Abstract
Approximately one-third of the Earth's photosynthetic CO2 assimilation occurs in a pyrenoid, an organelle containing the CO2-fixing enzyme Rubisco. How constituent proteins are recruited to the pyrenoid and how the organelle's subcompartments-membrane tubules, a surrounding phase-separated Rubisco matrix, and a peripheral starch sheath-are held together is unknown. Using the model alga Chlamydomonas reinhardtii, we found that pyrenoid proteins share a sequence motif. We show that the motif is necessary and sufficient to target proteins to the pyrenoid and that the motif binds to Rubisco, suggesting a mechanism for targeting. The presence of the Rubisco-binding motif on proteins that localize to the tubules and on proteins that localize to the matrix-starch sheath interface suggests that the motif holds the pyrenoid's three subcompartments together. Our findings advance our understanding of pyrenoid biogenesis and illustrate how a single protein motif can underlie the architecture of a complex multilayered phase-separated organelle.
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Affiliation(s)
- Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alan K Itakura
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Chun S Lau
- Department of Biology, University of York, York YO10 5DD, UK
| | - Gary Yates
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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21
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Elucidation and genetic intervention of CO2 concentration mechanism in Chlamydomonas reinhardtii for increased plant primary productivity. J Biosci 2020. [DOI: 10.1007/s12038-020-00080-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Chaperone Machineries of Rubisco – The Most Abundant Enzyme. Trends Biochem Sci 2020; 45:748-763. [DOI: 10.1016/j.tibs.2020.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/19/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
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23
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Oleksienko AA, Kot YG, Komaristaya VP. DNA-Specific DAPI Staining of the Pyrenoid Matrix During its Fission in Dunaliella salina (Dunal) Teodoresco (Chlorophyta). Curr Microbiol 2020; 77:3450-3459. [PMID: 32780204 DOI: 10.1007/s00284-020-02159-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 08/03/2020] [Indexed: 11/29/2022]
Abstract
The algal pyrenoid is a naked phase-separated liquid compartment inside the chloroplast consisting predominantly of densely packaged Rubisco and most often transversed by a system of lipid membranes. The pyrenoid participates in carbon-concentrating mechanisms of algae. During the cell division, the daughter cells of algae acquire the pyrenoids via their assembly or fission, the mechanisms of which are not fully understood. We suppose that the chloroplast nucleoid scaffolds the new pyrenoid like the cyanobacterial nucleoid positions carboxysomes before the cell division. This work was aimed at visualization and localization of the chloroplast DNA relative to the pyrenoid in synchronously dividing cells of Dunaliella salina with DNA-specific fluorescent DAPI stain through the fluorescent confocal microscope. The intense DNA-specific blue DAPI fluorescence was discovered in the pyrenoids matrix under the starch shell in the presumably pre-mitotic cells, during and following the pyrenoid fission. In the interphase cells, the chloroplast DNA localized both in the pyrenoid core and in several small nucleoids on the outer surface of the starch shell around the pyrenoid. The observations were compared with the literature data on the same and other algal species. The spatial pre-requisite exists in D. salina for the chloroplast nucleoid to scaffold the pyrenoid fission. A potential alternative explanation was declared being the algal pyrenoid as the chloroplast genetic center. The theoretical and practical implications of the findings were discussed.
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Affiliation(s)
- Anna A Oleksienko
- The School of Biology, V.N. Karazin Kharkiv National University, Svobody sq., 4, Kharkiv, 61022, Ukraine
| | - Yurii G Kot
- The School of Biology, V.N. Karazin Kharkiv National University, Svobody sq., 4, Kharkiv, 61022, Ukraine
| | - Victoria P Komaristaya
- The School of Biology, V.N. Karazin Kharkiv National University, Svobody sq., 4, Kharkiv, 61022, Ukraine.
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Goudet MMM, Orr DJ, Melkonian M, Müller KH, Meyer MT, Carmo-Silva E, Griffiths H. Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae. THE NEW PHYTOLOGIST 2020; 227:810-823. [PMID: 32249430 DOI: 10.1111/nph.16577] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO2 uptake (K0.5 ), carbon isotope discrimination (δ13 C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ13 C and pyrenoid ultrastructure between high and low CO2 conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.
