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Liu X, Li L, Zhao G, Xiong P. Optimization strategies for CO 2 biological fixation. Biotechnol Adv 2024; 73:108364. [PMID: 38642673 DOI: 10.1016/j.biotechadv.2024.108364] [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: 09/18/2023] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 04/22/2024]
Abstract
Global sustainable development faces a significant challenge in effectively utilizing CO2. Meanwhile, CO2 biological fixation offers a promising solution. CO2 has the highest oxidation state (+4 valence state), whereas typical multi‑carbon chemicals have lower valence states. The Gibbs free energy (ΔG) changes of CO2 reductive reactions are generally positive and this renders it necessary to input different forms of energy. Although biological carbon fixation processes are friendly to operate, the thermodynamic obstacles must be overcome. To make this reaction occur favorably and efficiently, diverse strategies to enhance CO2 biological fixation efficiency have been proposed by numerous researchers. This article reviews recent advances in optimizing CO2 biological fixation and intends to provide new insights into achieving efficient biological utilization of CO2. It first outlines the thermodynamic characteristics of diverse carbon fixation reactions and proposes optimization directions for CO2 biological fixation. A comprehensive overview of the catalytic mechanisms, optimization strategies, and challenges encountered by common carbon-fixing enzymes is then provided. Subsequently, potential routes for improving the efficiency of biological carbon fixation are discussed, including the ATP supply, reducing power supply, energy supply, reactor design, and carbon enrichment system modules. In addition, effective artificial carbon fixation pathways were summarized and analyzed. Finally, prospects are made for the research direction of continuously improving the efficiency of biological carbon fixation.
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Affiliation(s)
- Xiutao Liu
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China.
| | - Linqing Li
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China.
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China.
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2
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Liang J, Xiao K, Wang X, Hou T, Zeng C, Gao X, Wang B, Zhong C. Revisiting Solar Energy Flow in Nanomaterial-Microorganism Hybrid Systems. Chem Rev 2024. [PMID: 38900019 DOI: 10.1021/acs.chemrev.3c00831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Nanomaterial-microorganism hybrid systems (NMHSs), integrating semiconductor nanomaterials with microorganisms, present a promising platform for broadband solar energy harvesting, high-efficiency carbon reduction, and sustainable chemical production. While studies underscore its potential in diverse solar-to-chemical energy conversions, prevailing NMHSs grapple with suboptimal energy conversion efficiency. Such limitations stem predominantly from an insufficient systematic exploration of the mechanisms dictating solar energy flow. This review provides a systematic overview of the notable advancements in this nascent field, with a particular focus on the discussion of three pivotal steps of energy flow: solar energy capture, cross-membrane energy transport, and energy conversion into chemicals. While key challenges faced in each stage are independently identified and discussed, viable solutions are correspondingly postulated. In view of the interplay of the three steps in affecting the overall efficiency of solar-to-chemical energy conversion, subsequent discussions thus take an integrative and systematic viewpoint to comprehend, analyze and improve the solar energy flow in the current NMHSs of different configurations, and highlighting the contemporary techniques that can be employed to investigate various aspects of energy flow within NMHSs. Finally, a concluding section summarizes opportunities for future research, providing a roadmap for the continued development and optimization of NMHSs.
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Affiliation(s)
- Jun Liang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Kemeng Xiao
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianfeng Hou
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Cuiping Zeng
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiang Gao
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Bo Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chao Zhong
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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Shimizu T, Inui M. Novel aspects of ethylene glycol catabolism. Appl Microbiol Biotechnol 2024; 108:369. [PMID: 38861200 PMCID: PMC11166783 DOI: 10.1007/s00253-024-13179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/12/2024]
Abstract
Ethylene glycol (EG) is an industrially important two-carbon diol used as a solvent, antifreeze agent, and building block of polymers such as poly(ethylene terephthalate) (PET). Recently, the use of EG as a starting material for the production of bio-fuels or bio-chemicals is gaining attention as a sustainable process since EG can be derived from materials not competing with human food stocks including CO2, syngas, lignocellulolytic biomass, and PET waste. In order to design and construct microbial process for the conversion of EG to value-added chemicals, microbes capable of catabolizing EG such as Escherichia coli, Pseudomonas putida, Rhodococcus jostii, Ideonella sakaiensis, Paracoccus denitrificans, and Acetobacterium woodii are candidates of chassis for the construction of synthetic pathways. In this mini-review, we describe EG catabolic pathways and catabolic enzymes in these microbes, and further review recent advances in microbial conversion of EG to value-added chemicals by means of metabolic engineering. KEY POINTS: • Ethylene glycol is a potential next-generation feedstock for sustainable industry. • Microbial conversion of ethylene glycol to value-added chemicals is gaining attention. • Ethylene glycol-utilizing microbes are useful as chassis for synthetic pathways.
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Affiliation(s)
- Tetsu Shimizu
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto, 619-0292, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto, 619-0292, Japan.
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan.
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4
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Murillo-Lopez JA, Villegas-Escobar N, Vogt-Geisse S, Vöhringer-Martinez E. Molecular Environment Modulates CO 2 Liberation from Carboxy-Biotin. J Phys Chem B 2024; 128:5327-5335. [PMID: 38771940 DOI: 10.1021/acs.jpcb.4c00910] [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: 05/23/2024]
Abstract
Carboxy-biotin serves as a coenzyme in certain carboxylases, exhibiting the remarkable capability to transfer a carboxy group to specific substrates. This process is made possible by the presence of biotin, a unique molecule that consists of a sulfur-containing tetrahydrothiophene ring fused to a ureido group. It is covalently attached to the enzyme via a flexible linker, allowing for its functionality. Biotin-dependent carboxylases consist of two distinct domains. The first domain (BC) facilitates biotin carboxylation by utilizing ATP, while the second domain (CT) transfers CO2 to the substrate. The process of ATP-dependent carboxylation using bicarbonate in the biotin carboxylase domain (BC) is well-known. However, the precise mechanism by which CO2 is released in the carboxyltransferase domain (CT) is still not fully understood. We employed advanced computational chemistry methods to investigate the decarboxylation process of carboxy-biotin in various molecular environments and different protonation states. Regardless of the polarity of the molecular surroundings, decarboxylation only occurs spontaneously in the protonated form. To determine the protonation state of biotin in different environments, we established an accurate computational chemistry method for calculating the pKa value of carboxy-biotin, reaching sub-kcal/mol accuracy. Based on our findings, nonpolar environments, such as the active site of the carboxyltransferase domain, have the ability to cause the spontaneous release of CO2 from carboxy-biotin. The CO2 release takes place spontaneously from protonated carboxy-biotin, promoting the carboxylation of substrates.
