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Schada von Borzyskowski L, Hermann L, Kremer K, Barthel S, Pommerenke B, Glatter T, Paczia N, Bremer E, Erb TJ. Multiple levels of transcriptional regulation control glycolate metabolism in Paracoccus denitrificans. mBio 2024:e0152424. [PMID: 38953632 DOI: 10.1128/mbio.01524-24] [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: 05/24/2024] [Accepted: 06/02/2024] [Indexed: 07/04/2024] Open
Abstract
The hydroxyacid glycolate is a highly abundant carbon source in the environment. Glycolate is produced by unicellular photosynthetic organisms and excreted at petagram scales to the environment, where it serves as growth substrate for heterotrophic bacteria. In microbial metabolism, glycolate is first oxidized to glyoxylate by the enzyme glycolate oxidase. The recently described β-hydroxyaspartate cycle (BHAC) subsequently mediates the carbon-neutral assimilation of glyoxylate into central metabolism in ubiquitous Alpha- and Gammaproteobacteria. Although the reaction sequence of the BHAC was elucidated in Paracoccus denitrificans, little is known about the regulation of glycolate and glyoxylate assimilation in this relevant alphaproteobacterial model organism. Here, we show that regulation of glycolate metabolism in P. denitrificans is surprisingly complex, involving two regulators, the IclR-type transcription factor BhcR that acts as an activator for the BHAC gene cluster, and the GntR-type transcriptional regulator GlcR, a previously unidentified repressor that controls the production of glycolate oxidase. Furthermore, an additional layer of regulation is exerted at the global level, which involves the transcriptional regulator CceR that controls the switch between glycolysis and gluconeogenesis in P. denitrificans. Together, these regulators control glycolate metabolism in P. denitrificans, allowing the organism to assimilate glycolate together with other carbon substrates in a simultaneous fashion, rather than sequentially. Our results show that the metabolic network of Alphaproteobacteria shows a high degree of flexibility to react to the availability of multiple substrates in the environment.IMPORTANCEAlgae perform ca. 50% of the photosynthetic carbon dioxide fixation on our planet. In the process, they release the two-carbon molecule glycolate. Due to the abundance of algae, massive amounts of glycolate are released. Therefore, this molecule is available as a source of carbon for bacteria in the environment. Here, we describe the regulation of glycolate metabolism in the model organism Paracoccus denitrificans. This bacterium uses the recently characterized β-hydroxyaspartate cycle to assimilate glycolate in a carbon- and energy-efficient manner. We found that glycolate assimilation is dynamically controlled by three different transcriptional regulators: GlcR, BhcR, and CceR. This allows P. denitrificans to assimilate glycolate together with other carbon substrates in a simultaneous fashion. Overall, this flexible and multi-layered regulation of glycolate metabolism in P. denitrificans represents a resource-efficient strategy to make optimal use of this globally abundant molecule under fluctuating environmental conditions.
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Affiliation(s)
- Lennart Schada von Borzyskowski
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Lucas Hermann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Katharina Kremer
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sebastian Barthel
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Bianca Pommerenke
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
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2
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Zai X, Cordovez V, Zhu F, Zhao M, Diao X, Zhang F, Raaijmakers JM, Song C. C4 cereal and biofuel crop microbiomes. Trends Microbiol 2024:S0966-842X(24)00093-3. [PMID: 38772810 DOI: 10.1016/j.tim.2024.04.008] [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: 12/07/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/23/2024]
Abstract
Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.
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Affiliation(s)
- Xiaoyu Zai
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China
| | - Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China.
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3
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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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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [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: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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5
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Schulz-Mirbach H, Dronsella B, He H, Erb TJ. Creating new-to-nature carbon fixation: A guide. Metab Eng 2024; 82:12-28. [PMID: 38160747 DOI: 10.1016/j.ymben.2023.12.012] [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: 10/10/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Synthetic biology aims at designing new biological functions from first principles. These new designs allow to expand the natural solution space and overcome the limitations of naturally evolved systems. One example is synthetic CO2-fixation pathways that promise to provide more efficient ways for the capture and conversion of CO2 than natural pathways, such as the Calvin Benson Bassham (CBB) cycle of photosynthesis. In this review, we provide a practical guideline for the design and realization of such new-to-nature CO2-fixation pathways. We introduce the concept of "synthetic CO2-fixation", and give a general overview over the enzymology and topology of synthetic pathways, before we derive general principles for their design from their eight naturally evolved analogs. We provide a comprehensive summary of synthetic carbon-assimilation pathways and derive a step-by-step, practical guide from the theoretical design to their practical implementation, before ending with an outlook on new developments in the field.
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Affiliation(s)
- Helena Schulz-Mirbach
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Beau Dronsella
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Hai He
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, D-35043, Marburg, Germany.
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6
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Song S, Ye C, Jin Y, Dai H, Hu J, Lian J, Pan R. Peroxisome-based metabolic engineering for biomanufacturing and agriculture. Trends Biotechnol 2024:S0167-7799(24)00034-9. [PMID: 38423802 DOI: 10.1016/j.tibtech.2024.02.005] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Subcellular compartmentalization of metabolic pathways plays a crucial role in metabolic engineering. The peroxisome has emerged as a highly valuable and promising compartment for organelle engineering, particularly in the fields of biological manufacturing and agriculture. In this review, we summarize the remarkable achievements in peroxisome engineering in yeast, the industrially popular biomanufacturing chassis host, to produce various biocompounds. We also review progress in plant peroxisome engineering, a field that has already exhibited high potential in both biomanufacturing and agriculture. Moreover, we outline various experimentally validated strategies to improve the efficiency of engineered pathways in peroxisomes, as well as prospects of peroxisome engineering.
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Affiliation(s)
- Shuyan Song
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Cuifang Ye
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Yijun Jin
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
| | - Huaxin Dai
- Beijing Life Science Academy, Changping 102209, Beijing, China
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Jiazhang Lian
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China.
| | - Ronghui Pan
- State Key Laboratory of Rice Biology and Breeding, College of Chemical and Biological Engineering, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China.
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7
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Erb TJ. Photosynthesis 2.0: Realizing New-to-Nature CO 2-Fixation to Overcome the Limits of Natural Metabolism. Cold Spring Harb Perspect Biol 2024; 16:a041669. [PMID: 37848245 PMCID: PMC10835606 DOI: 10.1101/cshperspect.a041669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Synthetic biology provides opportunities to realize new-to-nature CO2-fixation metabolisms to overcome the limitations of natural photosynthesis. Two different strategies are currently being pursued: One is to realize engineered plants that feature carbon-neutral or carbon-negative (i.e., CO2-fixing) photorespiration metabolism, such as the tatronyl-CoA (TaCo) pathway, to boost CO2-uptake rates of photosynthesis between 20% and 60%. Another (arguably more radical) is to create engineered plants in which natural photosynthesis is fully replaced by an alternative CO2-fixation metabolism, such as the CETCH cycle, which carries the potential to improve CO2 uptake rates between 20% and 200%. These efforts could revolutionize plant engineering by expanding the capabilities of plant metabolism beyond the constraints of natural evolution to create highly improved crops addressing the challenges of climate change in the future.
