1
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Croce R, Carmo-Silva E, Cho YB, Ermakova M, Harbinson J, Lawson T, McCormick AJ, Niyogi KK, Ort DR, Patel-Tupper D, Pesaresi P, Raines C, Weber APM, Zhu XG. Perspectives on improving photosynthesis to increase crop yield. THE PLANT CELL 2024; 36:3944-3973. [PMID: 38701340 PMCID: PMC11449117 DOI: 10.1093/plcell/koae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024]
Abstract
Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin-Benson-Bassham (CBB) cycle. Additionally, we explore methods to increase carbon dioxide (CO2) concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.
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Affiliation(s)
- Roberta Croce
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, theNetherlands
| | | | - Young B Cho
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
| | - Maria Ermakova
- School of Biological Sciences, Faculty of Science, Monash University, Melbourne, VIC 3800, Australia
| | - Jeremy Harbinson
- Laboratory of Biophysics, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
| | - Alistair J McCormick
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
| | - Dhruv Patel-Tupper
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Paolo Pesaresi
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Christine Raines
- School of Life Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
| | - Xin-Guang Zhu
- Key Laboratory of Carbon Capture, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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2
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Shimakawa G, Demulder M, Flori S, Kawamoto A, Tsuji Y, Nawaly H, Tanaka A, Tohda R, Ota T, Matsui H, Morishima N, Okubo R, Wietrzynski W, Lamm L, Righetto RD, Uwizeye C, Gallet B, Jouneau PH, Gerle C, Kurisu G, Finazzi G, Engel BD, Matsuda Y. Diatom pyrenoids are encased in a protein shell that enables efficient CO 2 fixation. Cell 2024:S0092-8674(24)01031-6. [PMID: 39357521 DOI: 10.1016/j.cell.2024.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/13/2024] [Accepted: 09/06/2024] [Indexed: 10/04/2024]
Abstract
Pyrenoids are subcompartments of algal chloroplasts that increase the efficiency of Rubisco-driven CO2 fixation. Diatoms fix up to 20% of global CO2, but their pyrenoids remain poorly characterized. Here, we used in vivo photo-crosslinking to identify pyrenoid shell (PyShell) proteins, which we localized to the pyrenoid periphery of model pennate and centric diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana. In situ cryo-electron tomography revealed that pyrenoids of both diatom species are encased in a lattice-like protein sheath. Single-particle cryo-EM yielded a 2.4-Å-resolution structure of an in vitro TpPyShell1 lattice, which showed how protein subunits interlock. T. pseudonana TpPyShell1/2 knockout mutants had no PyShell sheath, altered pyrenoid morphology, and a high-CO2 requiring phenotype, with reduced photosynthetic efficiency and impaired growth under standard atmospheric conditions. The structure and function of the diatom PyShell provide a molecular view of how CO2 is assimilated in the ocean, a critical ecosystem undergoing rapid change.
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Affiliation(s)
- Ginga Shimakawa
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Manon Demulder
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Serena Flori
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshinori Tsuji
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hermanus Nawaly
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Atsuko Tanaka
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara 903-0213, Japan
| | - Rei Tohda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tadayoshi Ota
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Hiroaki Matsui
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Natsumi Morishima
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Ryosuke Okubo
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | | | - Lorenz Lamm
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; HelmholtzAI, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Ricardo D Righetto
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Clarisse Uwizeye
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Benoit Gallet
- University of Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Christoph Gerle
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
| | - Yusuke Matsuda
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan.
