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Croce R, Carmo-Silva E, Cho YB, Ermakova M, Harbinson J, Lawson T, McCormick AJ, Niyogi KK, Ort DR, Patel-Tupper D, Pesaresi P, Raines C, Weber APM, Zhu XG. Perspectives on improving photosynthesis to increase crop yield. THE PLANT CELL 2024; 36:3944-3973. [PMID: 38701340 PMCID: PMC11449117 DOI: 10.1093/plcell/koae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024]
Abstract
Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin-Benson-Bassham (CBB) cycle. Additionally, we explore methods to increase carbon dioxide (CO2) concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.
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Affiliation(s)
- Roberta Croce
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, theNetherlands
| | | | - Young B Cho
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
| | - Maria Ermakova
- School of Biological Sciences, Faculty of Science, Monash University, Melbourne, VIC 3800, Australia
| | - Jeremy Harbinson
- Laboratory of Biophysics, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
| | - Alistair J McCormick
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
| | - Dhruv Patel-Tupper
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Paolo Pesaresi
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Christine Raines
- School of Life Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf 40225, Germany
| | - Xin-Guang Zhu
- Key Laboratory of Carbon Capture, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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2
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Dowaidar M. Synthetic biology of metabolic cycles for Enhanced CO 2 capture and Sequestration. Bioorg Chem 2024; 153:107774. [PMID: 39260160 DOI: 10.1016/j.bioorg.2024.107774] [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: 06/03/2024] [Revised: 08/01/2024] [Accepted: 08/28/2024] [Indexed: 09/13/2024]
Abstract
In most organisms, the tri-carboxylic acid cycle (TCA cycle) is an essential metabolic system that is involved in both energy generation and carbon metabolism. Its uni-directionality, however, restricts its use in synthetic biology and carbon fixation. Here, it is describing the use of the modified TCA cycle, called the Tri-carboxylic acid Hooked to Ethylene by Enzyme Reactions and Amino acid Synthesis, the reductive tricarboxylic acid branch/4-hydroxybutyryl-CoA/ethylmalonyl-CoA/acetyl-CoA (THETA) cycle, in Escherichia coli for the purposes of carbon fixation and amino acid synthesis. Three modules make up the THETA cycle: (1) pyruvate to succinate transformation, (2) succinate to crotonyl-CoA change, and (3) crotonyl-CoA to acetyl-CoA and pyruvate change. It is presenting each module's viability in vivo and showing how it integrates into the E. coli metabolic network to support growth on minimal medium without the need for outside supplementation. Enzyme optimization, route redesign, and heterologous expression were used to get over metabolic roadblocks and produce functional modules. Furthermore, the THETA cycle may be improved by including components of the Carbon-Efficient Tri-Carboxylic Acid Cycle (CETCH cycle) to improve carbon fixation. THETA cycle's promise as a platform for applications in synthetic biology and carbon fixation.
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Affiliation(s)
- Moataz Dowaidar
- Bioengineering Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; Interdisciplinary Research Center for Hydrogen Technologies and Carbon Management, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia; Biosystems and Machines Research Center, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia.
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3
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Noor E, Liebermeister W. Optimal enzyme profiles in unbranched metabolic pathways. Interface Focus 2024; 14:20230029. [PMID: 38344407 PMCID: PMC10853694 DOI: 10.1098/rsfs.2023.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/19/2023] [Indexed: 05/09/2024] Open
Abstract
How to optimize the allocation of enzymes in metabolic pathways has been a topic of study for many decades. Although the general problem is complex and nonlinear, we have previously shown that it can be solved by convex optimization. In this paper, we focus on unbranched metabolic pathways with simplified enzymatic rate laws and derive analytic solutions to the optimization problem. We revisit existing solutions based on the limit of mass-action rate laws and present new solutions for other rate laws. Furthermore, we revisit a known relationship between flux control coefficients and enzyme abundances in optimal metabolic states. We generalize this relationship to models with density constraints on enzymes and metabolites, and present a new local relationship between optimal reaction elasticities and enzyme amounts. Finally, we apply our theory to derive simple kinetics-based formulae for protein allocation during bacterial growth.