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Affiliation(s)
- Tobias J Erb
- Max Planck Society, Germany, Department for Biochemistry & Synthetic Metabolism, Center for Synthetic Microbiology (SYNMIKRO) & Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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8
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Yang X, Zhang Y, Zhao G. Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems. Biotechnol Adv 2024; 70:108294. [PMID: 38013126 DOI: 10.1016/j.biotechadv.2023.108294] [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: 07/28/2023] [Revised: 10/26/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Synthetic biology is being increasingly used to establish novel carbon assimilation pathways and artificial autotrophic strains that can be used in low-carbon biomanufacturing. Currently, artificial pathway design has made significant progress from advocacy to practice within a relatively short span of just over ten years. However, there is still huge scope for exploration of pathway diversity, operational efficiency, and host suitability. The accelerated research process will bring greater opportunities and challenges. In this paper, we provide a comprehensive summary and interpretation of representative one-carbon assimilation pathway designs and artificial autotrophic strain construction work. In addition, we propose some feasible design solutions based on existing research results and patterns to promote the development and application of artificial autotrophy.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Curien G. A Practical Guide to the Representation of Protein Regulation in the Web Application ChloroKB. Methods Mol Biol 2024; 2776:305-320. [PMID: 38502513 DOI: 10.1007/978-1-0716-3726-5_19] [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] [Indexed: 03/21/2024]
Abstract
ChloroKB ( http://chlorokb.fr ) is a knowledge base providing synoptic representations of the metabolism of the model plant Arabidopsis thaliana and its regulation. Initially focused on plastid metabolism, ChloroKB now accounts for the metabolism throughout the cell. ChloroKB is based on the CellDesigner formalism. CellDesigner supports graphical notation and listing of the corresponding symbols based on the Systems Biology Graphical Notation. Thus, this formalism allows biologists to represent detailed biochemical processes in a way that can be easily understood and shared, facilitating communication between researchers. In this chapter, we will focus on a specificity of ChloroKB, the representation of multilayered regulation of protein activity. Information on regulation of protein activity is indeed central to understanding the plant response to fluctuating environmental conditions. However, the intrinsic diversity of the regulatory modes and the abundance of detail may hamper comprehension of the regulatory processes described in ChloroKB. With this chapter, ChloroKB users will be guided through the representation of these sophisticated biological processes of prime importance to understanding metabolism or for applied purposes. The descriptions provided, which summarize years of work and a broad bibliography in a few pages, can help speed up the integration of regulatory processes in kinetic models of plant metabolism.
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Affiliation(s)
- Gilles Curien
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble Cedex 9, France.
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10
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Plett A, Westhoff P, Linka N. Analysis of Photorespiratory Intermediates Under Transient Conditions by Mass Spectrometry. Methods Mol Biol 2024; 2792:187-194. [PMID: 38861088 DOI: 10.1007/978-1-0716-3802-6_15] [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] [Indexed: 06/12/2024]
Abstract
Photorespiration is an essential process of phototropic organisms caused by the limited ability of rubisco to distinguish between CO2 and O2. To understand the metabolic flux through the photorespiratory pathway, we combined a mass spectrometry-based approach with a shift experiment from elevated CO2 (3000 ppm) to ambient CO2 (390 ppm). Here, we describe a protocol for quantifying photorespiratory intermediates, starting from plant cultivation through extraction and evaluation.
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Affiliation(s)
- Anastasija Plett
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Philipp Westhoff
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, Germany.
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Xu H, Wang H, Zhang Y, Yang X, Lv S, Hou D, Mo C, Wassie M, Yu B, Hu T. A synthetic light-inducible photorespiratory bypass enhances photosynthesis to improve rice growth and grain yield. PLANT COMMUNICATIONS 2023; 4:100641. [PMID: 37349987 PMCID: PMC10721467 DOI: 10.1016/j.xplc.2023.100641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 04/25/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Bioengineering of photorespiratory bypasses is an effective strategy for improving plant productivity by modulating photosynthesis. In previous work, two photorespiratory bypasses, the GOC and GCGT bypasses, increased photosynthetic rates but decreased seed-setting rate in rice (Oryza sativa), probably owing to excess photosynthate accumulation in the stem. To solve this bottleneck, we successfully developed a new synthetic photorespiratory bypass (called the GMA bypass) in rice chloroplasts by introducing Oryza sativa glycolate oxidase 1 (OsGLO1), Cucurbita maxima malate synthase (CmMS), and Oryza sativa ascorbate peroxidase7 (OsAPX7) into the rice genome using a high-efficiency transgene stacking system. Unlike the GOC and GCGT bypass genes driven by constitutive promoters, OsGLO1 in GMA plants was driven by a light-inducible Rubisco small subunit promoter (pRbcS); its expression dynamically changed in response to light, producing a more moderate increase in photosynthate. Photosynthetic rates were significantly increased in GMA plants, and grain yields were significantly improved under greenhouse and field conditions. Transgenic GMA rice showed no reduction in seed-setting rate under either test condition, unlike previous photorespiratory-bypass rice, probably reflecting proper modulation of the photorespiratory bypass. Together, these results imply that appropriate engineering of the GMA bypass can enhance rice growth and grain yield without affecting seed-setting rate.
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Affiliation(s)
- Huawei Xu
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China.
| | - Huihui Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Yanwen Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Xiaoyi Yang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Shufang Lv
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Dianyun Hou
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Changru Mo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
| | - Misganaw Wassie
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bo Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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12
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Smith EN, van Aalst M, Tosens T, Niinemets Ü, Stich B, Morosinotto T, Alboresi A, Erb TJ, Gómez-Coronado PA, Tolleter D, Finazzi G, Curien G, Heinemann M, Ebenhöh O, Hibberd JM, Schlüter U, Sun T, Weber APM. Improving photosynthetic efficiency toward food security: Strategies, advances, and perspectives. MOLECULAR PLANT 2023; 16:1547-1563. [PMID: 37660255 DOI: 10.1016/j.molp.2023.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Photosynthesis in crops and natural vegetation allows light energy to be converted into chemical energy and thus forms the foundation for almost all terrestrial trophic networks on Earth. The efficiency of photosynthetic energy conversion plays a crucial role in determining the portion of incident solar radiation that can be used to generate plant biomass throughout a growth season. Consequently, alongside the factors such as resource availability, crop management, crop selection, maintenance costs, and intrinsic yield potential, photosynthetic energy use efficiency significantly influences crop yield. Photosynthetic efficiency is relevant to sustainability and food security because it affects water use efficiency, nutrient use efficiency, and land use efficiency. This review focuses specifically on the potential for improvements in photosynthetic efficiency to drive a sustainable increase in crop yields. We discuss bypassing photorespiration, enhancing light use efficiency, harnessing natural variation in photosynthetic parameters for breeding purposes, and adopting new-to-nature approaches that show promise for achieving unprecedented gains in photosynthetic efficiency.
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Affiliation(s)
- Edward N Smith
- Faculty of Science and Engineering, Molecular Systems Biology - Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Marvin van Aalst
- Institute of Quantitative and Theoretical Biology, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tiina Tosens
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | | | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry & Synthetic Metabolism, 35043 Marburg, Germany
| | - Paul A Gómez-Coronado
- Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry & Synthetic Metabolism, 35043 Marburg, Germany
| | - Dimitri Tolleter
- Interdisciplinary Research Institute of Grenoble, IRIG-LPCV, Grenoble Alpes University, CNRS, CEA, INRAE, 38000 Grenoble, France
| | - Giovanni Finazzi
- Interdisciplinary Research Institute of Grenoble, IRIG-LPCV, Grenoble Alpes University, CNRS, CEA, INRAE, 38000 Grenoble, France
| | - Gilles Curien
- Interdisciplinary Research Institute of Grenoble, IRIG-LPCV, Grenoble Alpes University, CNRS, CEA, INRAE, 38000 Grenoble, France
| | - Matthias Heinemann
- Faculty of Science and Engineering, Molecular Systems Biology - Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Julian M Hibberd
- Molecular Physiology, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Urte Schlüter
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tianshu Sun
- Molecular Physiology, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
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13
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Boisset ND, Favoino G, Meloni M, Jomat L, Cassier-Chauvat C, Zaffagnini M, Lemaire SD, Crozet P. Phosphoribulokinase abundance is not limiting the Calvin-Benson-Bassham cycle in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2023; 14:1230723. [PMID: 37719215 PMCID: PMC10501310 DOI: 10.3389/fpls.2023.1230723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/21/2023] [Indexed: 09/19/2023]
Abstract
Improving photosynthetic efficiency in plants and microalgae is of utmost importance to support the growing world population and to enable the bioproduction of energy and chemicals. Limitations in photosynthetic light conversion efficiency can be directly attributed to kinetic bottlenecks within the Calvin-Benson-Bassham cycle (CBBC) responsible for carbon fixation. A better understanding of these bottlenecks in vivo is crucial to overcome these limiting factors through bio-engineering. The present study is focused on the analysis of phosphoribulokinase (PRK) in the unicellular green alga Chlamydomonas reinhardtii. We have characterized a PRK knock-out mutant strain and showed that in the absence of PRK, Chlamydomonas cannot grow photoautotrophically while functional complementation with a synthetic construct allowed restoration of photoautotrophy. Nevertheless, using standard genetic elements, the expression of PRK was limited to 40% of the reference level in complemented strains and could not restore normal growth in photoautotrophic conditions suggesting that the CBBC is limited. We were subsequently able to overcome this initial limitation by improving the design of the transcriptional unit expressing PRK using diverse combinations of DNA parts including PRK endogenous promoter and introns. This enabled us to obtain strains with PRK levels comparable to the reference strain and even overexpressing strains. A collection of strains with PRK levels between 16% and 250% of WT PRK levels was generated and characterized. Immunoblot and growth assays revealed that a PRK content of ≈86% is sufficient to fully restore photoautotrophic growth. This result suggests that PRK is present in moderate excess in Chlamydomonas. Consistently, the overexpression of PRK did not increase photosynthetic growth indicating that that the endogenous level of PRK in Chlamydomonas is not limiting the Calvin-Benson-Bassham cycle under optimal conditions.
