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Huang Y, Xia P. Biomolecular condensates in plant cells: Mediating and integrating environmental signals and development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112178. [PMID: 38971467 DOI: 10.1016/j.plantsci.2024.112178] [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: 04/23/2024] [Revised: 06/23/2024] [Accepted: 06/30/2024] [Indexed: 07/08/2024]
Abstract
In response to the spatiotemporal coordination of various biochemical reactions and membrane-encapsulated organelles, plants appear to provide another effective mechanism for cellular organization by phase separation that allows the internal compartmentalization of cells to form a variety of membrane-less organelles. Most of the research on phase separation has centralized in various non-plant systems, such as yeast and animal systems. Recent studies have shown a remarkable correlation between the formation of condensates in plant systems and the formation of condensates in these systems. Moreover, the last decade has made new advances in phase separation research in the context of plant biology. Here, we provide an overview of the physicochemical forces and molecular factors that drive liquid-liquid phase separation in plant cells and the biochemical characterization of condensates. We then explore new developments in phase separation research specific to plants, discussing examples of condensates found in green plants and detailing their role in plant growth and development. We propose that phase separation may be a conserved organizational mechanism in plant evolution to help plants respond rapidly and effectively to various environmental stresses as sessile organisms.
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Affiliation(s)
- Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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2
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Hennacy JH, Atkinson N, Kayser-Browne A, Ergun SL, Franklin E, Wang L, Kafri M, Fauser F, Vilarrasa-Blasi J, Jinkerson RE, McCormick AJ, Jonikas MC. Biogenesis, engineering and function of membranes in the CO 2 -fixing pyrenoid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.603944. [PMID: 39211136 PMCID: PMC11361040 DOI: 10.1101/2024.08.08.603944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Approximately one-third of global CO 2 assimilation is performed by the pyrenoid 1 , a liquid-like organelle found in most algae and some plants 2 . Specialized membranes are hypothesized to drive CO 2 assimilation in the pyrenoid by delivering concentrated CO 2 3,4 , but their biogenesis and function have not been experimentally characterized. Here, we show that homologous proteins SAGA1 and MITH1 mediate the biogenesis of the pyrenoid membrane tubules in the model alga Chlamydomonas reinhardtii and are sufficient to reconstitute pyrenoid-traversing membranes in a heterologous system, the plant Arabidopsis thaliana . SAGA1 localizes to the regions where thylakoid membranes transition into tubules and is necessary to initiate tubule formation. MITH1 localizes to the tubules and is necessary for their extension through the pyrenoid. Tubule-deficient mutants exhibit growth defects under CO 2 -limiting conditions, providing evidence for the function of membrane tubules in CO 2 delivery to the pyrenoid. Furthermore, these mutants form multiple aberrant condensates of pyrenoid matrix, indicating that a normal tubule network promotes the coalescence of a single pyrenoid. The reconstitution of pyrenoid-traversing membranes in a plant represents a key milestone toward engineering a functional pyrenoid into crops for improving crop yields. More broadly, our study demonstrates the functional importance of pyrenoid membranes, identifies key biogenesis factors, and paves the way for the molecular characterization of pyrenoid membranes across the tree of life.
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3
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Yang X, Huang Y, Xia P. The property and function of proteins undergoing liquid-liquid phase separation in plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38808958 DOI: 10.1111/pce.14988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/30/2024]
Abstract
A wide variety of membrane-less organelles in cells play an essential role in regulating gene expression, RNA processing, plant growth and development, and helping organisms cope with changing external environments. In biology, liquid-liquid phase separation (LLPS) usually refers to a reversible process in which one or more specific molecular components are spontaneously separated from the bulk environment, producing two distinct liquid phases: concentrated and dilute. LLPS may be a powerful cellular compartmentalisation mechanism whereby biocondensates formed via LLPS when biomolecules exceed critical or saturating concentrations in the environment where they are found will be generated. It has been widely used to explain the formation of membrane-less organelles in organisms. LLPS studies in the context of plant physiology are now widespread, but most of the research is still focused on non-plant systems; the study of phase separation in plants needs to be more thorough. Proteins and nucleic acids are the main components involved in LLPS. This review summarises the specific features and properties of biomolecules undergoing LLPS in plants. We describe in detail these biomolecules' structural characteristics, the mechanism of formation of condensates, and the functions of these condensates. Finally, We summarised the phase separation mechanisms in plant growth, development, and stress adaptation.
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Affiliation(s)
- Xuejiao Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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4
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Payne-Dwyer A, Kumar G, Barrett J, Gherman LK, Hodgkinson M, Plevin M, Mackinder L, Leake MC, Schaefer C. Predicting Rubisco-Linker Condensation from Titration in the Dilute Phase. PHYSICAL REVIEW LETTERS 2024; 132:218401. [PMID: 38856270 DOI: 10.1103/physrevlett.132.218401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/09/2024] [Indexed: 06/11/2024]
Abstract
The condensation of Rubisco holoenzymes and linker proteins into "pyrenoids," a crucial supercharger of photosynthesis in algae, is qualitatively understood in terms of "sticker-and-spacer" theory. We derive semianalytical partition sums for small Rubisco-linker aggregates, which enable the calculation of both dilute-phase titration curves and dimerization diagrams. By fitting the titration curves to surface plasmon resonance and single-molecule fluorescence microscopy data, we extract the molecular properties needed to predict dimerization diagrams. We use these to estimate typical concentrations for condensation, and successfully compare these to microscopy observations.