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3
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Li T, Chen T, Chang P, Ge X, Chriscoli V, Dykes GF, Wang Q, Liu LN. Uncovering the roles of the scaffolding protein CsoS2 in mediating the assembly and shape of the α-carboxysome shell. mBio 2024:e0135824. [PMID: 39207096 DOI: 10.1128/mbio.01358-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
Carboxysomes are proteinaceous organelles featuring icosahedral protein shells that enclose the carbon-fixing enzymes, ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco), along with carbonic anhydrase. The intrinsically disordered scaffolding protein CsoS2 plays a vital role in the construction of α-carboxysomes through bridging the shell and cargo enzymes. The N-terminal domain of CsoS2 binds Rubisco and facilitates Rubisco packaging within the α-carboxysome, whereas the C-terminal domain of CsoS2 (CsoS2-C) anchors to the shell and promotes shell assembly. However, the role of the middle region of CsoS2 (CsoS2-M) has remained elusive. Here, we conducted in-depth examinations on the function of CsoS2-M in the assembly of the α-carboxysome shell by generating a series of recombinant shell variants in the absence of cargos. Our results reveal that CsoS2-M assists CsoS2-C in the assembly of the α-carboxysome shell and plays an important role in shaping the α-carboxysome shell through enhancing the association of shell proteins on both the facet-facet interfaces and flat shell facets. Moreover, CsoS2-M is responsible for recruiting the C-terminal truncated isoform of CsoS2, CsoS2A, into α-carboxysomes, which is crucial for Rubisco encapsulation and packaging. This study not only deepens our knowledge of how the carboxysome shell is constructed and regulated but also lays the groundwork for engineering and repurposing carboxysome-based nanostructures for diverse biotechnological purposes. IMPORTANCE Carboxysomes are a paradigm of organelle-like structures in cyanobacteria and many proteobacteria. These nanoscale compartments enclose Rubisco and carbonic anhydrase within an icosahedral virus-like shell to improve CO2 fixation, playing a vital role in the global carbon cycle. Understanding how the carboxysomes are formed is not only important for basic research studies but also holds promise for repurposing carboxysomes in bioengineering applications. In this study, we focuses on a specific scaffolding protein called CsoS2, which is involved in facilitating the assembly of α-type carboxysomes. By deciphering the functions of different parts of CsoS2, especially its middle region, we provide new insights into how CsoS2 drives the stepwise assembly of the carboxysome at the molecular level. This knowledge will guide the rational design and reprogramming of carboxysome nanostructures for many biotechnological applications.
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Affiliation(s)
- Tianpei Li
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ping Chang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Xingwu Ge
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Vincent Chriscoli
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
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4
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Turnšek JB, Oltrogge LM, Savage DF. Conserved and repetitive motifs in an intrinsically disordered protein drive ⍺-carboxysome assembly. J Biol Chem 2024; 300:107532. [PMID: 38971311 PMCID: PMC11365436 DOI: 10.1016/j.jbc.2024.107532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 07/08/2024] Open
Abstract
All cyanobacteria and some chemoautotrophic bacteria fix CO2 into sugars using specialized proteinaceous compartments called carboxysomes. Carboxysomes enclose the enzymes Rubisco and carbonic anhydrase inside a layer of shell proteins to increase the CO2 concentration for efficient carbon fixation by Rubisco. In the ⍺-carboxysome lineage, a disordered and highly repetitive protein named CsoS2 is essential for carboxysome formation and function. Without it, the bacteria require high CO2 to grow. How does a protein predicted to be lacking structure serve as the architectural scaffold for such a vital cellular compartment? In this study, we identify key residues present in the repeats of CsoS2, VTG and Y, which are necessary for building functional ⍺-carboxysomes in vivo. These highly conserved and repetitive residues contribute to the multivalent binding interaction and phase separation behavior between CsoS2 and shell proteins. We also demonstrate 3-component reconstitution of CsoS2, Rubisco, and shell proteins into spherical condensates and show the utility of reconstitution as a biochemical tool to study carboxysome biogenesis. The precise self-assembly of thousands of proteins is crucial for carboxysome formation, and understanding this process could enable their use in alternative biological hosts or industrial processes as effective tools to fix carbon.
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Affiliation(s)
- Julia B Turnšek
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA.
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5
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Zhang T, Liu D, Zhang Y, Chen L, Zhang W, Sun T. Biomedical engineering utilizing living photosynthetic cyanobacteria and microalgae: Current status and future prospects. Mater Today Bio 2024; 27:101154. [PMID: 39113912 PMCID: PMC11304071 DOI: 10.1016/j.mtbio.2024.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/24/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Cyanobacteria are the only prokaryotes capable of performing oxygenic photosynthesis on Earth. Besides their traditional roles serving as primary producers, cyanobacteria also synthesize abundant secondary metabolites including carotenoids, alkaloids, peptides, which have been reported to possess medicinal potentials. More importantly, the advancement of synthetic biology technology has further expanded their potential biomedical applications especially using living/engineered cyanobacteria, providing promising and attractive strategies for future disease treatments. To improve the understanding and to facilitate future applications, this review aims to discuss the current status and future prospects of cyanobacterial-based biomedical engineering. Firstly, specific properties of cyanobacteria related with biomedical applications like their natural products of bioactive compounds and heavy metal adsorption were concluded. Subsequently, based on these properties of cyanobacteria, we discussed the progress of their applications in various disease models like hypoxia microenvironment alleviation, wound healing, drug delivery, and so on. Finally, the future prospects including further exploration of cyanobacteria secondary metabolites, the integration of bioactive compounds synthesized by cyanobacteria in situ with medical diagnosis and treatment, and the optimization of in vivo application were critically presented. The review will promote the studies related with cyanobacteria-based biomedical engineering and its practical application in clinical trials in the future.