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Affiliation(s)
- Nicolas D. Boisset
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
- Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin, France
| | - Giusi Favoino
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
| | - Maria Meloni
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Lucile Jomat
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
| | - Corinne Cassier-Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Gif-sur-Yvette, France
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Stéphane D. Lemaire
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
| | - Pierre Crozet
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
- Polytech-Sorbonne, Sorbonne Université, Paris, France
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14
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Yogadasan N, Doxey AC, Chuong SDX. A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information. Genome Biol Evol 2023; 15:evad129. [PMID: 37462292 PMCID: PMC10368328 DOI: 10.1093/gbe/evad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
C4 photosynthesis is known to have at least 61 independent origins across plant lineages making it one of the most notable examples of convergent evolution. Of the >60 independent origins, a predicted 22-24 origins, encompassing greater than 50% of all known C4 species, exist within the Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) clade of the Poaceae family. This clade is therefore primed with species ideal for the study of genomic changes associated with the acquisition of the C4 photosynthetic trait. In this study, we take advantage of the growing availability of sequenced plastid genomes and employ a machine learning (ML) approach to screen for plastid genes harboring C3 and C4 distinguishing information in PACMAD species. We demonstrate that certain plastid-encoded protein sequences possess distinguishing and informative sequence information that allows them to train accurate ML C3/C4 classification models. Our RbcL-trained model, for example, informs a C3/C4 classifier with greater than 99% accuracy. Accurate prediction of photosynthetic type from individual sequences suggests biologically relevant, and potentially differing roles of these sequence products in C3 versus C4 metabolism. With this ML framework, we have identified several key sequences and sites that are most predictive of C3/C4 status, including RbcL, subunits of the NAD(P)H dehydrogenase complex, and specific residues within, further highlighting their potential significance in the evolution and/or maintenance of C4 photosynthetic machinery. This general approach can be applied to uncover intricate associations between other similar genotype-phenotype relationships.
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Affiliation(s)
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Simon D X Chuong
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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15
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Schada von Borzyskowski L, Schulz-Mirbach H, Troncoso Castellanos M, Severi F, Gómez-Coronado PA, Paczia N, Glatter T, Bar-Even A, Lindner SN, Erb TJ. Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol. Metab Eng 2023; 76:97-109. [PMID: 36731627 DOI: 10.1016/j.ymben.2023.01.011] [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: 08/07/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023]
Abstract
Ethylene glycol (EG) is a promising next generation feedstock for bioprocesses. It is a key component of the ubiquitous plastic polyethylene terephthalate (PET) and other polyester fibers and plastics, used in antifreeze formulations, and can also be generated by electrochemical conversion of syngas, which makes EG a key compound in a circular bioeconomy. The majority of biotechnologically relevant bacteria assimilate EG via the glycerate pathway, a wasteful metabolic route that releases CO2 and requires reducing equivalents as well as ATP. In contrast, the recently characterized β-hydroxyaspartate cycle (BHAC) provides a more efficient, carbon-conserving route for C2 assimilation. Here we aimed at overcoming the natural limitations of EG metabolism in the industrially relevant strain Pseudomonas putida KT2440 by replacing the native glycerate pathway with the BHAC. We first prototyped the core reaction sequence of the BHAC in Escherichia coli before establishing the complete four-enzyme BHAC in Pseudomonas putida. Directed evolution on EG resulted in an improved strain that exhibits 35% faster growth and 20% increased biomass yield compared to a recently reported P. putida strain that was evolved to grow on EG via the glycerate pathway. Genome sequencing and proteomics highlight plastic adaptations of the genetic and metabolic networks in response to the introduction of the BHAC into P. putida and identify key mutations for its further integration during evolution. Taken together, our study shows that the BHAC can be utilized as 'plug-and-play' module for the metabolic engineering of two important microbial platform organisms, paving the way for multiple applications for a more efficient and carbon-conserving upcycling of EG in the future.