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Affiliation(s)
- Juliana A Murillo-Lopez
- Departamento de Físico-Química Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4070139, Chile
| | - Nery Villegas-Escobar
- Departamento de Físico-Química Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4070139, Chile
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4070139, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4070139, Chile
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Su J, Wang P, Zhou W, Peydayesh M, Zhou J, Jin T, Donat F, Jin C, Xia L, Wang K, Ren F, Van der Meeren P, García de Arquer FP, Mezzenga R. Single-site iron-anchored amyloid hydrogels as catalytic platforms for alcohol detoxification. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01657-7. [PMID: 38740933 DOI: 10.1038/s41565-024-01657-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/21/2024] [Indexed: 05/16/2024]
Abstract
Constructing effective antidotes to reduce global health impacts induced by alcohol prevalence is a challenging topic. Despite the positive effects observed with intravenous applications of natural enzyme complexes, their insufficient activities and complicated usage often result in the accumulation of toxic acetaldehyde, which raises important clinical concerns, highlighting the pressing need for stable oral strategies. Here we present an effective solution for alcohol detoxification by employing a biomimetic-nanozyme amyloid hydrogel as an orally administered catalytic platform. We exploit amyloid fibrils derived from β-lactoglobulin, a readily accessible milk protein that is rich in coordinable nitrogen atoms, as a nanocarrier to stabilize atomically dispersed iron (ferrous-dominated). By emulating the coordination structure of the horseradish peroxidase enzyme, the single-site iron nanozyme demonstrates the capability to selectively catalyse alcohol oxidation into acetic acid, as opposed to the more toxic acetaldehyde. Administering the gelatinous nanozyme to mice suffering from alcohol intoxication significantly reduced their blood-alcohol levels (decreased by 55.8% 300 min post-alcohol intake) without causing additional acetaldehyde build-up. Our hydrogel further demonstrates a protective effect on the liver, while simultaneously mitigating intestinal damage and dysbiosis associated with chronic alcohol consumption, introducing a promising strategy in effective alcohol detoxification.
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Affiliation(s)
- Jiaqi Su
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
- Particle and Interfacial Technology Group, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Pengjie Wang
- Department of Nutrition and Health, Beijing Higher Institution Engineering Research Center of Animal Products, China Agricultural University, Beijing, China
| | - Wei Zhou
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Mohammad Peydayesh
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Jiangtao Zhou
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Tonghui Jin
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Felix Donat
- Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
| | - Cuiyuan Jin
- Institute of Translational Medicine, Zhejiang Shuren University, Zhejiang, China
| | - Lu Xia
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Kaiwen Wang
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fazheng Ren
- Department of Nutrition and Health, Beijing Higher Institution Engineering Research Center of Animal Products, China Agricultural University, Beijing, China
| | - Paul Van der Meeren
- Particle and Interfacial Technology Group, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - F Pelayo García de Arquer
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
- Department of Materials, ETH Zurich, Zurich, Switzerland.
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Li A, Cao X, Fu R, Guo S, Fei Q. Biocatalysis of CO 2 and CH 4: Key enzymes and challenges. Biotechnol Adv 2024; 72:108347. [PMID: 38527656 DOI: 10.1016/j.biotechadv.2024.108347] [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: 11/17/2023] [Revised: 03/10/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Mitigating greenhouse gas emissions is a critical challenge for promoting global sustainability. The utilization of CO2 and CH4 as substrates for the production of valuable products offers a promising avenue for establishing an eco-friendly economy. Biocatalysis, a sustainable process utilizing enzymes to facilitate biochemical reactions, plays a significant role in upcycling greenhouse gases. This review provides a comprehensive overview of the enzymes and associated reactions involved in the biocatalytic conversion of CO2 and CH4. Furthermore, the challenges facing the field are discussed, paving the way for future research directions focused on developing robust enzymes and systems for the efficient fixation of CO2 and CH4.
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Affiliation(s)
- Aipeng Li
- Xi'an Key Laboratory of C1 Compound Bioconversion Technology, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xupeng Cao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Rongzhan Fu
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an 710069, China
| | - Shuqi Guo
- Xi'an Key Laboratory of C1 Compound Bioconversion Technology, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Qiang Fei
- Xi'an Key Laboratory of C1 Compound Bioconversion Technology, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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7
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Kabasakal BV, Cotton CAR, Murray JW. Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA reductase controls the reaction. Biochimie 2024; 219:12-20. [PMID: 37952891 DOI: 10.1016/j.biochi.2023.11.003] [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: 08/11/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Malonyl-Coenzyme A Reductase (MCR) in Chloroflexus aurantiacus, a characteristic enzyme of the 3-hydroxypropionate (3-HP) cycle, catalyses the reduction of malonyl-CoA to 3-HP. MCR is a bi-functional enzyme; in the first step, malonyl-CoA is reduced to the free intermediate malonate semialdehyde by the C-terminal region of MCR, and this is further reduced to 3-HP by the N-terminal region of MCR. Here we present the crystal structures of both N-terminal and C-terminal regions of the MCR from C. aurantiacus. A catalytic mechanism is suggested by ligand and substrate bound structures, and structural and kinetic studies of MCR variants. Both MCR structures reveal one catalytic, and one non-catalytic SDR (short chain dehydrogenase/reductase) domain. C-terminal MCR has a lid domain which undergoes a conformational change and controls the reaction. In the proposed mechanism of the C-terminal MCR, the conversion of malonyl-CoA to malonate semialdehyde is based on the reduction of malonyl-CoA by NADPH, followed by the decomposition of the hemithioacetal to produce malonate semialdehyde and coenzyme A. Conserved arginines, Arg734 and Arg773 are proposed to play key roles in the mechanism and conserved Ser719, and Tyr737 are other essential residues forming an oxyanion hole for the substrate intermediates.
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Affiliation(s)
- Burak V Kabasakal
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK; Turkish Accelerator and Radiation Laboratory, Gölbaşı, 06830, Ankara, Turkiye
| | - Charles A R Cotton
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK; Cambrium GmbH, Max-Urich-Strasse 3, 13355, Berlin, Germany
| | - James W Murray
- Department of Life Sciences, Imperial College, Exhibition Road, London, SW7 2AZ, UK.
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8
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Wang J, Marks JH, Fortenberry RC, Kaiser RI. Interstellar formation of glyceric acid [HOCH 2CH(OH)COOH]-The simplest sugar acid. SCIENCE ADVANCES 2024; 10:eadl3236. [PMID: 38478624 PMCID: PMC10936953 DOI: 10.1126/sciadv.adl3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Glyceric acid [HOCH2CH(OH)COOH]-the simplest sugar acid-represents a key molecule in biochemical processes vital for metabolism in living organisms such as glycolysis. Although critically linked to the origins of life and identified in carbonaceous meteorites with abundances comparable to amino acids, the underlying mechanisms of its formation have remained elusive. Here, we report the very first abiotic synthesis of racemic glyceric acid via the barrierless radical-radical reaction of the hydroxycarbonyl radical (HOĊO) with 1,2-dihydroxyethyl (HOĊHCH2OH) radical in low-temperature carbon dioxide (CO2) and ethylene glycol (HOCH2CH2OH) ices. Using isomer-selective vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry, glyceric acid was identified in the gas phase based on the adiabatic ionization energies and isotopic substitution studies. This work reveals the key reaction pathways for glyceric acid synthesis through nonequilibrium reactions from ubiquitous precursor molecules, advancing our fundamental knowledge of the formation pathways of key biorelevant organics-sugar acids-in deep space.