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Affiliation(s)
- Tong Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Dailin Liu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Yingying Zhang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
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6
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Karthick PV, Senthil A, Djanaguiraman M, Anitha K, Kuttimani R, Boominathan P, Karthikeyan R, Raveendran M. Improving Crop Yield through Increasing Carbon Gain and Reducing Carbon Loss. PLANTS (BASEL, SWITZERLAND) 2024; 13:1317. [PMID: 38794389 PMCID: PMC11124956 DOI: 10.3390/plants13101317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 05/26/2024]
Abstract
Photosynthesis is a process where solar energy is utilized to convert atmospheric CO2 into carbohydrates, which forms the basis for plant productivity. The increasing demand for food has created a global urge to enhance yield. Earlier, the plant breeding program was targeting the yield and yield-associated traits to enhance the crop yield. However, the yield cannot be further improved without improving the leaf photosynthetic rate. Hence, in this review, various strategies to enhance leaf photosynthesis were presented. The most promising strategies were the optimization of Rubisco carboxylation efficiency, the introduction of a CO2 concentrating mechanism in C3 plants, and the manipulation of photorespiratory bypasses in C3 plants, which are discussed in detail. Improving Rubisco's carboxylation efficiency is possible by engineering targets such as Rubisco subunits, chaperones, and Rubisco activase enzyme activity. Carbon-concentrating mechanisms can be introduced in C3 plants by the adoption of pyrenoid and carboxysomes, which can increase the CO2 concentration around the Rubisco enzyme. Photorespiration is the process by which the fixed carbon is lost through an oxidative process. Different approaches to reduce carbon and nitrogen loss were discussed. Overall, the potential approaches to improve the photosynthetic process and the way forward were discussed in detail.
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Affiliation(s)
- Palanivelu Vikram Karthick
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (P.V.K.); (M.D.); (K.A.); (R.K.); (P.B.)
| | - Alagarswamy Senthil
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (P.V.K.); (M.D.); (K.A.); (R.K.); (P.B.)
| | - Maduraimuthu Djanaguiraman
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (P.V.K.); (M.D.); (K.A.); (R.K.); (P.B.)
| | - Kuppusamy Anitha
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (P.V.K.); (M.D.); (K.A.); (R.K.); (P.B.)
| | - Ramalingam Kuttimani
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (P.V.K.); (M.D.); (K.A.); (R.K.); (P.B.)
| | - Parasuraman Boominathan
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (P.V.K.); (M.D.); (K.A.); (R.K.); (P.B.)
| | - Ramasamy Karthikeyan
- Directorate of Crop Management, Tamil Nadu Agricultural University, Coimbatore 641003, India;
| | - Muthurajan Raveendran
- Directorate of Research, Tamil Nadu Agricultural University, Coimbatore 641003, India;
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Wang Y, Selivanovitch E, Douglas T. Enhancing Multistep Reactions: Biomimetic Design of Substrate Channeling Using P22 Virus-Like Particles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206906. [PMID: 36815387 PMCID: PMC10161098 DOI: 10.1002/advs.202206906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/09/2023] [Indexed: 05/06/2023]
Abstract
Many biocatalytic processes inside cells employ substrate channeling to control the diffusion of intermediates for improved efficiency of enzymatic cascade reactions. This inspirational mechanism offers a strategy for increasing efficiency of multistep biocatalysis, especially where the intermediates are expensive cofactors that require continuous regeneration. However, it is challenging to achieve substrate channeling artificially in vitro due to fast diffusion of small molecules. By mimicking some naturally occurring metabolons, nanoreactors are developed using P22 virus-like particles (VLPs), which enhance the efficiency of nicotinamide adenine dinucleotide (NAD)-dependent multistep biocatalysis by substrate channeling. In this design, NAD-dependent enzyme partners are coencapsulated inside the VLPs, while the cofactor is covalently tethered to the capsid interior through swing arms. The crowded environment inside the VLPs induces colocalization of the enzymes and the immobilized NAD, which shuttles between the enzymes for in situ regeneration without diffusing into the bulk solution. The modularity of the nanoreactors allows to tune their composition and consequently their overall activity, and also remodel them for different reactions by altering enzyme partners. Given the plasticity and versatility, P22 VLPs possess great potential for developing functional materials capable of multistep biotransformations with advantageous properties, including enhanced efficiency and economical usage of enzyme cofactors.
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Affiliation(s)
- Yang Wang
- Department of ChemistryIndiana University800 E Kirkwood AveBloomingtonIN47405USA
| | | | - Trevor Douglas
- Department of ChemistryIndiana University800 E Kirkwood AveBloomingtonIN47405USA
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8
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Goodchild-Michelman IM, Church GM, Schubert MG, Tang TC. Light and carbon: Synthetic biology toward new cyanobacteria-based living biomaterials. Mater Today Bio 2023; 19:100583. [PMID: 36846306 PMCID: PMC9945787 DOI: 10.1016/j.mtbio.2023.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023] Open
Abstract
Cyanobacteria are ideal candidates to use in developing carbon neutral and carbon negative technologies; they are efficient photosynthesizers and amenable to genetic manipulation. Over the past two decades, researchers have demonstrated that cyanobacteria can make sustainable, useful biomaterials, many of which are engineered living materials. However, we are only beginning to see such technologies applied at an industrial scale. In this review, we explore the ways in which synthetic biology tools enable the development of cyanobacteria-based biomaterials. First we give an overview of the ecological and biogeochemical importance of cyanobacteria and the work that has been done using cyanobacteria to create biomaterials so far. This is followed by a discussion of commonly used cyanobacteria strains and synthetic biology tools that exist to engineer cyanobacteria. Then, three case studies-bioconcrete, biocomposites, and biophotovoltaics-are explored as potential applications of synthetic biology in cyanobacteria-based materials. Finally, challenges and future directions of cyanobacterial biomaterials are discussed.
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Affiliation(s)
- Isabella M. Goodchild-Michelman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Tzu-Chieh Tang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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9
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Manning T, Birch R, Stevenson T, Nugent G, Whitney S. Bacterial Form II Rubisco can support wild-type growth and productivity in Solanum tuberosum cv. Desiree (potato) under elevated CO 2. PNAS NEXUS 2023; 2:pgac305. [PMID: 36743474 PMCID: PMC9896143 DOI: 10.1093/pnasnexus/pgac305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/22/2022] [Indexed: 02/05/2023]
Abstract
The last decade has seen significant advances in the development of approaches for improving both the light harvesting and carbon fixation pathways of photosynthesis by nuclear transformation, many involving multigene synthetic biology approaches. As efforts to replicate these accomplishments from tobacco into crops gather momentum, similar diversification is needed in the range of transgenic options available, including capabilities to modify crop photosynthesis by chloroplast transformation. To address this need, here we describe the first transplastomic modification of photosynthesis in a crop by replacing the native Rubisco in potato with the faster, but lower CO2-affinity and poorer CO2/O2 specificity Rubisco from the bacterium Rhodospirillum rubrum. High level production of R. rubrum Rubisco in the potRr genotype (8 to 10 µmol catalytic sites m2) allowed it to attain wild-type levels of productivity, including tuber yield, in air containing 0.5% (v/v) CO2. Under controlled environment growth at 25°C and 350 µmol photons m2 PAR, the productivity and leaf biochemistry of wild-type potato at 0.06%, 0.5%, or 1.5% (v/v) CO2 and potRr at 0.5% or 1.5% (v/v) CO2 were largely indistinguishable. These findings suggest that increasing the scope for enhancing productivity gains in potato by improving photosynthate production will necessitate improvement to its sink-potential, consistent with current evidence productivity gains by eCO2 fertilization for this crop hit a ceiling around 560 to 600 ppm CO2.