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Affiliation(s)
- Alex Payne-Dwyer
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
| | - Gaurav Kumar
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - James Barrett
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Laura K Gherman
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- York Structural Biology Laboratory, The University of York; York, YO10 5DD, United Kingdom
| | - Michael Hodgkinson
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Michael Plevin
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- York Structural Biology Laboratory, The University of York; York, YO10 5DD, United Kingdom
| | - Luke Mackinder
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Mark C Leake
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Charley Schaefer
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
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5
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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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6
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Li Q, Liu Y, Zhang X. Biomolecular condensates in plant RNA silencing: insights into formation, function, and stress responses. THE PLANT CELL 2024; 36:227-245. [PMID: 37772963 PMCID: PMC10827315 DOI: 10.1093/plcell/koad254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]
Abstract
Biomolecular condensates are dynamic structures formed through diverse mechanisms, including liquid-liquid phase separation. These condensates have emerged as crucial regulators of cellular processes in eukaryotic cells, enabling the compartmentalization of specific biological reactions while allowing for dynamic exchange of molecules with the surrounding environment. RNA silencing, a conserved gene regulatory mechanism mediated by small RNAs (sRNAs), plays pivotal roles in various biological processes. Multiple types of biomolecular condensate, including dicing bodies, processing bodies, small interfering RNA bodies, and Cajal bodies, have been identified as key players in RNA silencing pathways. These biomolecular condensates provide spatial compartmentation for the biogenesis, loading, action, and turnover of small RNAs. Moreover, they actively respond to stresses, such as viral infections, and modulate RNA silencing activities during stress responses. This review summarizes recent advances in understanding of dicing bodies and other biomolecular condensates involved in RNA silencing. We explore their formation, roles in RNA silencing, and contributions to antiviral resistance responses. This comprehensive overview provides insights into the functional significance of biomolecular condensates in RNA silencing and expands our understanding of their roles in gene expression and stress responses in plants.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- HainanYazhou Bay Seed Lab, Sanya, China
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7
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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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8
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Launay H, Avilan L, Gérard C, Parsiegla G, Receveur-Brechot V, Gontero B, Carriere F. Location of the photosynthetic carbon metabolism in microcompartments and separated phases in microalgal cells. FEBS Lett 2023; 597:2853-2878. [PMID: 37827572 DOI: 10.1002/1873-3468.14754] [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: 06/16/2023] [Revised: 09/04/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Carbon acquisition, assimilation and storage in eukaryotic microalgae and cyanobacteria occur in multiple compartments that have been characterised by the location of the enzymes involved in these functions. These compartments can be delimited by bilayer membranes, such as the chloroplast, the lumen, the peroxisome, the mitochondria or monolayer membranes, such as lipid droplets or plastoglobules. They can also originate from liquid-liquid phase separation such as the pyrenoid. Multiple exchanges exist between the intracellular microcompartments, and these are reviewed for the CO2 concentration mechanism, the Calvin-Benson-Bassham cycle, the lipid metabolism and the cellular energetic balance. Progress in microscopy and spectroscopic methods opens new perspectives to characterise the molecular consequences of the location of the proteins involved, including intrinsically disordered proteins.
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Affiliation(s)
- Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
| | - Luisana Avilan
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
| | - Cassy Gérard
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
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9
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Blikstad C, Dugan EJ, Laughlin TG, Turnšek JB, Liu MD, Shoemaker SR, Vogiatzi N, Remis JP, Savage DF. Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome. Proc Natl Acad Sci U S A 2023; 120:e2308600120. [PMID: 37862384 PMCID: PMC10614612 DOI: 10.1073/pnas.2308600120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2023] [Indexed: 10/22/2023] Open
Abstract
Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO2 fixation-Rubisco and carbonic anhydrase-and are the centerpiece of the bacterial CO2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO2 by carbonic anhydrase, producing a high CO2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus. We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.
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Affiliation(s)
- Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Thomas G. Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Julia B. Turnšek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Mira D. Liu
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Sophie R. Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Nikoleta Vogiatzi
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Jonathan P. Remis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- HHMI, University of California, Berkeley, CA94720
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10
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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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11
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Lau CS, Dowle A, Thomas GH, Girr P, Mackinder LCM. A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii. THE PLANT CELL 2023; 35:3260-3279. [PMID: 37195994 PMCID: PMC10473203 DOI: 10.1093/plcell/koad131] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 05/19/2023]
Abstract
Phase separation underpins many biologically important cellular events such as RNA metabolism, signaling, and CO2 fixation. However, determining the composition of a phase-separated organelle is often challenging due to its sensitivity to environmental conditions, which limits the application of traditional proteomic techniques like organellar purification or affinity purification mass spectrometry to understand their composition. In Chlamydomonas reinhardtii, Rubisco is condensed into a crucial phase-separated organelle called the pyrenoid that improves photosynthetic performance by supplying Rubisco with elevated concentrations of CO2. Here, we developed a TurboID-based proximity labeling technique in which proximal proteins in Chlamydomonas chloroplasts are labeled by biotin radicals generated from the TurboID-tagged protein. By fusing 2 core pyrenoid components with the TurboID tag, we generated a high-confidence pyrenoid proxiome that contains most known pyrenoid proteins, in addition to new pyrenoid candidates. Fluorescence protein tagging of 7 previously uncharacterized TurboID-identified proteins showed that 6 localized to a range of subpyrenoid regions. The resulting proxiome also suggests new secondary functions for the pyrenoid in RNA-associated processes and redox-sensitive iron-sulfur cluster metabolism. This developed pipeline can be used to investigate a broad range of biological processes in Chlamydomonas, especially at a temporally resolved suborganellar resolution.
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Affiliation(s)
- Chun Sing Lau
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Adam Dowle
- Department of Biology, University of York, York YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Luke C M Mackinder
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
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12
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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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13
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Wei S, Li F, Zhu N, Wei X, Wu P, Dang Z. Biomass production of Chlorella pyrenoidosa by filled sphere carrier reactor: Performance and mechanism. BIORESOURCE TECHNOLOGY 2023:129195. [PMID: 37207699 DOI: 10.1016/j.biortech.2023.129195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Microalgae-based Carbon Capture, Utilization and Storage is vital for mitigating global climate change. A filled sphere carrier reactor was developed to achieve high biomass production and carbon sequestration rate of Chlorella pyrenoidosa. By introducing air (0.04% CO2) into the reactor, the dry biomass production achieved 8.26 g/L with the optimized parameters of polyester carrier, 80% packing density, 5-fold concentrated nutrient combining 0.2 mol/L phosphate buffer. At simulated flue gas CO2 concentration of 7%, the dry biomass yield and carbon sequestration rate reached up to 9.98 g/L and 18.32 g/L/d in one day, which were as high as 249.5 and 79.65 times comparing with those of suspension culture at day 1, respectively. The mechanism was mainly attributed to the obvious intensification of electron transfer rate and remarkable increase of RuBisCO enzyme activity in the photosynthetic chloroplast matrix. This work provided a novel approach for potential microalgae-based carbon capture and storage.
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Affiliation(s)
- Sijing Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Fei Li
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Nengwu Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters of Ministry of Education, Guangzhou 510006, PR China; Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, PR China.