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Affiliation(s)
- Lennart Schada von Borzyskowski
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
| | - Helena Schulz-Mirbach
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mauricio Troncoso Castellanos
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Francesca Severi
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Paul A Gómez-Coronado
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Nicole Paczia
- Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany.
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16
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Rizzo P, Chavez BG, Leite Dias S, D'Auria JC. Plant synthetic biology: from inspiration to augmentation. Curr Opin Biotechnol 2023; 79:102857. [PMID: 36502769 DOI: 10.1016/j.copbio.2022.102857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Although it is still in its infancy, synthetic biology has the capacity to face scientific and societal problems related to modern agriculture. Innovations in cloning toolkits and genetic parts allow increased precision over gene expression in planta. We review the vast spectrum of available technologies providing a practical list of toolkits that take advantage of combinatorial power to introduce/alter metabolic pathways. We highlight that rational design is inspired by deep knowledge of natural and biochemical mechanisms. Finally, we provide several examples in which modern technologies have been applied to address these critical topics. Future applications in plants include not only pathway modifications but also prospects of augmenting plant anatomical features and developmental processes.
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Affiliation(s)
- Paride Rizzo
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - Benjamin G Chavez
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - Sara Leite Dias
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany
| | - John C D'Auria
- Metabolite Diversity Group, Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Correnstr. 3, D-06466 Seeland, Germany.
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17
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Jin K, Chen G, Yang Y, Zhang Z, Lu T. Strategies for manipulating Rubisco and creating photorespiratory bypass to boost C 3 photosynthesis: Prospects on modern crop improvement. PLANT, CELL & ENVIRONMENT 2023; 46:363-378. [PMID: 36444099 DOI: 10.1111/pce.14500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 06/16/2023]
Abstract
Photosynthesis is a process that uses solar energy to fix CO2 in the air and converts it into sugar, and ultimately powers almost all life activities on the earth. C3 photosynthesis is the most common form of photosynthesis in crops. Current efforts of increasing crop yields in response to growing global food requirement are mostly focused on improving C3 photosynthesis. In this review, we summarized the strategies of C3 photosynthesis improvement in terms of Rubisco properties and photorespiratory limitation. Potential engineered targets include Rubisco subunits and their catalytic sites, Rubisco assembly chaperones, and Rubisco activase. In addition, we reviewed multiple photorespiratory bypasses built by strategies of synthetic biology to reduce the release of CO2 and ammonia and minimize energy consumption by photorespiration. The potential strategies are suggested to enhance C3 photosynthesis and boost crop production.
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Affiliation(s)
- Kaining Jin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- Department of Plant Sciences, Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, The Netherlands
| | - Guoxin Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yirong Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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18
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Cavanagh AP, Slattery R, Kubien DS. Temperature-induced changes in Arabidopsis Rubisco activity and isoform expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:651-663. [PMID: 36124740 PMCID: PMC9833042 DOI: 10.1093/jxb/erac379] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/16/2022] [Indexed: 06/06/2023]
Abstract
In many plant species, expression of the nuclear encoded Rubisco small subunit (SSu) varies with environmental changes, but the functional role of any changes in expression remains unclear. In this study, we investigated the impact of differential expression of Rubisco SSu isoforms on carbon assimilation in Arabidopsis. Using plants grown at contrasting temperatures (10 °C and 30 °C), we confirm the previously reported temperature response of the four RbcS genes and extend this to protein expression, finding that warm-grown plants produce Rubisco containing ~65% SSu-B and cold-grown plants produce Rubisco with ~65% SSu-A as a proportion of the total pool of subunits. We find that these changes in isoform concentration are associated with kinetic changes to Rubisco in vitro: warm-grown plants produce a Rubisco having greater CO2 affinity (i.e. higher SC/O and lower KC) but lower kcatCO2 at warm measurement temperatures. Although warm-grown plants produce 38% less Rubisco than cold-grown plants on a leaf area basis, warm-grown plants can maintain similar rates of photosynthesis to cold-grown plants at ambient CO2 and 30 °C, indicating that the carboxylation capacity of warm-grown Rubisco is enhanced at warmer measurement temperatures, and is able to compensate for the lower Rubisco content in warm-grown plants. This association between SSu isoform expression and maintenance of Rubisco activity at high temperature suggests that SSu isoform expression could impact the temperature response of C3 photosynthesis.
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Affiliation(s)
| | - Rebecca Slattery
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David S Kubien
- Department of Biology, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
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19
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Dandekar T, Kunz M. Bioinformatics Connects Life with the Universe and All the Rest. Bioinformatics 2023. [DOI: 10.1007/978-3-662-65036-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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20
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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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21
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Wang Q, Yang H, Cao P, Chen F, Zhao L. Biosynthetic approaches to efficient assimilation of CO2via photorespiration modification in plant chassis. Front Bioeng Biotechnol 2022; 10:979627. [PMID: 36003537 PMCID: PMC9393500 DOI: 10.3389/fbioe.2022.979627] [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: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Plant chassis has emerged as the platform with great potential for bioproduction of high value-added products such as recombinant protein, vaccine and natural product. However, as the primary metabolic pathway, photorespiration results in the loss of photosynthetically fixed carbon compounds and limits the exploration of plant chassis. People are endeavored to reduce the photorespiration energy or carbon loss based on variation screening or genetic engineering. Insomuch as protein engineering of Rubisco has not resulted in the significant improvement of Rubisco specificity which is linked to the direct CO2 fixation, the biosynthetic approaches of photorespiration bypass are gaining much more attention and manifested great potentiality in conferring efficient assimilation of CO2 in plant chassis. In this review, we summarize the recent studies on the metabolic pathway design and implementation of photorespiration alternative pathway aiming to provide clues to efficiently enhance carbon fixation via the modification of photorespiration in plant chassis for bioproduction. These will benefit the development of plant synthetic metabolism for biorefineries via improvement of artificial carbon sequestration cycle, particularly for the mitigation of serious challenges such as extreme climate change, food and energy shortages in the future.
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Affiliation(s)
- Qing Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Hao Yang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Fangjian Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Lei Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- *Correspondence: Lei Zhao,
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22
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Abstract
Multiple proof-of-principle experiments and successful field trials have demonstrated that engineering photosynthesis is a viable strategy for improving crop yields. Advances to engineering technologies have accelerated efforts to improve photosynthesis, generating a large volume of published literature: this Review therefore aims to highlight the most promising results from the period February 2021 to January 2022. Recent research has demonstrated the importance of understanding the impact of changing climates on photosynthesis to ensure that proposed engineering strategies are resilient to climate change. Encouragingly, there have been several reports of strategies that have benefits at temperatures higher than current ambient conditions. There has also been success in engineering synthetic bypass pathways, providing support for the feasibility of a synthetic biology approach. Continued developments in all areas of engineering photosynthesis will be necessary for sustainably securing sufficient crop yields for the future. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sophie L Johnson
- Department of Plant Sciences, University of Oxford,Oxford, OX1 3RB,UK
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23
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Integration of Light and Auxin Signaling in Shade Plants: From Mechanisms to Opportunities in Urban Agriculture. Int J Mol Sci 2022; 23:ijms23073422. [PMID: 35408782 PMCID: PMC8998421 DOI: 10.3390/ijms23073422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/01/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
With intensification of urbanization throughout the world, food security is being threatened by the population surge, frequent occurrence of extreme climate events, limited area of available cultivated land, insufficient utilization of urban space, and other factors. Determining the means by which high-yielding and high-quality crops can be produced in a limited space is an urgent priority for plant scientists. Dense planting, vertical production, and indoor cultivation are effective ways to make full use of space and improve the crop yield. The results of physiological and molecular analyses of the model plant species Arabidopsis thaliana have shown that the plant response to shade is the key to regulating the plant response to changes in light intensity and quality by integrating light and auxin signals. In this study, we have summarized the major molecular mechanisms of shade avoidance and shade tolerance in plants. In addition, the biotechnological strategies of enhancing plant shade tolerance are discussed. More importantly, cultivating crop varieties with strong shade tolerance could provide effective strategies for dense planting, vertical production, and indoor cultivation in urban agriculture in the future.