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Affiliation(s)
- Tahnee Manning
- School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Rosemary Birch
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia
| | - Trevor Stevenson
- School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Gregory Nugent
- School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Spencer Whitney
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia
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10
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Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. The small subunit of Rubisco and its potential as an engineering target. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:543-561. [PMID: 35849331 PMCID: PMC9833052 DOI: 10.1093/jxb/erac309] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 05/06/2023]
Abstract
Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
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Affiliation(s)
- Yuwei Mao
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - Ella Catherall
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - Aranzazú Díaz-Ramos
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - George R L Greiff
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stavros Azinas
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Laura Gunn
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
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11
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Peng G, Jin H, Liu F, Yang X, Sui P, Lin S. Biomimetic ultrathin pepsomes for photo-controllable catalysis. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Lavania A, Carpenter WB, Oltrogge LM, Perez D, Turnšek JB, Savage DF, Moerner WE. Exploring Masses and Internal Mass Distributions of Single Carboxysomes in Free Solution Using Fluorescence and Interferometric Scattering in an Anti-Brownian Trap. J Phys Chem B 2022; 126:8747-8759. [PMID: 36282790 PMCID: PMC9639131 DOI: 10.1021/acs.jpcb.2c05939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/10/2022] [Indexed: 01/11/2023]
Abstract
Carboxysomes are self-assembled bacterial microcompartments that facilitate carbon assimilation by colocalizing the enzymes of CO2 fixation within a protein shell. These microcompartments can be highly heterogeneous in their composition and filling, so measuring the mass and loading of an individual carboxysome would allow for better characterization of its assembly and function. To enable detailed and extended characterizations of single nanoparticles in solution, we recently demonstrated an improved interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which tracks the position of a single nanoparticle via its scattering of a near-infrared beam and applies feedback to counteract its Brownian motion. Importantly, the scattering signal can be related to the mass of nanoscale proteinaceous objects, whose refractive indices are well-characterized. We calibrate single-particle scattering cross-section measurements in the ISABEL trap and determine individual carboxysome masses in the 50-400 MDa range by analyzing their scattering cross sections with a core-shell model. We further investigate carboxysome loading by combining mass measurements with simultaneous fluorescence reporting from labeled internal components. This method may be extended to other biological objects, such as viruses or extracellular vesicles, and can be combined with orthogonal fluorescence reporters to achieve precise physical and chemical characterization of individual nanoscale biological objects.
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Affiliation(s)
- Abhijit
A. Lavania
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California94305, United States
| | - William B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
| | - Julia B. Turnšek
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California94305, United States
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13
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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)
- Liat Adler
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Aranzazú Díaz-Ramos
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - 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
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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14
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Raba DA, Kerfeld CA. The potential of bacterial microcompartment architectures for phytonanotechnology. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:700-710. [PMID: 35855583 DOI: 10.1111/1758-2229.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
The application of nanotechnology to plants, termed phytonanotechnology, has the potential to revolutionize plant research and agricultural production. Advancements in phytonanotechnology will allow for the time-controlled and target-specific release of bioactive compounds and agrochemicals to alter and optimize conventional plant production systems. A diverse range of engineered nanoparticles with unique physiochemical properties is currently being investigated to determine their suitability for plants. Improvements in crop yield, disease resistance and nutrient and pesticide management are all possible using designed nanocarriers. However, despite these prospective benefits, research to thoroughly understand the precise activity, localization and potential phytotoxicity of these nanoparticles within plant systems is required. Protein-based bacterial microcompartment shell proteins that self-assemble into spherical shells, nanotubes and sheets could be of immense value for phytonanotechnology due to their ease of manipulation, multifunctionality, rapid and efficient producibility and biodegradability. In this review, we explore bacterial microcompartment-based architectures within the scope of phytonanotechnology.
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Affiliation(s)
- Daniel A Raba
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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15
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Using synthetic biology to improve photosynthesis for sustainable food production. J Biotechnol 2022; 359:1-14. [PMID: 36126804 DOI: 10.1016/j.jbiotec.2022.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 11/23/2022]
Abstract
Photosynthesis is responsible for the primary productivity and maintenance of life on Earth, boosting biological activity and contributing to the maintenance of the environment. In the past, traditional crop improvement was considered sufficient to meet food demands, but the growing demand for food coupled with climate change has modified this scenario over the past decades. However, advances in this area have not focused on photosynthesis per se but rather on fixed carbon partitioning. In short, other approaches must be used to meet an increasing agricultural demand. Thus, several paths may be followed, from modifications in leaf shape and canopy architecture, improving metabolic pathways related to CO2 fixation, the inclusion of metabolic mechanisms from other species, and improvements in energy uptake by plants. Given the recognized importance of photosynthesis, as the basis of the primary productivity on Earth, we here present an overview of the latest advances in attempts to improve plant photosynthetic performance. We focused on points considered key to the enhancement of photosynthesis, including leaf shape development, RuBisCO reengineering, Calvin-Benson cycle optimization, light use efficiency, the introduction of the C4 cycle in C3 plants and the inclusion of other CO2 concentrating mechanisms (CCMs). We further provide compelling evidence that there is still room for further improvements. Finally, we conclude this review by presenting future perspectives and possible new directions on this subject.