| | - Xiaorong Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Pingxiao Wu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters of Ministry of Education, Guangzhou 510006, PR China; Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou 510006, PR China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters of Ministry of Education, Guangzhou 510006, PR China; Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou 510006, PR China
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14
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Shimamura D, Yamano T, Niikawa Y, Hu D, Fukuzawa H. A pyrenoid-localized protein SAGA1 is necessary for Ca 2+-binding protein CAS-dependent expression of nuclear genes encoding inorganic carbon transporters in Chlamydomonas reinhardtii. PHOTOSYNTHESIS RESEARCH 2023; 156:181-192. [PMID: 36656499 DOI: 10.1007/s11120-022-00996-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/14/2022] [Indexed: 05/03/2023]
Abstract
Microalgae induce a CO2-concentrating mechanism (CCM) to maintain photosynthetic affinity for dissolved inorganic carbon (Ci) under CO2-limiting conditions. In the model alga Chlamydomonas reinhardtii, the pyrenoid-localized Ca2+-binding protein CAS is required to express genes encoding the Ci-transporters, high-light activated 3 (HLA3), and low-CO2-inducible protein A (LCIA). To identify new factors related to the regulation or components of the CCM, we isolated CO2-requiring mutants KO-60 and KO-62. These mutants had insertions of a hygromycin-resistant cartridge in the StArch Granules Abnormal 1 (SAGA1) gene, which is necessary to maintain the number of pyrenoids and the structure of pyrenoid tubules in the chloroplast. In both KO-60 and the previously identified saga1 mutant, expression levels of 532 genes were significantly reduced. Among them, 10 CAS-dependent genes, including HLA3 and LCIA, were not expressed in the saga1 mutants. While CAS was expressed normally at the protein levels, the localization of CAS was dispersed through the chloroplast rather than in the pyrenoid, even under CO2-limiting conditions. These results suggest that SAGA1 is necessary not only for maintenance of the pyrenoid structure but also for regulation of the nuclear genes encoding Ci-transporters through CAS-dependent retrograde signaling under CO2-limiting stress.
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Affiliation(s)
- Daisuke Shimamura
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Takashi Yamano
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan.
| | - Yuki Niikawa
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Donghui Hu
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan.
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15
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Nguyen ND, Pulsford SB, Hee WY, Rae BD, Rourke LM, Price GD, Long BM. Towards engineering a hybrid carboxysome. PHOTOSYNTHESIS RESEARCH 2023; 156:265-277. [PMID: 36892800 PMCID: PMC10154267 DOI: 10.1007/s11120-023-01009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/17/2023] [Indexed: 05/03/2023]
Abstract
Carboxysomes are bacterial microcompartments, whose structural features enable the encapsulated Rubisco holoenzyme to operate in a high-CO2 environment. Consequently, Rubiscos housed within these compartments possess higher catalytic turnover rates relative to their plant counterparts. This particular enzymatic property has made the carboxysome, along with associated transporters, an attractive prospect to incorporate into plant chloroplasts to increase future crop yields. To date, two carboxysome types have been characterized, the α-type that has fewer shell components and the β-type that houses a faster Rubisco. While research is underway to construct a native carboxysome in planta, work investigating the internal arrangement of carboxysomes has identified conserved Rubisco amino acid residues between the two carboxysome types which could be engineered to produce a new, hybrid carboxysome. In theory, this hybrid carboxysome would benefit from the simpler α-carboxysome shell architecture while simultaneously exploiting the higher Rubisco turnover rates in β-carboxysomes. Here, we demonstrate in an Escherichia coli expression system, that the Thermosynechococcus elongatus Form IB Rubisco can be imperfectly incorporated into simplified Cyanobium α-carboxysome-like structures. While encapsulation of non-native cargo can be achieved, T. elongatus Form IB Rubisco does not interact with the Cyanobium carbonic anhydrase, a core requirement for proper carboxysome functionality. Together, these results suggest a way forward to hybrid carboxysome formation.
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Affiliation(s)
- Nghiem Dinh Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Sacha B Pulsford
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, The Australian National University, Building 46, Sullivan's Creek Road, Acton, ACT, 2601, Australia
| | - Wei Yi Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Loraine M Rourke
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - G Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia.
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
- Division of Plant Sciences, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Canberra, ACT, 2601, Australia.
| | - Benedict M Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
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16
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Kupriyanova EV, Pronina NA, Los DA. Adapting from Low to High: An Update to CO 2-Concentrating Mechanisms of Cyanobacteria and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1569. [PMID: 37050194 PMCID: PMC10096703 DOI: 10.3390/plants12071569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.
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17
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Boeynaems S, Chong S, Gsponer J, Holt L, Milovanovic D, Mitrea DM, Mueller-Cajar O, Portz B, Reilly JF, Reinkemeier CD, Sabari BR, Sanulli S, Shorter J, Sontag E, Strader L, Stachowiak J, Weber SC, White M, Zhang H, Zweckstetter M, Elbaum-Garfinkle S, Kriwacki R. Phase Separation in Biology and Disease; Current Perspectives and Open Questions. J Mol Biol 2023; 435:167971. [PMID: 36690068 PMCID: PMC9970028 DOI: 10.1016/j.jmb.2023.167971] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023]
Abstract
In the past almost 15 years, we witnessed the birth of a new scientific field focused on the existence, formation, biological functions, and disease associations of membraneless bodies in cells, now referred to as biomolecular condensates. Pioneering studies from several laboratories [reviewed in1-3] supported a model wherein biomolecular condensates associated with diverse biological processes form through the process of phase separation. These and other findings that followed have revolutionized our understanding of how biomolecules are organized in space and time within cells to perform myriad biological functions, including cell fate determination, signal transduction, endocytosis, regulation of gene expression and protein translation, and regulation of RNA metabolism. Further, condensates formed through aberrant phase transitions have been associated with numerous human diseases, prominently including neurodegeneration and cancer. While in some cases, rigorous evidence supports links between formation of biomolecular condensates through phase separation and biological functions, in many others such links are less robustly supported, which has led to rightful scrutiny of the generality of the roles of phase separation in biology and disease.4-7 During a week-long workshop in March 2022 at the Telluride Science Research Center (TSRC) in Telluride, Colorado, ∼25 scientists addressed key questions surrounding the biomolecular condensates field. Herein, we present insights gained through these discussions, addressing topics including, roles of condensates in diverse biological processes and systems, and normal and disease cell states, their applications to synthetic biology, and the potential for therapeutically targeting biomolecular condensates.
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Affiliation(s)
- Steven Boeynaems
- Department of Molecular and Human Genetics, Therapeutic Innovation Center (THINC), Center for Alzheimer’s and Neurodegenerative Diseases (CAND), Dan L Duncan Comprehensive Cancer Center (DLDCCC), Baylor College of Medicine, Houston, TX 77030, USA and Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jörg Gsponer
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Liam Holt
- New York University School of Medicine, Institute for Systems Genetics, New York, NY 10016
| | - Drago Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
| | | | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | | | | | | | - Benjamin R. Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX
| | - Serena Sanulli
- Department of Genetics, Stanford University, Palo Alto, CA 94304
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily Sontag
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin
| | - Lucia Strader
- Department of Biology, Duke University, Durham, NC 27708 USA
| | - Jeanne Stachowiak
- University of Texas at Austin, Department of Biomedical Engineering, Austin, TX, USA
| | | | | | - Huaiying Zhang
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Shana Elbaum-Garfinkle
- Department of Biochemistry, The Graduate Center of the City University of New York, New York, NY and Structural Biology Initiative, Advanced Science Research Center, City University of New York, New York, NY
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee and Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, Tennessee
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18
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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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19
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Badger MR, Sharwood RE. Rubisco, the imperfect winner: it's all about the base. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:562-580. [PMID: 36412307 DOI: 10.1093/jxb/erac458] [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: 06/28/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles' heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth's multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco's catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.
