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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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2
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Ma Y, Shang Y, Stephanopoulos G. Engineering peroxisomal biosynthetic pathways for maximization of triterpene production in Yarrowia lipolytica. Proc Natl Acad Sci U S A 2024; 121:e2314798121. [PMID: 38261612 PMCID: PMC10835042 DOI: 10.1073/pnas.2314798121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Constructing efficient cell factories for product synthesis is frequently hampered by competing pathways and/or insufficient precursor supply. This is particularly evident in the case of triterpenoid biosynthesis in Yarrowia lipolytica, where squalene biosynthesis is tightly coupled to cytosolic biosynthesis of sterols essential for cell viability. Here, we addressed this problem by reconstructing the complete squalene biosynthetic pathway, starting from acetyl-CoA, in the peroxisome, thus harnessing peroxisomal acetyl-CoA pool and sequestering squalene synthesis in this organelle from competing cytosolic reactions. This strategy led to increasing the squalene levels by 1,300-fold relatively to native cytosolic synthesis. Subsequent enhancement of the peroxisomal acetyl-CoA supply by two independent approaches, 1) converting cellular lipid pool to peroxisomal acetyl-CoA and 2) establishing an orthogonal acetyl-CoA shortcut from CO2-derived acetate in the peroxisome, further significantly improved local squalene accumulation. Using these approaches, we constructed squalene-producing strains capable of yielding 32.8 g/L from glucose, and 31.6 g/L from acetate by employing a cofeeding strategy, in bioreactor fermentations. Our findings provide a feasible strategy for protecting intermediate metabolites that can be claimed by multiple reactions by engineering peroxisomes in Y. lipolytica as microfactories for the production of such intermediates and in particular acetyl-CoA-derived metabolites.
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Affiliation(s)
- Yongshuo Ma
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, Chinese Academy of Agricultural Sciences (CAAS)-Yunnan Normal University (YNNU)-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming650500, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy (Ministry of Education), Yunnan Normal University, Kunming650500, China
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
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3
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Boob AG, Chen J, Zhao H. Enabling pathway design by multiplex experimentation and machine learning. Metab Eng 2024; 81:70-87. [PMID: 38040110 DOI: 10.1016/j.ymben.2023.11.006] [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: 09/14/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures that arise from intermediate accumulation and reduced flux resulting from competing pathways within the host cell. Moreover, the conventional trial and error methods utilized in pathway optimization struggle to fully grasp the intricacies of installed pathways, leading to time-consuming and labor-intensive experiments, ultimately resulting in suboptimal yields. Considering these obstacles, there is a pressing need to explore the enzyme expression landscape and identify the optimal pathway configuration for enhanced production of molecules. This review delves into recent advancements in pathway engineering, with a focus on multiplex experimentation and machine learning techniques. These approaches play a pivotal role in overcoming the limitations of traditional methods, enabling exploration of a broader design space and increasing the likelihood of discovering optimal pathway configurations for enhanced production of molecules. We discuss several tools and strategies for pathway design, construction, and optimization for sustainable and cost-effective microbial production of molecules ranging from bulk to fine chemicals. We also highlight major successes in academia and industry through compelling case studies.
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Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Junyu Chen
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.
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4
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Ren X, Wang X, Zheng G, Wang S, Wang Q, Yuan M, Xu T, Xu J, Huang P, Ge M. