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Nguyen ND, Pulsford SB, Förster B, Rottet S, Rourke L, Long BM, Price GD. A carboxysome-based CO 2 concentrating mechanism for C 3 crop chloroplasts: advances and the road ahead. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:940-952. [PMID: 38321620 DOI: 10.1111/tpj.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
The introduction of the carboxysome-based CO2 concentrating mechanism (CCM) into crop plants has been modelled to significantly increase crop yields. This projection serves as motivation for pursuing this strategy to contribute to global food security. The successful implementation of this engineering challenge is reliant upon the transfer of a microcompartment that encapsulates cyanobacterial Rubisco, known as the carboxysome, alongside active bicarbonate transporters. To date, significant progress has been achieved with respect to understanding various aspects of the cyanobacterial CCM, and more recently, different components of the carboxysome have been successfully introduced into plant chloroplasts. In this Perspective piece, we summarise recent findings and offer new research avenues that will accelerate research in this field to ultimately and successfully introduce the carboxysome into crop plants for increased crop yields.
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Affiliation(s)
- Nghiem D Nguyen
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sacha B Pulsford
- Research School of Chemistry, Australian National University, 137 Sullivan's Ck Rd, Acton, Australian Capital Territory, 2601, Australia
| | - Britta Förster
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sarah Rottet
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Loraine Rourke
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Benedict M Long
- Discipline of Biological Sciences, School of Environmental and Life Sciences, ARC Centre of Excellence in Synthetic Biology, The University of Newcastle, University Drive, Callaghan, New South Wales, 2308, Australia
| | - G Dean Price
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
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2
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Li R, He Y, Chen J, Zheng S, Zhuang C. Research Progress in Improving Photosynthetic Efficiency. Int J Mol Sci 2023; 24:ijms24119286. [PMID: 37298238 DOI: 10.3390/ijms24119286] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Photosynthesis is the largest mass- and energy-conversion process on Earth, and it is the material basis for almost all biological activities. The efficiency of converting absorbed light energy into energy substances during photosynthesis is very low compared to theoretical values. Based on the importance of photosynthesis, this article summarizes the latest progress in improving photosynthesis efficiency from various perspectives. The main way to improve photosynthetic efficiency is to optimize the light reactions, including increasing light absorption and conversion, accelerating the recovery of non-photochemical quenching, modifying enzymes in the Calvin cycle, introducing carbon concentration mechanisms into C3 plants, rebuilding the photorespiration pathway, de novo synthesis, and changing stomatal conductance. These developments indicate that there is significant room for improvement in photosynthesis, providing support for improving crop yields and mitigating changes in climate conditions.
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Affiliation(s)
- Ruiqi Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Ying He
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Junyu Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shaoyan Zheng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Chuxiong Zhuang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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3
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Chen T, Hojka M, Davey P, Sun Y, Dykes GF, Zhou F, Lawson T, Nixon PJ, Lin Y, Liu LN. Engineering α-carboxysomes into plant chloroplasts to support autotrophic photosynthesis. Nat Commun 2023; 14:2118. [PMID: 37185249 PMCID: PMC10130085 DOI: 10.1038/s41467-023-37490-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/17/2023] [Indexed: 05/17/2023] Open
Abstract
The growth in world population, climate change, and resource scarcity necessitate a sustainable increase in crop productivity. Photosynthesis in major crops is limited by the inefficiency of the key CO2-fixing enzyme Rubisco, owing to its low carboxylation rate and poor ability to discriminate between CO2 and O2. In cyanobacteria and proteobacteria, carboxysomes function as the central CO2-fixing organelles that elevate CO2 levels around encapsulated Rubisco to enhance carboxylation. There is growing interest in engineering carboxysomes into crop chloroplasts as a potential route for improving photosynthesis and crop yields. Here, we generate morphologically correct carboxysomes in tobacco chloroplasts by transforming nine carboxysome genetic components derived from a proteobacterium. The chloroplast-expressed carboxysomes display a structural and functional integrity comparable to native carboxysomes and support autotrophic growth and photosynthesis of the transplastomic plants at elevated CO2. Our study provides proof-of-concept for a route to engineering fully functional CO2-fixing modules and entire CO2-concentrating mechanisms into chloroplasts to improve crop photosynthesis and productivity.
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Affiliation(s)
- Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Marta Hojka
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Philip Davey
- School of Life Sciences, University of Essex, Colchester, CO4 4SQ, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, CO4 4SQ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China.
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003, Qingdao, China.
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4
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Chen T, Riaz S, Davey P, Zhao Z, Sun Y, Dykes GF, Zhou F, Hartwell J, Lawson T, Nixon PJ, Lin Y, Liu LN. Producing fast and active Rubisco in tobacco to enhance photosynthesis. THE PLANT CELL 2023; 35:795-807. [PMID: 36471570 PMCID: PMC9940876 DOI: 10.1093/plcell/koac348] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/24/2022] [Accepted: 12/02/2022] [Indexed: 05/28/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) performs most of the carbon fixation on Earth. However, plant Rubisco is an intrinsically inefficient enzyme given its low carboxylation rate, representing a major limitation to photosynthesis. Replacing endogenous plant Rubisco with a faster Rubisco is anticipated to enhance crop photosynthesis and productivity. However, the requirement of chaperones for Rubisco expression and assembly has obstructed the efficient production of functional foreign Rubisco in chloroplasts. Here, we report the engineering of a Form 1A Rubisco from the proteobacterium Halothiobacillus neapolitanus in Escherichia coli and tobacco (Nicotiana tabacum) chloroplasts without any cognate chaperones. The native tobacco gene encoding Rubisco large subunit was genetically replaced with H. neapolitanus Rubisco (HnRubisco) large and small subunit genes. We show that HnRubisco subunits can form functional L8S8 hexadecamers in tobacco chloroplasts at high efficiency, accounting for ∼40% of the wild-type tobacco Rubisco content. The chloroplast-expressed HnRubisco displayed a ∼2-fold greater carboxylation rate and supported a similar autotrophic growth rate of transgenic plants to that of wild-type in air supplemented with 1% CO2. This study represents a step toward the engineering of a fast and highly active Rubisco in chloroplasts to improve crop photosynthesis and growth.
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Affiliation(s)
- Taiyu Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Saba Riaz
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Philip Davey
- School of Life Sciences, University of Essex, Colchester CO4 4SQ, UK
| | - Ziyu Zhao
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - James Hartwell
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester CO4 4SQ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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5
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Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. The small subunit of Rubisco and its potential as an engineering target. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:543-561. [PMID: 35849331 PMCID: PMC9833052 DOI: 10.1093/jxb/erac309] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 05/06/2023]
Abstract
Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
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Affiliation(s)
| | | | - Aranzazú Díaz-Ramos
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - George R L Greiff
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stavros Azinas
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Laura Gunn
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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6
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Rosado-Souza L, Yokoyama R, Sonnewald U, Fernie AR. Understanding source-sink interactions: Progress in model plants and translational research to crops. MOLECULAR PLANT 2023; 16:96-121. [PMID: 36447435 DOI: 10.1016/j.molp.2022.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/25/2022] [Indexed: 06/16/2023]
Abstract
Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration. While we have learned much about how environmental conditions and diseases impact crop yield, until recently considerably less was known concerning endogenous factors, including within-plant nutrient allocation. In this review, we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field. In this respect we detail efforts aimed at improving and/or combining C3, C4, and CAM modes of photosynthesis, altering the chloroplastic electron transport chain, modulating photorespiration, adopting bacterial/algal carbon-concentrating mechanisms, and enhancing nitrogen- and water-use efficiencies. Moreover, we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford. Although source, transport, and sink functions are all covered in this review, we focus on discussing source functions because the majority of research has been conducted in this field. Nevertheless, considerable recent evidence, alongside the evidence from classical studies, demonstrates that both transport and sink functions are also incredibly important determinants of yield. We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.
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Affiliation(s)
- Laise Rosado-Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Ryo Yokoyama
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Uwe Sonnewald
- Department of Biochemistry, University of Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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7
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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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8
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Structural insights into cyanobacterial RuBisCO assembly coordinated by two chaperones Raf1 and RbcX. Cell Discov 2022; 8:93. [PMID: 36123352 PMCID: PMC9485235 DOI: 10.1038/s41421-022-00436-9] [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] [Received: 02/28/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
RuBisCO is the most abundant enzyme in nature, catalyzing the fixation of CO2 in photosynthesis. Its common form consists of eight RbcL and eight RbcS subunits, the assembly of which requires a series of chaperones that include RbcX and RuBisCO accumulation factor 1 (Raf1). To understand how these RuBisCO-specific chaperones function during cyanobacterial RbcL8RbcS8 (L8S8) holoenzyme formation, we solved a 3.3-Å cryo-electron microscopy structure of a 32-subunit RbcL8Raf18RbcX16 (L8F8X16) assembly intermediate from Anabaena sp. PCC 7120. Comparison to the previously resolved L8F8 and L8X16 structures together with biochemical assays revealed that the L8F8X16 complex forms a rather dynamic structural intermediate, favoring RbcS displacement of Raf1 and RbcX. In vitro assays further demonstrated that both Raf1 and RbcX function to regulate RuBisCO condensate formation by restricting CcmM35 binding to the stably assembled L8S8 holoenzymes. Combined with previous findings, we propose a model on how Raf1 and RbcX work in concert to facilitate, and regulate, cyanobacterial RuBisCO assembly as well as disassembly of RuBisCO condensates.
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9
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Al-Hammady MA, Silva TF, Hussein HN, Saxena G, Modolo LV, Belasy MB, Westphal H, Farag MA. How do algae endosymbionts mediate for their coral host fitness under heat stress? A comprehensive mechanistic overview. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Iñiguez C, Aguiló-Nicolau P, Galmés J. Improving photosynthesis through the enhancement of Rubisco carboxylation capacity. Biochem Soc Trans 2021; 49:2007-2019. [PMID: 34623388 DOI: 10.1042/bst20201056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022]
Abstract
Rising human population, along with the reduction in arable land and the impacts of global change, sets out the need for continuously improving agricultural resource use efficiency and crop yield (CY). Bioengineering approaches for photosynthesis optimization have largely demonstrated the potential for enhancing CY. This review is focused on the improvement of Rubisco functioning, which catalyzes the rate-limiting step of CO2 fixation required for plant growth, but also catalyzes the ribulose-bisphosphate oxygenation initiating the carbon and energy wasteful photorespiration pathway. Rubisco carboxylation capacity can be enhanced by engineering the Rubisco large and/or small subunit genes to improve its catalytic traits, or by engineering the mechanisms that provide enhanced Rubisco expression, activation and/or elevated [CO2] around the active sites to favor carboxylation over oxygenation. Recent advances have been made in the expression, assembly and activation of foreign (either natural or mutant) faster and/or more CO2-specific Rubisco versions. Some components of CO2 concentrating mechanisms (CCMs) from bacteria, algae and C4 plants has been successfully expressed in tobacco and rice. Still, none of the transformed plant lines expressing foreign Rubisco versions and/or simplified CCM components were able to grow faster than wild type plants under present atmospheric [CO2] and optimum conditions. However, the results obtained up to date suggest that it might be achievable in the near future. In addition, photosynthetic and yield improvements have already been observed when manipulating Rubisco quantity and activation degree in crops. Therefore, engineering Rubisco carboxylation capacity continues being a promising target for the improvement in photosynthesis and yield.