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Affiliation(s)
- Murray R Badger
- Research School of Biology, Building 134 Linnaeus Way, Canberra ACT, 2601, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Bourke St, Richmond, NSW, 2753, Australia
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20
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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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21
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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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22
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Vazquez DS, Toledo PL, Gianotti AR, Ermácora MR. Protein conformation and biomolecular condensates. Curr Res Struct Biol 2022; 4:285-307. [PMID: 36164646 PMCID: PMC9508354 DOI: 10.1016/j.crstbi.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 10/27/2022] Open
Abstract
Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.
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Affiliation(s)
- Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
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23
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Gérard C, Carrière F, Receveur-Bréchot V, Launay H, Gontero B. A Trajectory of Discovery: Metabolic Regulation by the Conditionally Disordered Chloroplast Protein, CP12. Biomolecules 2022; 12:1047. [PMID: 36008940 PMCID: PMC9406205 DOI: 10.3390/biom12081047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
The chloroplast protein CP12, which is widespread in photosynthetic organisms, belongs to the intrinsically disordered proteins family. This small protein (80 amino acid residues long) presents a bias in its composition; it is enriched in charged amino acids, has a small number of hydrophobic residues, and has a high proportion of disorder-promoting residues. More precisely, CP12 is a conditionally disordered proteins (CDP) dependent upon the redox state of its four cysteine residues. During the day, reducing conditions prevail in the chloroplast, and CP12 is fully disordered. Under oxidizing conditions (night), its cysteine residues form two disulfide bridges that confer some stability to some structural elements. Like many CDPs, CP12 plays key roles, and its redox-dependent conditional disorder is important for the main function of CP12: the dark/light regulation of the Calvin-Benson-Bassham (CBB) cycle responsible for CO2 assimilation. Oxidized CP12 binds to glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase and thereby inhibits their activity. However, recent studies reveal that CP12 may have other functions beyond the CBB cycle regulation. In this review, we report the discovery of this protein, its features as a disordered protein, and the many functions this small protein can have.
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Affiliation(s)
| | | | | | - Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, FR3479, 31 Chemin J. Aiguier, CEDEX 9, 13 402 Marseille, France; (C.G.); (F.C.); (V.R.-B.)
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, FR3479, 31 Chemin J. Aiguier, CEDEX 9, 13 402 Marseille, France; (C.G.); (F.C.); (V.R.-B.)
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24
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Tsidilkovski L, Mohajerani F, Hagan MF. Microcompartment assembly around multicomponent fluid cargoes. J Chem Phys 2022; 156:245104. [PMID: 35778087 PMCID: PMC9249432 DOI: 10.1063/5.0089556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a complex of enzymes and other components involved in certain metabolic processes. The simulations demonstrate that the relative interaction strengths among the different cargo species play a key role in determining the amount of each species that is encapsulated, their spatial organization, and the nature of the shell assembly pathways. However, the shell protein–shell protein and shell protein–cargo component interactions that help drive assembly and encapsulation also influence cargo composition within certain parameter regimes. These behaviors are governed by a combination of thermodynamic and kinetic effects. In addition to elucidating how natural microcompartments encapsulate multiple components involved within reaction cascades, these results have implications for efforts in synthetic biology to colocalize alternative sets of molecules within microcompartments to accelerate specific reactions. More broadly, the results suggest that coupling between self-assembly and multicomponent liquid–liquid phase separation may play a role in the organization of the cellular cytoplasm.
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Affiliation(s)
- Lev Tsidilkovski
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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25
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Reduction in Phosphoribulokinase Amount and Re-Routing Metabolism in Chlamydomonas reinhardtii CP12 Mutants. Int J Mol Sci 2022; 23:ijms23052710. [PMID: 35269851 PMCID: PMC8910624 DOI: 10.3390/ijms23052710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
The chloroplast protein CP12 is involved in the dark/light regulation of the Calvin–Benson–Bassham cycle, in particular, in the dark inhibition of two enzymes: glyceraldehyde−3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), but other functions related to stress have been proposed. We knocked out the unique CP12 gene to prevent its expression in Chlamydomonas reinhardtii (ΔCP12). The growth rates of both wild-type and ΔCP12 cells were nearly identical, as was the GAPDH protein abundance and activity in both cell lines. On the contrary, the abundance of PRK and its specific activity were significantly reduced in ΔCP12, as revealed by relative quantitative proteomics. Isolated PRK lost irreversibly its activity over-time in vitro, which was prevented in the presence of recombinant CP12 in a redox-independent manner. We have identified amino acid residues in the CP12 protein that are required for this new function preserving PRK activity. Numerous proteins involved in redox homeostasis and stress responses were more abundant and the expressions of various metabolic pathways were also increased or decreased in the absence of CP12. These results highlight CP12 as a moonlighting protein with additional functions beyond its well-known regulatory role in carbon metabolism.
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26
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Abyzov A, Blackledge M, Zweckstetter M. Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry. Chem Rev 2022; 122:6719-6748. [PMID: 35179885 PMCID: PMC8949871 DOI: 10.1021/acs.chemrev.1c00774] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Motions in biomolecules
are critical for biochemical reactions.
In cells, many biochemical reactions are executed inside of biomolecular
condensates formed by ultradynamic intrinsically disordered proteins.
A deep understanding of the conformational dynamics of intrinsically
disordered proteins in biomolecular condensates is therefore of utmost
importance but is complicated by diverse obstacles. Here we review
emerging data on the motions of intrinsically disordered proteins
inside of liquidlike condensates. We discuss how liquid–liquid
phase separation modulates internal motions across a wide range of
time and length scales. We further highlight the importance of intermolecular
interactions that not only drive liquid–liquid phase separation
but appear as key determinants for changes in biomolecular motions
and the aging of condensates in human diseases. The review provides
a framework for future studies to reveal the conformational dynamics
of intrinsically disordered proteins in the regulation of biomolecular
condensate chemistry.