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24
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Taylor-Kearney LJ, Flashman E. Targeting plant cysteine oxidase activity for improved submergence tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:779-788. [PMID: 34817108 DOI: 10.1111/tpj.15605] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Plant cysteine oxidases (PCOs) are plant O2 -sensing enzymes. They catalyse the O2 -dependent step which initiates the proteasomal degradation of Group VII ethylene response transcription factors (ERF-VIIs) via the N-degron pathway. When submerged, plants experience a reduction in O2 availability; PCO activity therefore decreases and the consequent ERF-VII stabilisation leads to upregulation of hypoxia-responsive genes which enable adaptation to low O2 conditions. Resulting adaptations include entering an anaerobic quiescent state to maintain energy reserves and rapid growth to escape floodwater and allow O2 transport to submerged tissues. Stabilisation of ERF-VIIs has been linked to improved survival post-submergence in Arabidopsis, rice (Oryza sativa) and barley (Hordeum vulgare). Due to climate change and increasing flooding events, there is an interest in manipulating the PCO/ERF-VII interaction as a method of improving yields in flood-intolerant crops. An effective way of achieving this may be through PCO inhibition; however, complete ablation of PCO activity is detrimental to growth and phenotype, likely due to other PCO-mediated roles. Targeting PCOs will therefore require either temporary chemical inhibition or careful engineering of the enzyme structure to manipulate their O2 sensitivity and/or substrate specificity. Sufficient PCO structural and functional information should make this possible, given the potential to engineer site-directed mutagenesis in vivo using CRISPR-mediated base editing. Here, we discuss the knowledge still required for rational manipulation of PCOs to achieve ERF-VII stabilisation without a yield penalty. We also take inspiration from the biocatalysis field to consider how enzyme engineering could be accelerated as a wider strategy to improve plant stress tolerance and productivity.
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Affiliation(s)
| | - Emily Flashman
- Department of Chemistry, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Kang BH, Anderson CT, Arimura SI, Bayer E, Bezanilla M, Botella MA, Brandizzi F, Burch-Smith TM, Chapman KD, Dünser K, Gu Y, Jaillais Y, Kirchhoff H, Otegui MS, Rosado A, Tang Y, Kleine-Vehn J, Wang P, Zolman BK. A glossary of plant cell structures: Current insights and future questions. THE PLANT CELL 2022; 34:10-52. [PMID: 34633455 PMCID: PMC8846186 DOI: 10.1093/plcell/koab247] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 05/03/2023]
Abstract
In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.
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Affiliation(s)
- Byung-Ho Kang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Charles T Anderson
- Department of Biology and Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Shin-ichi Arimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Emmanuelle Bayer
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, Villenave d'Ornon F-33140, France
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Miguel A Botella
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortifruticultura Subtropical y Mediterránea “La Mayora,” Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga 29071, Spain
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Kai Dünser
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Yangnan Gu
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Abel Rosado
- Department of Botany, University of British Columbia, Vancouver V6T1Z4, Canada
| | - Yu Tang
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Jürgen Kleine-Vehn
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bethany Karlin Zolman
- Department of Biology, University of Missouri, St. Louis, St. Louis, Missouri 63121, USA
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Kerchev PI, Van Breusegem F. Improving oxidative stress resilience in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:359-372. [PMID: 34519111 DOI: 10.1111/tpj.15493] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 05/22/2023]
Abstract
Originally conceived as harmful metabolic byproducts, reactive oxygen species (ROS) are now recognized as an integral part of numerous cellular programs. Thanks to their diverse physicochemical properties, compartmentalized production, and tight control exerted by the antioxidant machinery they activate signaling pathways that govern plant growth, development, and defense. Excessive ROS levels are often driven by adverse changes in environmental conditions, ultimately causing oxidative stress. The associated negative impact on cellular constituents have been a major focus of decade-long research efforts to improve the oxidative stress resilience by boosting the antioxidant machinery in model and crop species. We highlight the role of enzymatic and non-enzymatic antioxidants as integral factors of multiple signaling cascades beyond their mere function to prevent oxidative damage under adverse abiotic stress conditions.
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Affiliation(s)
- Pavel I Kerchev
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300, Brno, Czech Republic
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
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