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Affiliation(s)
- Jia Wang
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Joshua H. Marks
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Ryan C. Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Ralf I. Kaiser
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
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Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Wu W, Tong Y, Chen P. Regulation Strategy of Nanostructured Engineering on Indium-Based Materials for Electrocatalytic Conversion of CO 2. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305562. [PMID: 37845037 DOI: 10.1002/smll.202305562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/23/2023] [Indexed: 10/18/2023]
Abstract
Electrochemical carbon dioxide reduction (CO2 RR), as an emerging technology, can combine with sustainable energies to convert CO2 into high value-added products, providing an effective pathway to realize carbon neutrality. However, the high activation energy of CO2 , low mass transfer, and competitive hydrogen evolution reaction (HER) leads to the unsatisfied catalytic activity. Recently, Indium (In)-based materials have attracted significant attention in CO2 RR and a series of regulation strategies of nanostructured engineering are exploited to rationally design various advanced In-based electrocatalysts, which forces the necessary of a comprehensive and fundamental summary, but there is still a scarcity. Herein, this review provides a systematic discussion of the nanostructure engineering of In-based materials for the efficient electrocatalytic conversion of CO2 to fuels. These efficient regulation strategies including morphology, size, composition, defects, surface modification, interfacial structure, alloying, and single-atom structure, are summarized for exploring the internal relationship between the CO2 RR performance and the physicochemical properties of In-based catalysts. The correlation of electronic structure and adsorption behavior of reaction intermediates are highlighted to gain in-depth understanding of catalytic reaction kinetics for CO2 RR. Moreover, the challenges and opportunities of In-based materials are proposed, which is expected to inspire the development of other effective catalysts for CO2 RR.
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Affiliation(s)
- Wenbo Wu
- School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Yun Tong
- School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Pengzuo Chen
- School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
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11
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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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12
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Gorter de Vries PJ, Mol V, Sonnenschein N, Jensen TØ, Nielsen AT. Probing efficient microbial CO 2 utilisation through metabolic and process modelling. Microb Biotechnol 2024; 17:e14414. [PMID: 38380934 PMCID: PMC10880515 DOI: 10.1111/1751-7915.14414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
Acetogenic gas fermentation is increasingly studied as a promising technology to upcycle carbon-rich waste gasses. Currently the product range is limited, and production yields, rates and titres for a number of interesting products do not allow for economically viable processes. By pairing process modelling and host-agnostic metabolic modelling, we compare fermentation conditions and various products to optimise the processes. The models were then used in a simulation of an industrial-scale bubble column reactor. We find that increased temperatures favour gas transfer rates, particularly for the valuable and limiting H2 , while furthermore predicting an optimal feed composition of 9:1 mol H2 to mol CO2 . Metabolically, the increased non-growth associated maintenance requirements of thermophiles favours the formation of catabolic products. To assess the expansion of the product portfolio beyond acetate, both a product volatility analysis and a metabolic pathway model were implemented. In-situ recovery of volatile products is shown to be within range for acetone but challenging due to the extensive evaporation of water, while the direct production of more valuable compounds by acetogens is metabolically unfavourable compared to acetate and ethanol. We discuss alternative approaches to overcome these challenges to utilise acetogenic CO2 fixation to produce a wider range of carbon negative chemicals.
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Affiliation(s)
- Philip J. Gorter de Vries
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Viviënne Mol
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| | - Torbjørn Ølshøj Jensen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
- AgainSøborgDenmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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13
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Chen PR, Xia PF. Carbon recycling with synthetic CO 2 fixation pathways. Curr Opin Biotechnol 2024; 85:103023. [PMID: 38007984 DOI: 10.1016/j.copbio.2023.103023] [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: 09/15/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023]
Abstract
Carbon dioxide (CO2) is the node of alleviating global climate change and supporting living organisms on Earth. Currently, the warming climate and the growing population demand enhanced CO2 fixation for a sustainable future, which stimulates innovations in biotechnology to tackle these challenges. To this endeavor, synthetic biology and metabolic engineering are enabling a promising approach to engineer synthetic carbon fixation in heterotrophic organisms combining the advantages of both autotrophs and heterotrophs. Here, we review the current advances in constructing synthetic CO2 fixation pathways and discuss the underlying design principles with confronting challenges. Moreover, we highlight the application scenarios of these designs at different concentrations of CO2, and how sustainable bioproduction can be improved. We also foresee the future of engineering synthetic carbon fixation pathways for carbon recycling.
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Affiliation(s)
- Pei-Ru Chen
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China.
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14
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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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15
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Ducrot L, López IL, Orrego AH, López-Gallego F. Coenzyme A Thioester Intermediates as Platform Molecules in Cell-Free Chemical Biomanufacturing. Chembiochem 2024; 25:e202300673. [PMID: 37994376 DOI: 10.1002/cbic.202300673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/06/2023] [Indexed: 11/24/2023]
Abstract
The in vitro synthesis of Coenzyme A (CoA)-thioester intermediates opens new avenues to transform simple molecules into more complex and multifunctional ones by assembling cell-free biosynthetic cascades. In this review, we have systematically cataloged known CoA-dependent enzyme reactions that have been successfully implemented in vitro. To faciliate their identification, we provide their UniProt ID when available. Based on this catalog, we have organized enzymes into three modules: activation, modification, and removal. i) The activation module includes enzymes capable of fusing CoA with organic molecules. ii) The modification module includes enzymes capable of catalyzing chemical modifications in the structure of acyl-CoA intermediates. And iii) the removal module includes enzymes able to remove the CoA and release an organic molecule different from the one activated in the upstream. Based on these reactions, we constructed a reaction network that summarizes the most relevant CoA-dependent biosynthetic pathways reported until today. From the information available in the articles, we have plotted the total turnover number of CoA as a function of the product titer, observing a positive correlation between both parameters. Therefore, the success of a CoA-dependent in vitro pathway depends on its ability to regenerate CoA, but also to regenerate other cofactors such as NAD(P)H and ATP.
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Affiliation(s)
- Laurine Ducrot
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Idania L López
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Alejandro H Orrego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
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16
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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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17
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Zhou P, Gao C, Song W, Wei W, Wu J, Liu L, Chen X. Engineering status of protein for improving microbial cell factories. Biotechnol Adv 2024; 70:108282. [PMID: 37939975 DOI: 10.1016/j.biotechadv.2023.108282] [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: 05/12/2023] [Revised: 10/23/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023]
Abstract
With the development of metabolic engineering and synthetic biology, microbial cell factories (MCFs) have provided an efficient and sustainable method to synthesize a series of chemicals from renewable feedstocks. However, the efficiency of MCFs is usually limited by the inappropriate status of protein. Thus, engineering status of protein is essential to achieve efficient bioproduction with high titer, yield and productivity. In this review, we summarize the engineering strategies for metabolic protein status, including protein engineering for boosting microbial catalytic efficiency, protein modification for regulating microbial metabolic capacity, and protein assembly for enhancing microbial synthetic capacity. Finally, we highlight future challenges and prospects of improving microbial cell factories by engineering status of protein.
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Affiliation(s)
- Pei Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China.
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18
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Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202309305. [PMID: 38516574 PMCID: PMC10952289 DOI: 10.1002/ange.202309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 03/23/2024]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
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Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - John Davidson
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center National Renewable Energy Laboratory Golden CO USA
- BOTTLE Consortium Golden CO USA
| | - Anthony P Green
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
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19
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Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. Angew Chem Int Ed Engl 2023; 62:e202309305. [PMID: 37651344 PMCID: PMC10952156 DOI: 10.1002/anie.202309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2 ) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
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Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - John Davidson
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Elizabeth L. Bell
- Renewable Resources and Enabling Sciences CenterNational Renewable Energy LaboratoryGoldenCOUSA
- BOTTLE ConsortiumGoldenCOUSA
| | - Anthony P. Green
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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20
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Marchal D, Schulz L, Schuster I, Ivanovska J, Paczia N, Prinz S, Zarzycki J, Erb TJ. Machine Learning-Supported Enzyme Engineering toward Improved CO 2-Fixation of Glycolyl-CoA Carboxylase. ACS Synth Biol 2023; 12:3521-3530. [PMID: 37983631 PMCID: PMC10729300 DOI: 10.1021/acssynbio.3c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023]
Abstract
Glycolyl-CoA carboxylase (GCC) is a new-to-nature enzyme that catalyzes the key reaction in the tartronyl-CoA (TaCo) pathway, a synthetic photorespiration bypass that was recently designed to improve photosynthetic CO2 fixation. GCC was created from propionyl-CoA carboxylase (PCC) through five mutations. However, despite reaching activities of naturally evolved biotin-dependent carboxylases, the quintuple substitution variant GCC M5 still lags behind 4-fold in catalytic efficiency compared to its template PCC and suffers from futile ATP hydrolysis during CO2 fixation. To further improve upon GCC M5, we developed a machine learning-supported workflow that reduces screening efforts for identifying improved enzymes. Using this workflow, we present two novel GCC variants with 2-fold increased carboxylation rate and 60% reduced energy demand, respectively, which are able to address kinetic and thermodynamic limitations of the TaCo pathway. Our work highlights the potential of combining machine learning and directed evolution strategies to reduce screening efforts in enzyme engineering.
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Affiliation(s)
- Daniel
G. Marchal
- Department
of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Luca Schulz
- Department
of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | | | | | - Nicole Paczia
- Core
Facility for Metabolomics and Small Molecule Mass Spectrometry, Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Simone Prinz
- Central
Electron Microscopy Facility, Max-Planck-Institute
of Biophysics, Frankfurt 60438, Germany
| | - Jan Zarzycki
- Department
of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Tobias J. Erb
- Department
of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
- SYNMIKRO
Center for Synthetic Microbiology, Marburg 35032, Germany
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21
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Qiao Y, Ma W, Zhang S, Guo F, Liu K, Jiang Y, Wang Y, Xin F, Zhang W, Jiang M. Artificial multi-enzyme cascades and whole-cell transformation for bioconversion of C1 compounds: Advances, challenge and perspectives. Synth Syst Biotechnol 2023; 8:578-583. [PMID: 37706206 PMCID: PMC10495606 DOI: 10.1016/j.synbio.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Artificial multi-enzyme cascades bear great potential for bioconversion of C1 compounds to value-added chemicals. Over the past decade, massive efforts have been devoted to constructing multi-enzyme cascades to produce glycolic acid, rare functional sugars and even starch from C1 compounds. However, in contrast to traditional fermentation utilizing C1 compounds with the expectation of competitive economic performance in future industrialization, multi-enzyme cascades systems in the proof-of-concept phase are facing the challenges of upscaling. Here, we offered an overview of the recent advances in the construction of in vitro multi-enzyme cascades and whole-cell transformation using C1 compounds as substrate. In addition, the existing challenges and possible solutions were also discussed aiming to combine the strengths of in vitro and in vivo multi-enzyme cascades systems for upscaling.
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Affiliation(s)
- Yangyi Qiao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
| | - Wenyue Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
| | - Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
| | - Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
| | - Kang Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
| | - Yanxia Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211800, PR China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, PR China
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22
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Wagner N, Wen L, Frazão CJR, Walther T. Next-generation feedstocks methanol and ethylene glycol and their potential in industrial biotechnology. Biotechnol Adv 2023; 69:108276. [PMID: 37918546 DOI: 10.1016/j.biotechadv.2023.108276] [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: 09/04/2023] [Revised: 10/13/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
Microbial fermentation processes are expected to play an important role in reducing dependence on fossil-based raw materials for the production of everyday chemicals. In order to meet the growing demand for biotechnological products in the future, alternative carbon sources that do not compete with human nutrition must be exploited. The chemical conversion of the industrially emitted greenhouse gas CO2 into microbially utilizable platform chemicals such as methanol represents a sustainable strategy for the utilization of an abundant carbon source and has attracted enormous scientific interest in recent years. A relatively new approach is the microbial synthesis of products from the C2-compound ethylene glycol, which can also be synthesized from CO2 and non-edible biomass and, in addition, can be recovered from plastic waste. Here we summarize the main chemical routes for the synthesis of methanol and ethylene glycol from sustainable resources and give an overview of recent metabolic engineering work for establishing natural and synthetic microbial assimilation pathways. The different metabolic routes for C1 and C2 alcohol-dependent bioconversions were compared in terms of their theoretical maximum yields and their oxygen requirements for a wide range of value-added products. Assessment of the process engineering challenges for methanol and ethylene glycol-based fermentations underscores the theoretical advantages of new synthetic metabolic routes and advocates greater consideration of ethylene glycol, a C2 substrate that has received comparatively little attention to date.
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Affiliation(s)
- Nils Wagner
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Linxuan Wen
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Cláudio J R Frazão
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Thomas Walther
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany.
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23
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Yu Y, Pi S, Ke T, Zhou B, Chao W, Yang Y, Li Z, Li G, Ren N, Gao X, Lu L. Artificial Soil-Like Material Enhances CO 2 Bio-Valorization into Chemicals in Gas Fermentation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:53488-53497. [PMID: 37929338 DOI: 10.1021/acsami.3c12627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Gas fermentation offers a carbon-neutral route for producing industrial feedstocks using autotrophic microbes to convert carbon dioxide (CO2) in waste gases, such as industrial emissions and biogas, into valuable chemicals or biofuels. However, slow microbial metabolism owing to low gaseous solubility causes significant challenges in gas fermentation. Although chemical or genetic manipulations have been explored to improve gas fermentation, they are either nonsustainable or complex. Herein, an artificial soil-like material (SLM) inspired by natural soil was fabricated to improve the growth and metabolism ofCupriavidus necatorfor enhanced poly-β-hydroxybutyrate (PHB) biosynthesis from CO2 and hydrogen (H2). Porous SLM comprises low-cost nanoclay, boehmite, and starch and serves as a biocarrier to facilitate the colonization of bacteria and delivery of CO2 to bacteria. With 3.0 g/L SLM addition, the solubility of CO2 in water increased by ∼4 times and biomass and PHB production boosted by 29 and 102%, respectively, in the 24 h culture. In addition, a positive modulation was observed in the metabolism of PHB biosynthesis. PHB biosynthesis-associated gene expression was found to be enhanced in response to the SLM addition. The concentrations of intermediates in the metabolic pathway of PHB biosynthesis, such as pyruvate and acetyl-CoA, as well as reducing energy (ATP and NADPH) significantly increased with SLM addition. SLM also demonstrated the merits of easy fabrication, high stability, recyclability, and plasticity, thereby indicating its considerable potential for large-scale application in gas fermentation.
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Affiliation(s)
- Yongjie Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Shanshan Pi
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Tan Ke
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Baiqin Zhou
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Weixiang Chao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Yang Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Zhida Li
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Guifeng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Xiang Gao
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology of CAS, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academic of Science, Shenzhen 518000, China
| | - Lu Lu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
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24
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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: 0] [Impact Index Per Article: 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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25
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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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26
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Phan UT, Jeon BW, Kim YH. Microbial engineering of Methylorubrum extorquens AM1 to enhance CO 2 conversion into formate. Enzyme Microb Technol 2023; 168:110264. [PMID: 37244213 DOI: 10.1016/j.enzmictec.2023.110264] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Methylorubrum extorquens AM1 has the potential to consume C1 feedstock to produce a wide range of biomaterials, from bioplastic to pharmaceutical. However, the synthetic biology tools for engineering M. extorquens AM1 need to be employed for precise control of recombinant enzyme expression. In this study, we presented an approach to improve the expression level of formate dehydrogenase 1 from M. extorquens AM1 (MeFDH1) using an efficient terminator and 5'-untranslated region (5'-UTR) design for enhanced carbon dioxide (CO2) conversion activity of whole-cell biocatalyst. The rrnB terminator significantly increased mRNA levels of MeFDH1 alpha and beta subunits by 8.2-fold and 11-fold, respectively, compared to the T7 terminator. Moreover, enzyme production was 1.6-fold higher with 2.1 mg/wet cell weight (WCW) using rrnB terminator. Homologous 5'-untranslated regions (5'-UTR) determined based on proteomics data and UTR designer also influenced the expression level of MeFDH1. The 5'-UTR of the formaldehyde activating enzyme (fae) was the strongest, with 2.5-fold higher expression than that of the control sequence (T7g-10L). Furthermore, the electrochemical reaction of recombinant strains as whole-cell biocatalysts was investigated for their applicability to CO2 conversion, showing enhanced formate productivity. The recombinant strain containing the 5'-UTR sequence of fae exhibited formate productivity of 5.0 mM/h, 2.3-fold higher than that of the control strain (T7). Overall, this study suggested practical applications for CO2 conversion into bioavailable formate and provided valuable insights for recombinant expression systems in methylotrophic strains.
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Affiliation(s)
- Uyen Thu Phan
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea.
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27
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Pfister P, Diehl C, Hammarlund E, Carrillo M, Erb TJ. Enhancing the Substrate Specificity of Clostridium Succinyl-CoA Reductase for Synthetic Biology and Biocatalysis. Biochemistry 2023. [PMID: 37207322 DOI: 10.1021/acs.biochem.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Succinyl-CoA reductase (SucD) is an acylating aldehyde reductase that catalyzes the NADPH-dependent reduction of succinyl-CoA to succinic semialdehyde. The reaction sequence from succinate to crotonyl-CoA is of particular interest for several new-to-nature CO2-fixation pathways, such as the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, in which SucD plays a key role. However, pathways like the CETCH cycle feature several CoA-ester intermediates, which could be potentially side substrates for this enzyme. Here, we show that the side reaction for most CETCH cycle metabolites is relatively small (<2%) with the exception of mesaconyl-C1-CoA (16%), which represents a competing substrate in this pathway. We addressed this promiscuity by solving the crystal structure of a SucD of Clostridium kluyveri in complex with NADP+ and mesaconyl-C1-CoA. We further identified two residues (Lys70 and Ser243) that coordinate mesaconyl-C1-CoA at the active site. We targeted those residues with site-directed mutagenesis to improve succinyl-CoA over mesaconyl-C1-CoA reduction. The best resulting SucD variant, K70R, showed a strongly reduced side activity for mesaconyl-C1-CoA, but the substitution also reduced the specific activity for succinyl-CoA by a factor of 10. Transferring the same mutations into a SucD homologue from Clostridium difficile similarly decreases the side reaction of this enzyme for mesaconyl-C1-CoA from 12 to 2%, notably without changing the catalytic efficiency for succinyl-CoA. Overall, our structure-based engineering efforts provided a highly specific enzyme of interest for several applications in biocatalysis and synthetic biology.
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Affiliation(s)
- Pascal Pfister
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Christoph Diehl
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Eric Hammarlund
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Martina Carrillo
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, Karl-von-Frisch Str., 14, 35032 Marburg, Germany
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28
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Nattermann M, Wenk S, Pfister P, He H, Lee SH, Szymanski W, Guntermann N, Zhu F, Nickel L, Wallner C, Zarzycki J, Paczia N, Gaißert N, Franciò G, Leitner W, Gonzalez R, Erb TJ. Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo. Nat Commun 2023; 14:2682. [PMID: 37160875 PMCID: PMC10170137 DOI: 10.1038/s41467-023-38072-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/14/2023] [Indexed: 05/11/2023] Open
Abstract
Formate can be envisioned at the core of a carbon-neutral bioeconomy, where it is produced from CO2 by (electro-)chemical means and converted into value-added products by enzymatic cascades or engineered microbes. A key step in expanding synthetic formate assimilation is its thermodynamically challenging reduction to formaldehyde. Here, we develop a two-enzyme route in which formate is activated to formyl phosphate and subsequently reduced to formaldehyde. Exploiting the promiscuity of acetate kinase and N-acetyl-γ-glutamyl phosphate reductase, we demonstrate this phosphate (Pi)-based route in vitro and in vivo. We further engineer a formyl phosphate reductase variant with improved formyl phosphate conversion in vivo by suppressing cross-talk with native metabolism and interface the Pi route with a recently developed formaldehyde assimilation pathway to enable C2 compound formation from formate as the sole carbon source in Escherichia coli. The Pi route therefore offers a potent tool in expanding the landscape of synthetic formate assimilation.
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Affiliation(s)
- Maren Nattermann
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sebastian Wenk
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Pascal Pfister
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hai He
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Seung Hwan Lee
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Witold Szymanski
- Institute of Translational Proteomics, Philipps University, Marburg, Germany
| | - Nils Guntermann
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
| | - Fayin Zhu
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | | | | | - Jan Zarzycki
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Giancarlo Franciò
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
| | - Walter Leitner
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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29
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Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023; 64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.
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Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian Li
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
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30
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Lee JK, Liu YT, Hu JJ, Aphasizheva I, Aphasizhev R, Zhou ZH. CryoEM reveals oligomeric isomers of a multienzyme complex and assembly mechanics. J Struct Biol X 2023; 7:100088. [PMID: 37128595 PMCID: PMC10148081 DOI: 10.1016/j.yjsbx.2023.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/13/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023] Open
Abstract
Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly lead to serious illness in humans, known as propionic acidemia. Here, we report the cryogenic electron microscopy (cryoEM) structures and assembly of different oligomeric isomers of endogenous PCC from the parasitic protozoan Leishmania tarentolae (LtPCC). These structures and their statistical distribution reveal the mechanics of PCC assembly and disassembly at equilibrium. We show that, in solution, endogenous LtPCC β-subunits form stable homohexamers, to which different numbers of α-subunits attach. Sorting LtPCC particles into seven classes (i.e., oligomeric formulae α0β6, α1β6, α2β6, α3β6, α4β6, α5β6, α6β6) enables formulation of a model for PCC assembly. Our results suggest how multimerization regulates PCC enzymatic activity and showcase the utility of cryoEM in revealing the statistical mechanics of reaction pathways.
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Affiliation(s)
- Jane K.J. Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Psychology, UCLA, Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Jason J. Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Mathematics, UCLA, Los Angeles, CA 90095, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
- Department of Biochemistry, BUMC, Boston, MA 02118, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
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31
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Frazão CJR, Wagner N, Rabe K, Walther T. Construction of a synthetic metabolic pathway for biosynthesis of 2,4-dihydroxybutyric acid from ethylene glycol. Nat Commun 2023; 14:1931. [PMID: 37024485 PMCID: PMC10079672 DOI: 10.1038/s41467-023-37558-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Ethylene glycol is an attractive two-carbon alcohol substrate for biochemical product synthesis as it can be derived from CO2 or syngas at no sacrifice to human food stocks. Here, we disclose a five-step synthetic metabolic pathway enabling the carbon-conserving biosynthesis of the versatile platform molecule 2,4-dihydroxybutyric acid (DHB) from this compound. The linear pathway chains ethylene glycol dehydrogenase, D-threose aldolase, D-threose dehydrogenase, D-threono-1,4-lactonase, D-threonate dehydratase and 2-oxo-4-hydroxybutyrate reductase enzyme activities in succession. We screen candidate enzymes with D-threose dehydrogenase and D-threonate dehydratase activities on cognate substrates with conserved carbon-centre stereochemistry. Lastly, we show the functionality of the pathway by its expression in an Escherichia coli strain and production of 1 g L-1 and 0.8 g L-1 DHB from, respectively, glycolaldehyde or ethylene glycol.
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Affiliation(s)
- Cláudio J R Frazão
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Nils Wagner
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Kenny Rabe
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany
| | - Thomas Walther
- Institute of Natural Materials Technology, TU Dresden, 01062, Dresden, Germany.
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32
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Recent progress in the synthesis of advanced biofuel and bioproducts. Curr Opin Biotechnol 2023; 80:102913. [PMID: 36854202 DOI: 10.1016/j.copbio.2023.102913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/27/2023]
Abstract
Energy is one of the most complex fields of study and an issue that influences nearly every aspect of modern life. Over the past century, combustion of fossil fuels, particularly in the transportation sector, has been the dominant form of energy release. Refining of petroleum and natural gas into liquid transportation fuels is also the centerpiece of the modern chemical industry used to produce materials, solvents, and other consumer goods. In the face of global climate change, the world is searching for alternative, sustainable means of producing energy carriers and chemical building blocks. The use of biofuels in engines predates modern refinery optimization and today represents a small but significant fraction of liquid transportation fuels burnt each year. Similarly, white biotechnology has been used to produce many natural products through fermentation. The evolution of recombinant DNA technology into modern synthetic biology has expanded the scope of biofuels and bioproducts that can be made by biocatalysts. This opinion examines the current trends in this research space, highlighting the substantial growth in computational tools and the growing influence of renewable electricity in the design of metabolic engineering strategies. In short, advanced biofuel and bioproduct synthesis remains a vibrant and critically important field of study whose focus is shifting away from the conversion of lignocellulosic biomass toward a broader consideration of how to reduce carbon dioxide to fuels and chemical products.
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33
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Park H, Wang W, Min SH, Ren Y, Shin K, Han X. Artificial organelles for sustainable chemical energy conversion and production in artificial cells: Artificial mitochondrion and chloroplasts. BIOPHYSICS REVIEWS 2023; 4:011311. [PMID: 38510162 PMCID: PMC10903398 DOI: 10.1063/5.0131071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/17/2023] [Indexed: 03/22/2024]
Abstract
Sustainable energy conversion modules are the main challenges for building complex reaction cascades in artificial cells. Recent advances in biotechnology have enabled this sustainable energy supply, especially the adenosine triphosphate (ATP), by mimicking the organelles, which are the core structures for energy conversion in living cells. Three components are mainly shared by the artificial organelles: the membrane compartment separating the inner and outer parts, membrane proteins for proton translocation, and the molecular rotary machine for ATP synthesis. Depending on the initiation factors, they are further categorized into artificial mitochondrion and artificial chloroplasts, which use chemical nutrients for oxidative phosphorylation and light for photosynthesis, respectively. In this review, we summarize the essential components needed for artificial organelles and then review the recent progress on two different artificial organelles. Recent strategies, purified and identified proteins, and working principles are discussed. With more study on the artificial mitochondrion and artificial chloroplasts, they are expected to be very powerful tools, allowing us to achieve complex cascading reactions in artificial cells, like the ones that happen in real cells.