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Affiliation(s)
- Anton Abyzov
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Martin Blackledge
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble, France.,CEA, DSV, IBS, 38044 Grenoble, France.,CNRS, IBS, 38044 Grenoble, France
| | - Markus Zweckstetter
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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27
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Pyo AG, Zhang Y, Wingreen NS. Surface tension and super-stoichiometric surface enrichment in two-component biomolecular condensates. iScience 2022; 25:103852. [PMID: 35198903 PMCID: PMC8851291 DOI: 10.1016/j.isci.2022.103852] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/28/2021] [Accepted: 01/26/2022] [Indexed: 11/24/2022] Open
Abstract
Cells can achieve internal organization by exploiting liquid-liquid phase separation to form biomolecular condensates. Here we focus on the surface properties of condensates composed of two multivalent associative polymers held together by one-to-one "sticker" bonds. Using coarse-grained molecular-dynamics simulations, we study the influence of component stoichiometry on condensate surface properties. We find that unequal stoichiometry results in enrichment of the majority species at the interface and a sharp reduction of surface tension. To relate these two effects, we show that the reduction in surface tension scales linearly with the excess concentration of free binding sites at the interface. Our results imply that each excess free site contributes an approximately fixed additional energy and entropy to the interface, with the latter dominating such that enrichment of free majority sites lowers the surface tension. Our work provides insight into novel physical mechanisms by which cells can regulate condensate surface properties.
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Affiliation(s)
- Andrew G.T. Pyo
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Yaojun Zhang
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Physics and Astronomy and Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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28
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Yamano T, Toyokawa C, Shimamura D, Matsuoka T, Fukuzawa H. CO2-dependent migration and relocation of LCIB, a pyrenoid-peripheral protein in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2022; 188:1081-1094. [PMID: 34791500 PMCID: PMC8825250 DOI: 10.1093/plphys/kiab528] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/15/2021] [Indexed: 05/18/2023]
Abstract
Most microalgae overcome the difficulty of acquiring inorganic carbon (Ci) in aquatic environments by inducing a CO2-concentrating mechanism (CCM). In the green alga Chlamydomonas reinhardtii, two distinct photosynthetic acclimation states have been described under CO2-limiting conditions (low-CO2 [LC] and very low-CO2 [VLC]). LC-inducible protein B (LCIB), structurally characterized as carbonic anhydrase, localizes in the chloroplast stroma under CO2-supplied and LC conditions. In VLC conditions, it migrates to aggregate around the pyrenoid, where the CO2-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase is enriched. Although the physiological importance of LCIB localization changes in the chloroplast has been shown, factors necessary for the localization changes remain uncertain. Here, we examined the effect of pH, light availability, photosynthetic electron flow, and protein synthesis on the localization changes, along with measuring Ci concentrations. LCIB dispersed or localized in the basal region of the chloroplast stroma at 8.3-15 µM CO2, whereas LCIB migrated toward the pyrenoid at 6.5 µM CO2. Furthermore, LCIB relocated toward the pyrenoid at 2.6-3.4 µM CO2, even in cells in the dark or treated with 3-(3,4-dichlorophenyl)-1,1-dimethylurea and cycloheximide in light. In contrast, in the mutant lacking CCM1, a master regulator of CCM, LCIB remained dispersed even at 4.3 µM CO2. Meanwhile, a simultaneous expression of LCIC, an interacting protein of LCIB, induced the localization of several speckled structures at the pyrenoid periphery. These results suggest that the localization changes of LCIB require LCIC and are controlled by CO2 concentration with ∼7 µM as the boundary.
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Affiliation(s)
- Takashi Yamano
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Chihana Toyokawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Daisuke Shimamura
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Toshiki Matsuoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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29
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Zhang C, Zhao W, Duvall SW, Kowallis KA, Childers WS. Regulation of the activity of bacterial histidine kinase PleC by the scaffolding protein PodJ. J Biol Chem 2022; 298:101683. [PMID: 35124010 PMCID: PMC8980812 DOI: 10.1016/j.jbc.2022.101683] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Scaffolding proteins can customize the response of signaling networks to support cell development and behaviors. PleC is a bifunctional histidine kinase whose signaling activity coordinates asymmetric cell division to yield a motile swarmer cell and a stalked cell in the gram-negative bacterium Caulobacter crescentus. Past studies have shown that PleC’s switch in activity from kinase to phosphatase correlates with a change in its subcellular localization pattern from diffuse to localized at the new cell pole. Here we investigated how the bacterial scaffolding protein PodJ regulates the subcellular positioning and activity of PleC. We reconstituted the PleC-PodJ signaling complex through both heterologous expressions in Escherichia coli and in vitro studies. In vitro, PodJ phase separates as a biomolecular condensate that recruits PleC and inhibits its kinase activity. We also constructed an in vivo PleC-CcaS chimeric histidine kinase reporter assay and demonstrated using this method that PodJ leverages its intrinsically disordered region to bind to PleC’s PAS sensory domain and regulate PleC-CcaS signaling. Regulation of the PleC-CcaS was most robust when PodJ was concentrated at the cell poles and was dependent on the allosteric coupling between PleC-CcaS’s PAS sensory domain and its downstream histidine kinase domain. In conclusion, our in vitro biochemical studies suggest that PodJ phase separation may be coupled to changes in PleC enzymatic function. We propose that this coupling of phase separation and allosteric regulation may be a generalizable phenomenon among enzymes associated with biomolecular condensates.
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30
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Neofotis P, Temple J, Tessmer OL, Bibik J, Norris N, Pollner E, Lucker B, Weraduwage SM, Withrow A, Sears B, Mogos G, Frame M, Hall D, Weissman J, Kramer DM. The induction of pyrenoid synthesis by hyperoxia and its implications for the natural diversity of photosynthetic responses in Chlamydomonas. eLife 2021; 10:67565. [PMID: 34936552 PMCID: PMC8694700 DOI: 10.7554/elife.67565] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/13/2021] [Indexed: 12/31/2022] Open
Abstract
In algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO2. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, in Chlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO2 or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO2 or hyperoxia. Consistent with this view, the photorespiratory by-product, H2O2, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H2O2 signaling, and pyrenoid morphologies.