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16
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Metskas LA, Ortega D, Oltrogge LM, Blikstad C, Lovejoy DR, Laughlin TG, Savage DF, Jensen GJ. Rubisco forms a lattice inside alpha-carboxysomes. Nat Commun 2022; 13:4863. [PMID: 35982043 PMCID: PMC9388693 DOI: 10.1038/s41467-022-32584-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 08/04/2022] [Indexed: 02/07/2023] Open
Abstract
Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image α-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 μM. This characterization of Rubisco cargo inside the α-carboxysome provides insight into the balance between order and disorder in microcompartment organization.
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Affiliation(s)
- Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Biological Sciences Department, Purdue University, West Lafayette, IN, USA.
- Chemistry Department, Purdue University, West Lafayette, IN, USA.
| | - Davi Ortega
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Derik R Lovejoy
- Biological Sciences Department, Purdue University, West Lafayette, IN, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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17
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Sugawara T, Kaneko K. Chemophoresis engine: A general mechanism of ATPase-driven cargo transport. PLoS Comput Biol 2022; 18:e1010324. [PMID: 35877681 PMCID: PMC9363008 DOI: 10.1371/journal.pcbi.1010324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 08/09/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Cell polarity regulates the orientation of the cytoskeleton members that directs intracellular transport for cargo-like organelles, using chemical gradients sustained by ATP or GTP hydrolysis. However, how cargo transports are directly mediated by chemical gradients remains unknown. We previously proposed a physical mechanism that enables directed movement of cargos, referred to as chemophoresis. According to the mechanism, a cargo with reaction sites is subjected to a chemophoresis force in the direction of the increased concentration. Based on this, we introduce an extended model, the chemophoresis engine, as a general mechanism of cargo motion, which transforms chemical free energy into directed motion through the catalytic ATP hydrolysis. We applied the engine to plasmid motion in a ParABS system to demonstrate the self-organization system for directed plasmid movement and pattern dynamics of ParA-ATP concentration, thereby explaining plasmid equi-positioning and pole-to-pole oscillation observed in bacterial cells and in vitro experiments. We mathematically show the existence and stability of the plasmid-surfing pattern, which allows the cargo-directed motion through the symmetry-breaking transition of the ParA-ATP spatiotemporal pattern. We also quantitatively demonstrate that the chemophoresis engine can work even under in vivo conditions. Finally, we discuss the chemophoresis engine as one of the general mechanisms of hydrolysis-driven intracellular transport. The formation of organelle/macromolecule patterns depending on chemical concentration under non-equilibrium conditions, first observed during macroscopic morphogenesis, has recently been observed at the intracellular level as well, and its relevance as intracellular morphogen has been demonstrated in the case of bacterial cell division. These studies have discussed how cargos maintain positional information provided by chemical concentration gradients/localization. However, how cargo transports are directly mediated by chemical gradients remains unknown. Based on the previously proposed mechanism of chemotaxis-like behavior of cargos (referred to as chemophoresis), we introduce a chemophoresis engine as a physicochemical mechanism of cargo motion, which transforms chemical free energy to directed motion. The engine is based on the chemophoresis force to make cargoes move in the direction of the increasing ATPase(-ATP) concentration and an enhanced catalytic ATPase hydrolysis at the positions of the cargoes. Applying the engine to ATPase-driven movement of plasmid-DNAs in bacterial cells, we constructed a mathematical model to demonstrate the self-organization for directed plasmid motion and pattern dynamics of ATPase concentration, as is consistent with in vitro and in vivo experiments. We propose that this chemophoresis engine works as a general mechanism of hydrolysis-driven intracellular transport.