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Affiliation(s)
- Hyun Park
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, South Korea
| | - Weichen Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Seo Hyeon Min
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, South Korea
| | - Yongshuo Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, South Korea
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
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34
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Li C, Gao X, Qi H, Zhang W, Li L, Wei C, Wei M, Sun X, Wang S, Wang L, Ji Y, Mao S, Zhu Z, Tanokura M, Lu F, Qin HM. Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening. Angew Chem Int Ed Engl 2023; 62:e202216721. [PMID: 36658306 DOI: 10.1002/anie.202216721] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
Biosynthesis of D-allulose has been achieved using ketose 3-epimerases (KEases), but its application is limited by poor catalytic performance. In this study, we redesigned a genetically encoded biosensor based on a D-allulose-responsive transcriptional regulator for real-time monitoring of D-allulose. An ultrahigh-throughput droplet-based microfluidic screening platform was further constructed by coupling with this D-allulose-detecting biosensor for the directed evolution of the KEases. Structural analysis of Sinorhizobium fredii D-allulose 3-epimerase (SfDAE) revealed that a highly flexible helix/loop region exposes or occludes the catalytic center as an essential lid conformation regulating substrate recognition. We reprogrammed SfDAE using structure-guided rational design and directed evolution, in which a mutant M3-2 was identified with 17-fold enhanced catalytic efficiency. Our research offers a paradigm for the design and optimization of a biosensor-based microdroplet screening platform.
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Affiliation(s)
- Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Xin Gao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Hongbin Qi
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Wei Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Lei Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Cancan Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Meijing Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Xiaoxuan Sun
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Shusen Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Liyan Wang
- Luoyang BIO-Industry Technology Innovation Center, Luoyang, 471000, Henan, China
| | - Yingbin Ji
- Luoyang BIO-Industry Technology Innovation Center, Luoyang, 471000, Henan, China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, China
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35
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Teshima M, Willers VP, Sieber V. Cell-free enzyme cascades - application and transition from development to industrial implementation. Curr Opin Biotechnol 2023; 79:102868. [PMID: 36563481 DOI: 10.1016/j.copbio.2022.102868] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
In the vision to realize a circular economy aiming for net carbon neutrality or even negativity, cell-free bioconversion of sustainable and renewable resources emerged as a promising strategy. The potential of in vitro systems is enormous, delivering technological, ecological, and ethical added values. Innovative concepts arose in cell-free enzymatic conversions to reduce process waste production and preserve fossil resources, as well as to redirect and assimilate released industrial pollutions back into the production cycle again. However, the great challenge in the near future will be the jump from a concept to an industrial application. The transition process in industrial implementation also requires economic aspects such as productivity, scalability, and cost-effectiveness. Here, we briefly review the latest proof-of-concept cascades using carbon dioxide and other C1 or lignocellulose-derived chemicals as blueprints to efficiently recycle greenhouse gases, as well as cutting-edge technologies to maturate these concepts to industrial pilot plants.
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Affiliation(s)
- Mariko Teshima
- Technical University of Munich, Campus Straubing, 94315 Straubing, Germany
| | | | - Volker Sieber
- Technical University of Munich, Campus Straubing, 94315 Straubing, Germany; SynBioFoundry@TUM, Technical University of Munich, 94315 Straubing, Germany; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia.
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36
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Engineering Microorganisms to Produce Bio-Based Monomers: Progress and Challenges. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bioplastics are polymers made from sustainable bio-based feedstocks. While the potential of producing bio-based monomers in microbes has been investigated for decades, their economic feasibility is still unsatisfactory compared with petroleum-derived methods. To improve the overall synthetic efficiency of microbial cell factories, three main strategies were summarized in this review: firstly, implementing approaches to improve the microbial utilization ability of cheap and abundant substrates; secondly, developing methods at enzymes, pathway, and cellular levels to enhance microbial production performance; thirdly, building technologies to enhance microbial pH, osmotic, and metabolites stress tolerance. Moreover, the challenges of, and some perspectives on, exploiting microorganisms as efficient cell factories for producing bio-based monomers are also discussed.
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37
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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: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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38
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Hu JJ, Lee JKJ, Liu YT, Yu C, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH. Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase. Structure 2023; 31:100-110.e4. [PMID: 36543169 PMCID: PMC9825669 DOI: 10.1016/j.str.2022.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. α6β6 LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking α6β6 LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.
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Affiliation(s)
- Jason J Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Mathematics, UCLA, Los Angeles, CA 90095, USA
| | - Jane K J Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Psychology, UCLA, Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA; Department of Biochemistry, BUMC, Boston, MA 02118, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA.
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39
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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40
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Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
This review summarises the methods available for directed evolution, including mutagenesis and variant selection techniques. The advantages and disadvantages of each technique are presented, and future challenges in the field are discussed.
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Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - John T. Heap
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
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41
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Suryatin Alim G, Suzuki T, Honda K. Cell-Free Production and Regeneration of Cofactors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:29-49. [PMID: 37306696 DOI: 10.1007/10_2023_222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cofactors, such as adenosine triphosphate, nicotinamide adenine dinucleotide, and coenzyme A, are involved in nearly 50% of enzymatic reactions and widely used in biocatalytic production of useful chemicals. Although commercial production of cofactors has been mostly dependent on extraction from microbial cells, this approach has a theoretical limitation to achieve a high-titer, high-yield production of cofactors owing to the tight regulation of cofactor biosynthesis in living cells. Besides the cofactor production, their regeneration is also a key challenge to enable continuous use of costly cofactors and improve the feasibility of enzymatic chemical manufacturing. Construction and implementation of enzyme cascades for cofactor biosynthesis and regeneration in a cell-free environment can be a promising approach to these challenges. In this chapter, we present the available tools for cell-free cofactor production and regeneration, the pros and cons, and how they can contribute to promote the industrial application of enzymes.
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Affiliation(s)
- Gladwin Suryatin Alim
- Department of Chemistry, University of Basel, Basel, Switzerland
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Takuma Suzuki
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, Osaka, Japan.
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.
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42
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Recent progress in the engineering of C1-utilizing microbes. Curr Opin Biotechnol 2022; 78:102836. [PMID: 36334444 DOI: 10.1016/j.copbio.2022.102836] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The global climate crisis has led to the transition toward the sustainable production of chemicals and fuels with a low carbon footprint. Microbial utilization of one-carbon (C1) substrates, such as carbon dioxide, carbon monoxide, methane, formate, and methanol, may be a promising replacement for the current fossil fuel-based industry. However, natural C1-utilizing microbes are currently unsuitable for industrial applications because of their slow growth and low carbon conversion efficiency, which results in low productivity and yield. Here, we review the recent achievements in engineering C1-utilizing microbes with improved carbon assimilation efficiency and describe the development of synthetic microorganisms by introducing natural C1 assimilation pathways in non-C1-utilizing microbes. Finally, we outline the future directions for realizing the industrial potential of C1-utilizing microbes.