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Affiliation(s)
- Peter Neofotis
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Joshua Temple
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
| | - Oliver L Tessmer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Jacob Bibik
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Nicole Norris
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Eric Pollner
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Ben Lucker
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Sarathi M Weraduwage
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States.,Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, United States
| | - Alecia Withrow
- Center for Advanced Microscopy, Michigan State University, East Lansing, United States
| | - Barbara Sears
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Greg Mogos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Melinda Frame
- Center for Advanced Microscopy, Michigan State University, East Lansing, United States
| | - David Hall
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Joseph Weissman
- Corporate Strategic Research, ExxonMobil, Annandale, United States
| | - David M Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
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31
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The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos. J Biol Chem 2021; 298:101476. [PMID: 34890642 PMCID: PMC8718961 DOI: 10.1016/j.jbc.2021.101476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/15/2023] Open
Abstract
The CO2-fixing enzyme rubisco is responsible for almost all carbon fixation. This process frequently requires rubisco activase (Rca) machinery, which couples ATP hydrolysis to the removal of inhibitory sugar phosphates, including the rubisco substrate ribulose 1,5-bisphosphate (RuBP). Rubisco is sometimes compartmentalized in carboxysomes, bacterial microcompartments that enable a carbon dioxide concentrating mechanism (CCM). Characterized carboxysomal rubiscos, however, are not prone to inhibition, and often no activase machinery is associated with these enzymes. Here, we characterize two carboxysomal rubiscos of the form IAC clade that are associated with CbbQO-type Rcas. These enzymes release RuBP at a much lower rate than the canonical carboxysomal rubisco from Synechococcus PCC6301. We found that CbbQO-type Rcas encoded in carboxysome gene clusters can remove RuBP and the tight-binding transition state analog carboxy-arabinitol 1,5-bisphosphate from cognate rubiscos. The Acidithiobacillus ferrooxidans genome encodes two form IA rubiscos associated with two sets of cbbQ and cbbO genes. We show that the two CbbQO activase systems display specificity for the rubisco enzyme encoded in the same gene cluster, and this property can be switched by substituting the C-terminal three residues of the large subunit. Our findings indicate that the kinetic and inhibitory properties of proteobacterial form IA rubiscos are diverse and predict that Rcas may be necessary for some α-carboxysomal CCMs. These findings will have implications for efforts aiming to introduce biophysical CCMs into plants and other hosts for improvement of carbon fixation of crops.
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32
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Xu X, Zheng C, Lu D, Song CP, Zhang L. Phase separation in plants: New insights into cellular compartmentalization. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1835-1855. [PMID: 34314106 DOI: 10.1111/jipb.13152] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/16/2021] [Indexed: 05/16/2023]
Abstract
A fundamental challenge for cells is how to coordinate various biochemical reactions in space and time. To achieve spatiotemporal control, cells have developed organelles that are surrounded by lipid bilayer membranes. Further, membraneless compartmentalization, a process induced by dynamic physical association of biomolecules through phase transition offers another efficient mechanism for intracellular organization. While our understanding of phase separation was predominantly dependent on yeast and animal models, recent findings have provided compelling evidence for emerging roles of phase separation in plants. In this review, we first provide an overview of the current knowledge of phase separation, including its definition, biophysical principles, molecular features and regulatory mechanisms. Then we summarize plant-specific phase separation phenomena and describe their functions in plant biological processes in great detail. Moreover, we propose that phase separation is an evolutionarily conserved and efficient mechanism for cellular compartmentalization which allows for distinct metabolic processes and signaling pathways, and is especially beneficial for the sessile lifestyle of plants to quickly and efficiently respond to the changing environment.
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Affiliation(s)
- Xiumei Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Canhui Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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33
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Gao Z, Zhang W, Chang R, Zhang S, Yang G, Zhao G. Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells. Front Microbiol 2021; 12:751880. [PMID: 34759902 PMCID: PMC8573418 DOI: 10.3389/fmicb.2021.751880] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous examples of microbial phase-separated biomolecular condensates have now been identified following advances in fluorescence imaging and single molecule microscopy technologies. The structure, function, and potential applications of these microbial condensates are currently receiving a great deal of attention. By neatly compartmentalizing proteins and their interactors in membrane-less organizations while maintaining free communication between these macromolecules and the external environment, microbial cells are able to achieve enhanced metabolic efficiency. Typically, these condensates also possess the ability to rapidly adapt to internal and external changes. The biological functions of several phase-separated condensates in small bacterial cells show evolutionary convergence with the biological functions of their eukaryotic paralogs. Artificial microbial membrane-less organelles are being constructed with application prospects in biocatalysis, biosynthesis, and biomedicine. In this review, we provide an overview of currently known biomolecular condensates driven by liquid-liquid phase separation (LLPS) in microbial cells, and we elaborate on their biogenesis mechanisms and biological functions. Additionally, we highlight the major challenges and future research prospects in studying microbial LLPS.
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Affiliation(s)
| | | | | | | | - Guiwen Yang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guoyan Zhao
- College of Life Science, Shandong Normal University, Jinan, China
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34
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Abstract
Hypoxia inhibits the tricarboxylic acid (TCA) cycle and leaves glycolysis as the primary metabolic pathway responsible for converting glucose into usable energy. However, the mechanisms that compensate for this loss in energy production due to TCA cycle inactivation remain poorly understood. Glycolysis enzymes are typically diffuse and soluble in the cytoplasm under normoxic conditions. In contrast, recent studies have revealed dynamic compartmentalization of glycolysis enzymes in response to hypoxic stress in yeast, C. elegans and mammalian cells. These messenger ribonucleoprotein (mRNP) structures, termed glycolytic (G) bodies in yeast, lack membrane enclosure and display properties of phase-separated biomolecular condensates. Disruption of condensate formation correlates with defects such as impaired synaptic function in C. elegans neurons and decreased glucose flux in yeast. Concentrating glycolysis enzymes into condensates may lead to their functioning as 'metabolons' that enhance rates of glucose utilization for increased energy production. Besides condensates, glycolysis enzymes functionally associate in other organisms and specific tissues through protein-protein interactions and membrane association. However, as discussed in this Review, the functional consequences of coalescing glycolytic machinery are only just beginning to be revealed. Through ongoing studies, we anticipate the physiological importance of metabolic regulation mediated by the compartmentalization of glycolysis enzymes will continue to emerge.
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Affiliation(s)
- Gregory G Fuller
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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35
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Abstract
Wang and Jonikas take a look at an unconventional organelle, the pyrenoid.
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Affiliation(s)
- Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA.
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36
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Fahim A, Annunziata O. Effect of a Good buffer on the fate of metastable protein-rich droplets near physiological composition. Int J Biol Macromol 2021; 186:519-527. [PMID: 34265335 DOI: 10.1016/j.ijbiomac.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Metastable protein-rich microdroplets are produced from liquid-liquid phase separation (LLPS) of protein aqueous solutions. These globules can be intermediates for the formation of other protein-rich phases. Lysozyme aqueous solutions undergo LLPS around 0 °C in the presence of NaCl near physiological conditions. Here, it is shown that insertion of small amounts of 4-(2-hydroxyethyl)-1-piperazineethanesulfonate (HEPES, 0.1 M) as a second additive to lysozyme-NaCl-water solutions near physiological ionic strength (0.2 M) is an essential step for triggering conversion of protein-rich droplets into another phase. Specifically, LLPS induced by cooling reproducibly leads to a rapid and high-yield formation of compact tetragonal crystalline microparticles only in the presence of HEPES. These microcrystals exhibit small size (1-3 μm), narrow size distribution and guest-binding properties. The temperature-concentration phase diagram shows a characteristic topology with LLPS boundary metastable with respect to tetragonal microcrystals, which in turn become less stable than rod-shaped orthorhombic crystals above 40 °C. Interestingly, dynamic light scattering, hydrogen-ion titrations and isothermal titration calorimetry reveal that lysozyme-HEPES interactions were found to be weakly attractive and exothermic. Our findings indicate that additives of salting-in type can represent an important factor controlling the fate of metastable protein-rich microdroplets relevant to drug formulations, femtosecond crystallography, and potential implications in protein-driven cytoplasmic compartmentalization.