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Affiliation(s)
- Myriam M M Goudet
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, 50674, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, 45141, Essen, Germany
| | - Karin H Müller
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | | | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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Hennacy JH, Jonikas MC. Prospects for Engineering Biophysical CO 2 Concentrating Mechanisms into Land Plants to Enhance Yields. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:461-485. [PMID: 32151155 PMCID: PMC7845915 DOI: 10.1146/annurev-arplant-081519-040100] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Although cyanobacteria and algae represent a small fraction of the biomass of all primary producers, their photosynthetic activity accounts for roughly half of the daily CO2 fixation that occurs on Earth. These microorganisms are able to accomplish this feat by enhancing the activity of the CO2-fixing enzyme Rubisco using biophysical CO2 concentrating mechanisms (CCMs). Biophysical CCMs operate by concentrating bicarbonate and converting it into CO2 in a compartment that houses Rubisco (in contrast with other CCMs that concentrate CO2 via an organic intermediate, such as malate in the case of C4 CCMs). This activity provides Rubisco with a high concentration of its substrate, thereby increasing its reaction rate. The genetic engineering of a biophysical CCM into land plants is being pursued as a strategy to increase crop yields. This review focuses on the progress toward understanding the molecular components of cyanobacterial and algal CCMs, as well as recent advances toward engineering these components into land plants.
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Affiliation(s)
- Jessica H Hennacy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA; ,
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Orr DJ, Worrall D, Lin MT, Carmo-Silva E, Hanson MR, Parry MAJ. Hybrid Cyanobacterial-Tobacco Rubisco Supports Autotrophic Growth and Procarboxysomal Aggregation. PLANT PHYSIOLOGY 2020; 182:807-818. [PMID: 31744936 PMCID: PMC6997680 DOI: 10.1104/pp.19.01193] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/05/2019] [Indexed: 05/22/2023]
Abstract
Much of the research aimed at improving photosynthesis and crop productivity attempts to overcome shortcomings of the primary CO2-fixing enzyme Rubisco. Cyanobacteria utilize a CO2-concentrating mechanism (CCM), which encapsulates Rubisco with poor specificity but a relatively fast catalytic rate within a carboxysome microcompartment. Alongside the active transport of bicarbonate into the cell and localization of carbonic anhydrase within the carboxysome shell with Rubisco, cyanobacteria are able to overcome the limitations of Rubisco via localization within a high-CO2 environment. As part of ongoing efforts to engineer a β-cyanobacterial CCM into land plants, we investigated the potential for Rubisco large subunits (LSU) from the β-cyanobacterium Synechococcus elongatus (Se) to form aggregated Rubisco complexes with the carboxysome linker protein CcmM35 within tobacco (Nicotiana tabacum) chloroplasts. Transplastomic plants were produced that lacked cognate Se Rubisco small subunits (SSU) and expressed the Se LSU in place of tobacco LSU, with and without CcmM35. Plants were able to form a hybrid enzyme utilizing tobacco SSU and the Se LSU, allowing slow autotrophic growth in high CO2 CcmM35 was able to form large Rubisco aggregates with the Se LSU, and these incorporated small amounts of native tobacco SSU. Plants lacking the Se SSU showed delayed growth, poor photosynthetic capacity, and significantly reduced Rubisco activity compared with both wild-type tobacco and lines expressing the Se SSU. These results demonstrate the ability of the Se LSU and CcmM35 to form large aggregates without the cognate Se SSU in planta, harboring active Rubisco that enables plant growth, albeit at a much slower pace than plants expressing the cognate Se SSU.
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Affiliation(s)
- Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Dawn Worrall
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Myat T Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850
| | - Elizabete Carmo-Silva
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
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27
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Mukherjee A, Moroney JV. How protein - protein interactions contribute to pyrenoid formation in Chlamydomonas. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5033-5035. [PMID: 31613970 PMCID: PMC6793438 DOI: 10.1093/jxb/erz299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This article comments on:Atkinson N, Velanis CN, Wunder T, Clarke DJ, Mueller-Cajar O, McCormick AJ. 2019. The pyrenoidal linker protein EPYC1 phase separates with hybrid Arabidopsis-Chlamydomonas Rubisco through interactions with the algal Rubisco small subunit. Journal of Experimental Botany, 70, 5271–5285.
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Affiliation(s)
- Ananya Mukherjee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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