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Affiliation(s)
- Takeshi Sugawara
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Kunihiko Kaneko
- Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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18
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Singh AK, Santos-Merino M, Sakkos JK, Walker BJ, Ducat DC. Rubisco regulation in response to altered carbon status in the cyanobacterium Synechococcus elongatus PCC 7942. PLANT PHYSIOLOGY 2022; 189:874-888. [PMID: 35201348 PMCID: PMC9157067 DOI: 10.1093/plphys/kiac065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/22/2021] [Indexed: 05/19/2023]
Abstract
Photosynthetic organisms possess a variety of mechanisms to achieve balance between absorbed light (source) and the capacity to metabolically utilize or dissipate this energy (sink). While regulatory processes that detect changes in metabolic status/balance are relatively well studied in plants, analogous pathways remain poorly characterized in photosynthetic microbes. Here, we explored systemic changes that result from alterations in carbon availability in the model cyanobacterium Synechococcus elongatus PCC 7942 by taking advantage of an engineered strain where influx/efflux of a central carbon metabolite, sucrose, can be regulated experimentally. We observed that induction of a high-flux sucrose export pathway leads to depletion of internal carbon storage pools (glycogen) and concurrent increases in estimates of photosynthetic activity. Further, a proteome-wide analysis and fluorescence reporter-based analysis revealed that upregulated factors following the activation of the metabolic sink are concentrated on ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) and auxiliary modules involved in Rubisco maturation. Carboxysome number and Rubisco activity also increased following engagement of sucrose secretion. Conversely, reversing the flux of sucrose by feeding exogenous sucrose through the heterologous transporter resulted in increased glycogen pools, decreased Rubisco abundance, and carboxysome reorganization. Our data suggest that Rubisco activity and organization are key variables connected to regulatory pathways involved in metabolic balancing in cyanobacteria.
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Affiliation(s)
- Amit K Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - Jonathan K Sakkos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - Berkley J Walker
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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19
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Carpenter W, Lavania AA, Borden JS, Oltrogge LM, Perez D, Dahlberg PD, Savage DF, Moerner WE. Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution. J Phys Chem Lett 2022; 13:4455-4462. [PMID: 35549289 PMCID: PMC9150107 DOI: 10.1021/acs.jpclett.2c00782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diffusion of biological nanoparticles in solution impedes our ability to continuously monitor individual particles and measure their physical and chemical properties. To overcome this, we previously developed the interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which uses scattering to localize a particle and applies electrokinetic forces that counteract Brownian motion, thus enabling extended observation. Here we present an improved ISABEL trap that incorporates a near-infrared scatter illumination beam and rapidly interleaves 405 and 488 nm fluorescence excitation reporter beams. With the ISABEL trap, we monitored the internal redox environment of individual carboxysomes labeled with the ratiometric redox reporter roGFP2. Carboxysomes widely vary in scattering contrast (reporting on size) and redox-dependent ratiometric fluorescence. Furthermore, we used redox sensing to explore the chemical kinetics within intact carboxysomes, where bulk measurements may contain unwanted contributions from aggregates or interfering fluorescent proteins. Overall, we demonstrate the ISABEL trap's ability to sensitively monitor nanoscale biological objects, enabling new experiments on these systems.
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Affiliation(s)
- William
B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Abhijit A. Lavania
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Julia S. Borden
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National
Accelerator Laboratory, Menlo Park, California 94025, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
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20
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Abstract
Carbon dioxide is a major greenhouse gas, and its fixation and transformation are receiving increasing attention. Biofixation of CO2 is an eco–friendly and efficient way to reduce CO2, and six natural CO2 fixation pathways have been identified in microorganisms and plants. In this review, the six pathways along with the most recent identified variant pathway were firstly comparatively characterized. The key metabolic process and enzymes of the CO2 fixation pathways were also summarized. Next, the enzymes of Rubiscos, biotin-dependent carboxylases, CO dehydrogenase/acetyl-CoA synthase, and 2-oxoacid:ferredoxin oxidoreductases, for transforming inorganic carbon (CO2, CO, and bicarbonate) to organic chemicals, were specially analyzed. Then, the factors including enzyme properties, CO2 concentrating, energy, and reducing power requirements that affect the efficiency of CO2 fixation were discussed. Recent progress in improving CO2 fixation through enzyme and metabolic engineering was then summarized. The artificial CO2 fixation pathways with thermodynamical and/or energetical advantages or benefits and their applications in biosynthesis were included as well. The challenges and prospects of CO2 biofixation and conversion are discussed.