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Affiliation(s)
- Concepción Iñiguez
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
- Department of Ecology, Faculty of Sciences, University of Málaga, Málaga, Spain
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
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11
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Zhang J, Liu G, Carvajal AI, Wilson RH, Cai Z, Li Y. Discovery of a readily heterologously expressed Rubisco from the deep sea with potential for CO 2 capture. BIORESOUR BIOPROCESS 2021; 8:86. [PMID: 38650243 PMCID: PMC10992382 DOI: 10.1186/s40643-021-00439-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/27/2021] [Indexed: 11/10/2022] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), the key CO2-fixing enzyme in photosynthesis, is notorious for its low carboxylation. We report a highly active and assembly-competent Form II Rubisco from the endosymbiont of a deep-sea tubeworm Riftia pachyptila (RPE Rubisco), which shows a 50.5% higher carboxylation efficiency than that of a high functioning Rubisco from Synechococcus sp. PCC7002 (7002 Rubisco). It is a simpler hexamer with three pairs of large subunit homodimers around a central threefold symmetry axis. Compared with 7002 Rubisco, it showed a 3.6-fold higher carbon capture efficiency in vivo using a designed CO2 capture model. The simple structure, high carboxylation efficiency, easy heterologous soluble expression/assembly make RPE Rubisco a ready-to-deploy enzyme for CO2 capture that does not require complex co-expression of chaperones. The chemosynthetic CO2 fixation machinery of chemolithoautotrophs, CO2-fixing endosymbionts, may be more efficient than previously realized with great potential for next-generation microbial CO2 sequestration platforms.
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Affiliation(s)
- Junli Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Guoxia Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Alonso I Carvajal
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Robert H Wilson
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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12
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Lin MT, Orr DJ, Worrall D, Parry MAJ, Carmo-Silva E, Hanson MR. A procedure to introduce point mutations into the Rubisco large subunit gene in wild-type plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:876-887. [PMID: 33576096 DOI: 10.1111/tpj.15196] [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: 04/10/2020] [Revised: 01/22/2021] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Photosynthetic inefficiencies limit the productivity and sustainability of crop production and the resilience of agriculture to future societal and environmental challenges. Rubisco is a key target for improvement as it plays a central role in carbon fixation during photosynthesis and is remarkably inefficient. Introduction of mutations to the chloroplast-encoded Rubisco large subunit rbcL is of particular interest for improving the catalytic activity and efficiency of the enzyme. However, manipulation of rbcL is hampered by its location in the plastome, with many species recalcitrant to plastome transformation, and by the plastid's efficient repair system, which can prevent effective maintenance of mutations introduced with homologous recombination. Here we present a system where the introduction of a number of silent mutations into rbcL within the model plant Nicotiana tabacum facilitates simplified screening via additional restriction enzyme sites. This system was used to successfully generate a range of transplastomic lines from wild-type N. tabacum with stable point mutations within rbcL in 40% of the transformants, allowing assessment of the effect of these mutations on Rubisco assembly and activity. With further optimization the approach offers a viable way forward for mutagenic testing of Rubisco function in planta within tobacco and modification of rbcL in other crops where chloroplast transformation is feasible. The transformation strategy could also be applied to introduce point mutations in other chloroplast-encoded genes.
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Affiliation(s)
- Myat T Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Dawn Worrall
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Elizabete Carmo-Silva
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster, LA1 4YQ, UK
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
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Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803. Biosci Rep 2021; 40:222317. [PMID: 32149336 PMCID: PMC7133116 DOI: 10.1042/bsr20193325] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.
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Koester RP, Pignon CP, Kesler DC, Willison RS, Kang M, Shen Y, Priest HD, Begemann MB, Cook KA, Bannon GA, Oufattole M. Transgenic insertion of the cyanobacterial membrane protein ictB increases grain yield in Zea mays through increased photosynthesis and carbohydrate production. PLoS One 2021; 16:e0246359. [PMID: 33539477 PMCID: PMC7861388 DOI: 10.1371/journal.pone.0246359] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/18/2021] [Indexed: 11/19/2022] Open
Abstract
The C4 crop maize (Zea mays) is the most widely grown cereal crop worldwide and is an essential feedstock for food and bioenergy. Improving maize yield is important to achieve food security and agricultural sustainability in the 21st century. One potential means to improve crop productivity is to enhance photosynthesis. ictB, a membrane protein that is highly conserved across cyanobacteria, has been shown to improve photosynthesis, and often biomass, when introduced into diverse C3 plant species. Here, ictB from Synechococcus sp. strain PCC 7942 was inserted into maize using Agrobacterium-mediated transformation. In three controlled-environment experiments, ictB insertion increased leaf starch and sucrose content by up to 25% relative to controls. Experimental field trials in four growing seasons, spanning the Midwestern United States (Summers 2018 & 2019) and Argentina (Winter 2018 & 2019), showed an average of 3.49% grain yield improvement, by as much as 5.4% in a given season and up to 9.4% at certain trial locations. A subset of field trial locations was used to test for modification of ear traits and ФPSII, a proxy for photosynthesis. Results suggested that yield gain in transgenics could be associated with increased ФPSII, and the production of longer, thinner ears with more kernels. ictB localized primarily to the microsome fraction of leaf bundle-sheath cells, but not to chloroplasts. Extramembrane domains of ictB interacted in vitro with proteins involved in photosynthesis and carbohydrate metabolism. To our knowledge, this is the first published evidence of ictB insertion into a species using C4 photosynthesis and the largest-scale demonstration of grain yield enhancement from ictB insertion in planta. Results show that ictB is a valuable yield gene in the economically important crop maize, and are an important proof of concept that transgenic manipulation of photosynthesis can be used to create economically viable crop improvement traits.
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Affiliation(s)
| | | | - Dylan C Kesler
- Benson Hill, St. Louis, Missouri, United States of America
| | | | - Miyoung Kang
- Benson Hill, St. Louis, Missouri, United States of America
| | - Yu Shen
- Benson Hill, St. Louis, Missouri, United States of America
| | - Henry D Priest
- Benson Hill, St. Louis, Missouri, United States of America
| | | | - Kevin A Cook
- Benson Hill, St. Louis, Missouri, United States of America
| | - Gary A Bannon
- Benson Hill, St. Louis, Missouri, United States of America
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Donovan S, Mao Y, Orr DJ, Carmo-Silva E, McCormick AJ. CRISPR-Cas9-Mediated Mutagenesis of the Rubisco Small Subunit Family in Nicotiana tabacum. Front Genome Ed 2020; 2:605614. [PMID: 34713229 PMCID: PMC8525408 DOI: 10.3389/fgeed.2020.605614] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
Engineering the small subunit of the key CO2-fixing enzyme Rubisco (SSU, encoded by rbcS) in plants currently poses a significant challenge, as many plants have polyploid genomes and SSUs are encoded by large multigene families. Here, we used CRISPR-Cas9-mediated genome editing approach to simultaneously knock-out multiple rbcS homologs in the model tetraploid crop tobacco (Nicotiana tabacum cv. Petit Havana). The three rbcS homologs rbcS_S1a, rbcS_S1b and rbcS_T1 account for at least 80% of total rbcS expression in tobacco. In this study, two multiplexing guide RNAs (gRNAs) were designed to target homologous regions in these three genes. We generated tobacco mutant lines with indel mutations in all three genes, including one line with a 670 bp deletion in rbcS-T1. The Rubisco content of three selected mutant lines in the T1 generation was reduced by ca. 93% and mutant plants accumulated only 10% of the total biomass of wild-type plants. As a second goal, we developed a proof-of-principle approach to simultaneously introduce a non-native rbcS gene while generating the triple SSU knockout by co-transformation into a wild-type tobacco background. Our results show that CRISPR-Cas9 is a viable tool for the targeted mutagenesis of rbcS families in polyploid species and will contribute to efforts aimed at improving photosynthetic efficiency through expression of superior non-native Rubisco enzymes in plants.
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Affiliation(s)
- Sophie Donovan
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yuwei Mao
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Douglas J. Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | | | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Flamholz AI, Dugan E, Blikstad C, Gleizer S, Ben-Nissan R, Amram S, Antonovsky N, Ravishankar S, Noor E, Bar-Even A, Milo R, Savage DF. Functional reconstitution of a bacterial CO 2 concentrating mechanism in Escherichia coli. eLife 2020; 9:59882. [PMID: 33084575 PMCID: PMC7714395 DOI: 10.7554/elife.59882] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation via the Calvin cycle. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an Escherichia coli strain engineered to depend on rubisco carboxylation for growth. Expression of 20 CCM genes enabled E. coli to grow by fixing CO2 from ambient air into biomass, with growth in ambient air depending on the components of the CCM. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, thereby laying the groundwork for deeper study and engineering of the cell biology supporting CO2 assimilation in diverse organisms.
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Affiliation(s)
- Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Sumedha Ravishankar
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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Khumsupan P, Kozlowska MA, Orr DJ, Andreou AI, Nakayama N, Patron N, Carmo-Silva E, McCormick AJ. Generating and characterizing single- and multigene mutants of the Rubisco small subunit family in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5963-5975. [PMID: 32734287 DOI: 10.1093/jxb/eraa316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
The primary CO2-fixing enzyme Rubisco limits the productivity of plants. The small subunit of Rubisco (SSU) can influence overall Rubisco levels and catalytic efficiency, and is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. However, SSUs are encoded by a family of nuclear rbcS genes in plants, which makes them challenging to engineer and study. Here we have used CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] and T-DNA insertion lines to generate a suite of single and multiple gene knockout mutants for the four members of the rbcS family in Arabidopsis, including two novel mutants 2b3b and 1a2b3b. 1a2b3b contained very low levels of Rubisco (~3% relative to the wild-type) and is the first example of a mutant with a homogenous Rubisco pool consisting of a single SSU isoform (1B). Growth under near-outdoor levels of light demonstrated Rubisco-limited growth phenotypes for several SSU mutants and the importance of the 1A and 3B isoforms. We also identified 1a1b as a likely lethal mutation, suggesting a key contributory role for the least expressed 1B isoform during early development. The successful use of CRISPR/Cas here suggests that this is a viable approach for exploring the functional roles of SSU isoforms in plants.
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Affiliation(s)
- Panupon Khumsupan
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Marta A Kozlowska
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Andreas I Andreou
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Naomi Nakayama
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicola Patron
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Chaperone Machineries of Rubisco – The Most Abundant Enzyme. Trends Biochem Sci 2020; 45:748-763. [DOI: 10.1016/j.tibs.2020.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/19/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
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Yadav SK, Khatri K, Rathore MS, Jha B. Ectopic Expression of a Transmembrane Protein KaCyt b 6 from a Red Seaweed Kappaphycus alvarezii in Transgenic Tobacco Augmented the Photosynthesis and Growth. DNA Cell Biol 2020:dna.2020.5479. [PMID: 32865429 DOI: 10.1089/dna.2020.5479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cytochrome b6f complex is a thylakoid membrane-localized protein and catalyses the transfer of electrons from plastoquinol to plastocyanin in photosynthetic electron transport chain. In the present study, Cytochrome b6 (KaCyt b6) gene from Kappaphycus alvarezii (a red seaweed) was overexpressed in tobacco. A 935 base pair (bp) long KaCyt b6 cDNA contained an open reading frame of 648 bp encoding a protein of 215 amino acids with an expected isoelectric point of 8.67 and a molecular mass of 24.37 kDa. The KaCyt b6 gene was overexpressed in tobacco under control of CaMV35S promoter. The transgenic tobacco had higher electron transfer rate and photosynthetic yield over wild-type and vector control tobacco. The KaCyt b6 tobacco also exhibited significantly higher photosynthetic gas exchange (PN) and improved water use efficiency. The transgenic plants had higher ratio of PN and intercellular CO2. The KaCyt b6 transgenic tobacco showed higher estimates of photosystem II quantum yield, higher activity of the water-splitting complex, PSII photochemistry, and photochemical quenching. The basal quantum yield of nonphotochemical processes in PSII was recorded lower in KaCyt b6 tobacco. Transgenic tobacco contained higher contents of carotenoids and total chlorophyll and also had better ratios of chlorophyll a and b, and carotenoids and total chlorophyll contents hence improved photosynthetic efficiency and production of sugar and starch. The KaCyt b6 transgenic plants performed superior under control and greenhouse conditions. To the best of our knowledge through literature survey, this is the first report on characterization of KaCyt b6 gene from K. alvarezii for enhanced photosynthetic efficiency and growth in tobacco.
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Affiliation(s)
- Sweta K Yadav
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kusum Khatri
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Applied Phycology and Biotechnology, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, India
| | - Mangal S Rathore
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Applied Phycology and Biotechnology, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, India
| | - Bhavanath Jha
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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