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Affiliation(s)
- Aisha Fahim
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie St., Sid Richardson Bldg. #438, Fort Worth, TX 76129, USA
| | - Onofrio Annunziata
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie St., Sid Richardson Bldg. #438, Fort Worth, TX 76129, USA..
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37
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Santhanagopalan I, Wong R, Mathur T, Griffiths H. Orchestral manoeuvres in the light: crosstalk needed for regulation of the Chlamydomonas carbon concentration mechanism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4604-4624. [PMID: 33893473 PMCID: PMC8320531 DOI: 10.1093/jxb/erab169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 05/19/2023]
Abstract
The inducible carbon concentration mechanism (CCM) in Chlamydomonas reinhardtii has been well defined from a molecular and ultrastructural perspective. Inorganic carbon transport proteins, and strategically located carbonic anhydrases deliver CO2 within the chloroplast pyrenoid matrix where Rubisco is packaged. However, there is little understanding of the fundamental signalling and sensing processes leading to CCM induction. While external CO2 limitation has been believed to be the primary cue, the coupling between energetic supply and inorganic carbon demand through regulatory feedback from light harvesting and photorespiration signals could provide the original CCM trigger. Key questions regarding the integration of these processes are addressed in this review. We consider how the chloroplast functions as a crucible for photosynthesis, importing and integrating nuclear-encoded components from the cytoplasm, and sending retrograde signals to the nucleus to regulate CCM induction. We hypothesize that induction of the CCM is associated with retrograde signals associated with photorespiration and/or light stress. We have also examined the significance of common evolutionary pressures for origins of two co-regulated processes, namely the CCM and photorespiration, in addition to identifying genes of interest involved in transcription, protein folding, and regulatory processes which are needed to fully understand the processes leading to CCM induction.
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Affiliation(s)
- Indu Santhanagopalan
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Rachel Wong
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Tanya Mathur
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
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38
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Diel Variations of Extracellular Microcystin Influence the Subcellular Dynamics of RubisCO in Microcystis aeruginosa PCC 7806. Microorganisms 2021; 9:microorganisms9061265. [PMID: 34200971 PMCID: PMC8230624 DOI: 10.3390/microorganisms9061265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/02/2022] Open
Abstract
The ubiquitous freshwater cyanobacterium Microcystis is remarkably successful, showing a high tolerance against fluctuations in environmental conditions. It frequently forms dense blooms which can accumulate significant amounts of the hepatotoxin microcystin, which plays an extracellular role as an infochemical but also acts intracellularly by interacting with proteins of the carbon metabolism, notably with the CO2 fixing enzyme RubisCO. Here we demonstrate a direct link between external microcystin and its intracellular targets. Monitoring liquid cultures of Microcystis in a diel experiment revealed fluctuations in the extracellular microcystin content that correlate with an increase in the binding of microcystin to intracellular proteins. Concomitantly, reversible relocation of RubisCO from the cytoplasm to the cell’s periphery was observed. These variations in RubisCO localization were especially pronounced with cultures grown at higher cell densities. We replicated these effects by adding microcystin externally to cultures grown under continuous light. Thus, we propose that microcystin may be part of a fast response to conditions of high light and low carbon that contribute to the metabolic flexibility and the success of Microcystis in the field.
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39
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Abstract
Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.
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40
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Launay H, Shao H, Bornet O, Cantrelle FX, Lebrun R, Receveur-Brechot V, Gontero B. Flexibility of Oxidized and Reduced States of the Chloroplast Regulatory Protein CP12 in Isolation and in Cell Extracts. Biomolecules 2021; 11:biom11050701. [PMID: 34066751 PMCID: PMC8151241 DOI: 10.3390/biom11050701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
In the chloroplast, Calvin–Benson–Bassham enzymes are active in the reducing environment created in the light by electrons from the photosystems. In the dark, these enzymes are inhibited, mainly caused by oxidation of key regulatory cysteine residues. CP12 is a small protein that plays a role in this regulation with four cysteine residues that undergo a redox transition. Using amide-proton exchange with solvent, measured by nuclear magnetic resonance (NMR) and mass-spectrometry, we confirmed that reduced CP12 is intrinsically disordered. Using real-time NMR, we showed that the oxidation of the two disulfide bridges is simultaneous. In oxidized CP12, the C23–C31 pair is in a region that undergoes a conformational exchange in the NMR-intermediate timescale. The C66–C75 pair is in the C-terminus that folds into a stable helical turn. We confirmed that these structural states exist in a physiologically relevant environment: a cell extract from Chlamydomonas reinhardtii. Consistent with these structural equilibria, the reduction is slower for the C66–C75 pair than for the C23–C31 pair. The redox mid-potentials for the two cysteine pairs differ and are similar to those found for glyceraldehyde 3-phosphate dehydrogenase and phosphoribulokinase, consistent with the regulatory role of CP12.
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Affiliation(s)
- Helene Launay
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
- Correspondence: (H.L.); (B.G.)
| | - Hui Shao
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
| | - Olivier Bornet
- NMR Platform, Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, F-13009 Marseille, France;
| | - Francois-Xavier Cantrelle
- CNRS, ERL9002, Integrative Structural Biology, Univ. Lille, F-59658 Lille, France;
- U1167, INSERM, CHU Lille, Institut Pasteur de Lille, F-59019 Lille, France
| | - Regine Lebrun
- Plate-forme Protéomique, Marseille Protéomique (MaP), IMM FR 3479, 31 Chemin Joseph Aiguier, F-13009 Marseille, France;
| | | | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
- Correspondence: (H.L.); (B.G.)