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Affiliation(s)
- Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
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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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Zhong W, Li H, Wang Y. Design and Construction of Artificial Biological Systems for One-Carbon Utilization. BIODESIGN RESEARCH 2023; 5:0021. [PMID: 37915992 PMCID: PMC10616972 DOI: 10.34133/bdr.0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
The third-generation (3G) biorefinery aims to use microbial cell factories or enzymatic systems to synthesize value-added chemicals from one-carbon (C1) sources, such as CO2, formate, and methanol, fueled by renewable energies like light and electricity. This promising technology represents an important step toward sustainable development, which can help address some of the most pressing environmental challenges faced by modern society. However, to establish processes competitive with the petroleum industry, it is crucial to determine the most viable pathways for C1 utilization and productivity and yield of the target products. In this review, we discuss the progresses that have been made in constructing artificial biological systems for 3G biorefineries in the last 10 years. Specifically, we highlight the representative works on the engineering of artificial autotrophic microorganisms, tandem enzymatic systems, and chemo-bio hybrid systems for C1 utilization. We also prospect the revolutionary impact of these developments on biotechnology. By harnessing the power of 3G biorefinery, scientists are establishing a new frontier that could potentially revolutionize our approach to industrial production and pave the way for a more sustainable future.
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Affiliation(s)
- Wei Zhong
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
| | - Hailong Li
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
- School of Materials Science and Engineering,
Zhejiang University, Zhejiang Province, Hangzhou 310000, PR China
| | - Yajie Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J. Erb
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K. Winkler
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M. Glueck
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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Schulz-Mirbach H, Müller A, Wu T, Pfister P, Aslan S, Schada von Borzyskowski L, Erb TJ, Bar-Even A, Lindner SN. On the flexibility of the cellular amination network in E coli. eLife 2022; 11:e77492. [PMID: 35876664 PMCID: PMC9436414 DOI: 10.7554/elife.77492] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
Ammonium (NH4+) is essential to generate the nitrogenous building blocks of life. It gets assimilated via the canonical biosynthetic routes to glutamate and is further distributed throughout metabolism via a network of transaminases. To study the flexibility of this network, we constructed an Escherichia coli glutamate auxotrophic strain. This strain allowed us to systematically study which amino acids serve as amine sources. We found that several amino acids complemented the auxotrophy either by producing glutamate via transamination reactions or by their conversion to glutamate. In this network, we identified aspartate transaminase AspC as a major connector between many amino acids and glutamate. Additionally, we extended the transaminase network by the amino acids β-alanine, alanine, glycine, and serine as new amine sources and identified d-amino acid dehydrogenase (DadA) as an intracellular amino acid sink removing substrates from transaminase reactions. Finally, ammonium assimilation routes producing aspartate or leucine were introduced. Our study reveals the high flexibility of the cellular amination network, both in terms of transaminase promiscuity and adaptability to new connections and ammonium entry points.
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Affiliation(s)
| | - Alexandra Müller
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Tong Wu
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Pascal Pfister
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Selçuk Aslan
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Lennart Schada von Borzyskowski
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Institute of Biology Leiden, Leiden UniversityLeidenNetherlands
| | - Tobias J Erb
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Department of Biochemistry, Charité – Universitätsmedizin BerlinBerlinGermany
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Luo S, Lin PP, Nieh LY, Liao GB, Tang PW, Chen C, Liao JC. A cell-free self-replenishing CO2-fixing system. Nat Catal 2022. [DOI: 10.1038/s41929-022-00746-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AbstractBiological CO2 fixation is so far the most effective means for CO2 reduction at scale and accounts for most of the CO2 fixed on Earth. Through this process, carbon is fixed in cellular components and biomass during organismal growth. To uncouple CO2 fixation from growth and cellular regulation, cell-free CO2 fixation systems represent an alternative approach since the rate can be independently manipulated. Here we designed an oxygen-insensitive, self-replenishing CO2 fixation system with opto-sensing. The system comprises a synthetic reductive glyoxylate and pyruvate synthesis (rGPS) cycle and the malyl-CoA-glycerate (MCG) pathway to produce acetyl-coenzyme A (CoA), pyruvate and malate from CO2, which are also intermediates in the cycle. We solved various problems associated with the in vitro system, and implemented opto-sensing modules to control the regeneration of cofactors. We accomplished sustained operation for 6 hours with a CO2-fixing rate comparable to or greater than typical CO2 fixation rates of photosynthetic or lithoautotrophic organisms.
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9
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Engineering the Reductive Glycine Pathway: A Promising Synthetic Metabolism Approach for C1-Assimilation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:299-350. [DOI: 10.1007/10_2021_181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Löwe H, Kremling A. Corrigendum to "In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways". BIODESIGN RESEARCH 2021; 2021:9756012. [PMID: 37849949 PMCID: PMC10521723 DOI: 10.34133/2021/9756012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2023] Open
Abstract
[This corrects the article DOI: 10.34133/2021/9898316.].
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Affiliation(s)
- Hannes Löwe
- Systems Biotechnology, Technical University of Munich, Germany
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