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43
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Orsi E, Claassens NJ, Nikel PI, Lindner SN. Optimizing microbial networks through metabolic bypasses. Biotechnol Adv 2022; 60:108035. [PMID: 36096403 DOI: 10.1016/j.biotechadv.2022.108035] [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: 03/26/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023]
Abstract
Metabolism has long been considered as a relatively stiff set of biochemical reactions. This somewhat outdated and dogmatic view has been challenged over the last years, as multiple studies exposed unprecedented plasticity of metabolism by exploring rational and evolutionary modifications within the metabolic network of cell factories. Of particular importance is the emergence of metabolic bypasses, which consist of enzymatic reaction(s) that support unnatural connections between metabolic nodes. Such novel topologies can be generated through the introduction of heterologous enzymes or by upregulating native enzymes (sometimes relying on promiscuous activities thereof). Altogether, the adoption of bypasses resulted in an expansion in the capacity of the host's metabolic network, which can be harnessed for bioproduction. In this review, we discuss modifications to the canonical architecture of central carbon metabolism derived from such bypasses towards six optimization purposes: stoichiometric gain, overcoming kinetic limitations, solving thermodynamic barriers, circumventing toxic intermediates, uncoupling product synthesis from biomass formation, and altering redox cofactor specificity. The metabolic costs associated with bypass-implementation are likewise discussed, including tailoring their design towards improving bioproduction.
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Affiliation(s)
- Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany.
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44
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Polidoro D, Perosa A, Rodríguez-Castellón E, Canton P, Castoldi L, Rodríguez-Padrón D, Selva M. Metal-Free N-Doped Carbons for Solvent-Less CO 2 Fixation Reactions: A Shrimp Shell Valorization Opportunity. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:13835-13848. [PMID: 36845462 PMCID: PMC9942530 DOI: 10.1021/acssuschemeng.2c04443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/20/2022] [Indexed: 06/17/2023]
Abstract
High anthropogenic CO2 emissions are among the main causes of climate change. Herein, we investigate the use of CO2 for the synthesis of organic cyclic carbonates on metal-free nitrogen-doped carbon catalysts obtained from chitosan, chitin, and shrimp shell wastes, both in batch and in continuous flow (CF). The catalysts were characterized by N2 physisorption, CO2-temperature-programmed desorption, X-ray photoelectron spectroscopy, scanning electron microscopy, and CNHS elemental analysis, and all reactivity tests were run in the absence of solvents. Under batch conditions, the catalyst obtained by calcination of chitin exhibited excellent performance in the conversion of epichlorohydrin (selected as a model epoxide), resulting in the corresponding cyclic carbonate with 96% selectivity at complete conversion, at 150 °C and 30 bar CO2, for 4 h. On the other hand, in a CF regime, a quantitative conversion and a carbonate selectivity >99% were achieved at 150 °C, by using the catalyst obtained from shrimp waste. Remarkably, the material displayed an outstanding stability over a reaction run time of 180 min. The robustness of the synthetized catalysts was confirmed by their good operational stability and reusability: ca. (75 ± 3)% of the initial conversion was achieved/retained by all systems, after six recycles. Also, additional batch experiments proved that the catalysts were successful on different terminal and internal epoxides.
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Affiliation(s)
- Daniele Polidoro
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari di Venezia, 30123 Venezia, Italy
| | - Alvise Perosa
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari di Venezia, 30123 Venezia, Italy
| | - Enrique Rodríguez-Castellón
- Department
of Inorganic Chemistry, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Patrizia Canton
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari di Venezia, 30123 Venezia, Italy
| | - Lidia Castoldi
- Laboratory
of Catalysis and Catalytic Processes, Dipartimento di Energia, Politecnico di Milano, Via La Masa 34, 20156 Milano, Italy
| | - Daily Rodríguez-Padrón
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari di Venezia, 30123 Venezia, Italy
| | - Maurizio Selva
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università
Ca’ Foscari di Venezia, 30123 Venezia, Italy
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45
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Gomide MDS, Leitão MDC, Coelho CM. Biocircuits in plants and eukaryotic algae. FRONTIERS IN PLANT SCIENCE 2022; 13:982959. [PMID: 36212277 PMCID: PMC9545776 DOI: 10.3389/fpls.2022.982959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As one of synthetic biology's foundations, biocircuits are a strategy of genetic parts assembling to recognize a signal and to produce a desirable output to interfere with a biological function. In this review, we revisited the progress in the biocircuits technology basis and its mandatory elements, such as the characterization and assembly of functional parts. Furthermore, for a successful implementation, the transcriptional control systems are a relevant point, and the computational tools help to predict the best combinations among the biological parts planned to be used to achieve the desirable phenotype. However, many challenges are involved in delivering and stabilizing the synthetic structures. Some research experiences, such as the golden crops, biosensors, and artificial photosynthetic structures, can indicate the positive and limiting aspects of the practice. Finally, we envision that the modulatory structural feature and the possibility of finer gene regulation through biocircuits can contribute to the complex design of synthetic chromosomes aiming to develop plants and algae with new or improved functions.
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Affiliation(s)
- Mayna da Silveira Gomide
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
- School of Medicine, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - Matheus de Castro Leitão
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
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46
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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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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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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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Suzuki Y, Taniguchi K, Nam Hoang H, Tamura M, Matsuda T. Rate enhancement of lipase-catalyzed reaction using CO2-expanded liquids as solvents for chiral tetralol synthesis. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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50
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Abstract
Carbon dioxide is a major greenhouse gas, and its fixation and transformation are receiving increasing attention. Biofixation of CO2 is an eco–friendly and efficient way to reduce CO2, and six natural CO2 fixation pathways have been identified in microorganisms and plants. In this review, the six pathways along with the most recent identified variant pathway were firstly comparatively characterized. The key metabolic process and enzymes of the CO2 fixation pathways were also summarized. Next, the enzymes of Rubiscos, biotin-dependent carboxylases, CO dehydrogenase/acetyl-CoA synthase, and 2-oxoacid:ferredoxin oxidoreductases, for transforming inorganic carbon (CO2, CO, and bicarbonate) to organic chemicals, were specially analyzed. Then, the factors including enzyme properties, CO2 concentrating, energy, and reducing power requirements that affect the efficiency of CO2 fixation were discussed. Recent progress in improving CO2 fixation through enzyme and metabolic engineering was then summarized. The artificial CO2 fixation pathways with thermodynamical and/or energetical advantages or benefits and their applications in biosynthesis were included as well. The challenges and prospects of CO2 biofixation and conversion are discussed.
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