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41
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Sołtys K, Wycisk K, Ożyhar A. Liquid-liquid phase separation of the intrinsically disordered AB region of hRXRγ is driven by hydrophobic interactions. Int J Biol Macromol 2021; 183:936-949. [PMID: 33971237 DOI: 10.1016/j.ijbiomac.2021.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
Nuclear receptors (NRs) are a family of transcription factors that are regulated endogenously by small lipophilic ligands. Recently, liquid-liquid phase separation (LLPS) has appeared as a new aspect of NR function. In the human retinoid X receptor γ (hRXRγ), the inherently disordered AB region undergoes LLPS via homotypic multivalent interactions. To better understand the functions of liquid condensates, a clear view of the molecular interactions underlying the LLPS are required. The phase separation propensity of the AB region of hRXRγ (AB_hRXG) at a high NaCl concentration, a lower critical solution temperature behavior, and also sensitivity to kosmotropic salts and 1,6-hexanediol, which all indicate the importance of hydrophobic interactions in the formation of AB_hRXG liquid condensates, is presented in the paper. Additionally, molecular crowding agents and TMAO shift the equilibrium, in turn enabling phase transition at lower AB_hRXG concentrations. Although the LLPS of the proteins can lead to aggregation, AB_hRXG liquid condensates are not aggregation prone. Interestingly, the formation of AB_hRXG liquid condensates has an impact on the rest of the receptor, as AB_hRXG liquid condensates recruit the remaining fragment of hRXRγ into the droplets. The ability of AB_hRXG to undergo LLPS might be important for gene expression regulation.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Krzysztof Wycisk
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
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42
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Rubisco proton production can drive the elevation of CO 2 within condensates and carboxysomes. Proc Natl Acad Sci U S A 2021; 118:2014406118. [PMID: 33931502 PMCID: PMC8106323 DOI: 10.1073/pnas.2014406118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Membraneless organelles containing the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are a common feature of organisms utilizing CO2 concentrating mechanisms to enhance photosynthetic carbon acquisition. In cyanobacteria and proteobacteria, the Rubisco condensate is encapsulated in a proteinaceous shell, collectively termed a carboxysome, while some algae and hornworts have evolved Rubisco condensates known as pyrenoids. In both cases, CO2 fixation is enhanced compared with the free enzyme. Previous mathematical models have attributed the improved function of carboxysomes to the generation of elevated CO2 within the organelle via a colocalized carbonic anhydrase (CA) and inwardly diffusing HCO3 -, which have accumulated in the cytoplasm via dedicated transporters. Here, we present a concept in which we consider the net of two protons produced in every Rubisco carboxylase reaction. We evaluate this in a reaction-diffusion compartment model to investigate functional advantages these protons may provide Rubisco condensates and carboxysomes, prior to the evolution of HCO3 - accumulation. Our model highlights that diffusional resistance to reaction species within a condensate allows Rubisco-derived protons to drive the conversion of HCO3 - to CO2 via colocalized CA, enhancing both condensate [CO2] and Rubisco rate. Protonation of Rubisco substrate (RuBP) and product (phosphoglycerate) plays an important role in modulating internal pH and CO2 generation. Application of the model to putative evolutionary ancestors, prior to contemporary cellular HCO3 - accumulation, revealed photosynthetic enhancements along a logical sequence of advancements, via Rubisco condensation, to fully formed carboxysomes. Our model suggests that evolution of Rubisco condensation could be favored under low CO2 and low light environments.
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43
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Kim J, Lee H, Lee HG, Seo PJ. Get closer and make hotspots: liquid-liquid phase separation in plants. EMBO Rep 2021; 22:e51656. [PMID: 33913240 DOI: 10.15252/embr.202051656] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/14/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless compartments in a cell and allows the spatiotemporal organization of biochemical reactions by concentrating macromolecules locally. In plants, LLPS defines cellular reaction hotspots, and stimulus-responsive LLPS is tightly linked to a variety of cellular and biological functions triggered by exposure to various internal and external stimuli, such as stress responses, hormone signaling, and temperature sensing. Here, we provide an overview of the current understanding of physicochemical forces and molecular factors that drive LLPS in plant cells. We illustrate how the biochemical features of cellular condensates contribute to their biological functions. Additionally, we highlight major challenges for the comprehensive understanding of biological LLPS, especially in view of the dynamic and robust organization of biochemical reactions underlying plastic responses to environmental fluctuations in plants.
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Affiliation(s)
- Jiwoo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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44
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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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45
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Mohajerani F, Sayer E, Neil C, Inlow K, Hagan MF. Mechanisms of Scaffold-Mediated Microcompartment Assembly and Size Control. ACS NANO 2021; 15:4197-4212. [PMID: 33683101 PMCID: PMC8058603 DOI: 10.1021/acsnano.0c05715] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This article describes a theoretical and computational study of the dynamical assembly of a protein shell around a complex consisting of many cargo molecules and long, flexible scaffold molecules. Our study is motivated by bacterial microcompartments, which are proteinaceous organelles that assemble around a condensed droplet of enzymes and reactants. As in many examples of cytoplasmic liquid-liquid phase separation, condensation of the microcompartment interior cargo is driven by flexible scaffold proteins that have weak multivalent interactions with the cargo. Our results predict that the shell size, amount of encapsulated cargo, and assembly pathways depend sensitively on properties of the scaffold, including its length and valency of scaffold-cargo interactions. Moreover, the ability of self-assembling protein shells to change their size to accommodate scaffold molecules of different lengths depends crucially on whether the spontaneous curvature radius of the protein shell is smaller or larger than a characteristic elastic length scale of the shell. Beyond natural microcompartments, these results have important implications for synthetic biology efforts to target alternative molecules for encapsulation by microcompartments or viral shells. More broadly, the results elucidate how cells exploit coupling between self-assembly and liquid-liquid phase separation to organize their interiors.
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Affiliation(s)
- Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Evan Sayer
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Christopher Neil
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Koe Inlow
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
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46
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Zhang Y, Xu B, Weiner BG, Meir Y, Wingreen NS. Decoding the physical principles of two-component biomolecular phase separation. eLife 2021; 10:62403. [PMID: 33704061 PMCID: PMC7952089 DOI: 10.7554/elife.62403] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/18/2021] [Indexed: 01/02/2023] Open
Abstract
Cells possess a multiplicity of non-membrane-bound compartments, which form via liquid-liquid phase separation. These condensates assemble and dissolve as needed to enable central cellular functions. One important class of condensates is those composed of two associating polymer species that form one-to-one specific bonds. What are the physical principles that underlie phase separation in such systems? To address this question, we employed coarse-grained molecular dynamics simulations to examine how the phase boundaries depend on polymer valence, stoichiometry, and binding strength. We discovered a striking phenomenon – for sufficiently strong binding, phase separation is suppressed at rational polymer stoichiometries, which we termed the magic-ratio effect. We further developed an analytical dimer-gel theory that confirmed the magic-ratio effect and disentangled the individual roles of polymer properties in shaping the phase diagram. Our work provides new insights into the factors controlling the phase diagrams of biomolecular condensates, with implications for natural and synthetic systems.
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Affiliation(s)
- Yaojun Zhang
- Center for the Physics of Biological Function, Princeton University, Princeton, United States
| | - Bin Xu
- Department of Physics, Princeton University, Princeton, United States
| | - Benjamin G Weiner
- Department of Physics, Princeton University, Princeton, United States
| | - Yigal Meir
- Department of Physics, Princeton University, Princeton, United States.,Department of Physics, Ben Gurion University of the Negev, Beersheba, Israel.,Department of Molecular Biology, Princeton University, Princeton, United States
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
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47
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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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48
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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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49
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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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50
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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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