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21
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Abstract
Carboxysomes are anabolic bacterial microcompartments that play an essential role in carbon fixation in cyanobacteria and some chemoautotrophs. This self-assembling organelle encapsulates the key CO2-fixing enzymes, Rubisco, and carbonic anhydrase using a polyhedral protein shell that is constructed by hundreds of shell protein paralogs. The α-carboxysome from the chemoautotroph Halothiobacillus neapolitanus serves as a model system in fundamental studies and synthetic engineering of carboxysomes. In this study, we adopted a QconCAT-based quantitative mass spectrometry approach to determine the stoichiometric composition of native α-carboxysomes from H. neapolitanus. We further performed an in-depth comparison of the protein stoichiometry of native α-carboxysomes and their recombinant counterparts heterologously generated in Escherichia coli to evaluate the structural variability and remodeling of α-carboxysomes. Our results provide insight into the molecular principles that mediate carboxysome assembly, which may aid in rational design and reprogramming of carboxysomes in new contexts for biotechnological applications. IMPORTANCE A wide range of bacteria use special protein-based organelles, termed bacterial microcompartments, to encase enzymes and reactions to increase the efficiency of biological processes. As a model bacterial microcompartment, the carboxysome contains a protein shell filled with the primary carbon fixation enzyme Rubisco. The self-assembling organelle is generated by hundreds of proteins and plays important roles in converting carbon dioxide to sugar, a process known as carbon fixation. In this study, we uncovered the exact stoichiometry of all building components and the structural plasticity of the functional α-carboxysome, using newly developed quantitative mass spectrometry together with biochemistry, electron microscopy, and enzymatic assay. The study advances our understanding of the architecture and modularity of natural carboxysomes. The knowledge learned from natural carboxysomes will suggest feasible ways to produce functional carboxysomes in other hosts, such as crop plants, with the overwhelming goal of boosting cell metabolism and crop yields.
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22
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Treece TR, Gonzales JN, Pressley JR, Atsumi S. Synthetic Biology Approaches for Improving Chemical Production in Cyanobacteria. Front Bioeng Biotechnol 2022; 10:869195. [PMID: 35372310 PMCID: PMC8965691 DOI: 10.3389/fbioe.2022.869195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 11/15/2022] Open
Abstract
Biological chemical production has gained traction in recent years as a promising renewable alternative to traditional petrochemical based synthesis. Of particular interest in the field of metabolic engineering are photosynthetic microorganisms capable of sequestering atmospheric carbon dioxide. CO2 levels have continued to rise at alarming rates leading to an increasingly uncertain climate. CO2 can be sequestered by engineered photosynthetic microorganisms and used for chemical production, representing a renewable production method for valuable chemical commodities such as biofuels, plastics, and food additives. The main challenges in using photosynthetic microorganisms for chemical production stem from the seemingly inherent limitations of carbon fixation and photosynthesis resulting in slower growth and lower average product titers compared to heterotrophic organisms. Recently, there has been an increase in research around improving photosynthetic microorganisms as renewable chemical production hosts. This review will discuss the various efforts to overcome the intrinsic inefficiencies of carbon fixation and photosynthesis, including rewiring carbon fixation and photosynthesis, investigating alternative carbon fixation pathways, installing sugar catabolism to supplement carbon fixation, investigating newly discovered fast growing photosynthetic species, and using new synthetic biology tools such as CRISPR to radically alter metabolism.
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Affiliation(s)
- Tanner R. Treece
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Jake N. Gonzales
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Joseph R. Pressley
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
- *Correspondence: Shota Atsumi,
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23
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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24
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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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Tullman-Ercek D, Warren M. Editorial overview: Bacterial microcompartments to the fore as metabolism is put in its place. Curr Opin Microbiol 2021; 64:159-161. [PMID: 34740525 DOI: 10.1016/j.mib.2021.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA.
| | - Martin Warren
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, UK
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Zang K, Wang H, Hartl FU, Hayer-Hartl M. Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis. Nat Struct Mol Biol 2021; 28:909-922. [PMID: 34759380 PMCID: PMC8580825 DOI: 10.1038/s41594-021-00676-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/28/2021] [Indexed: 12/01/2022]
Abstract
Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the β-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of γCAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The γCAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the γCAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before β-carboxysome shell formation.
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Affiliation(s)
- Kun Zang
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Huping Wang
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
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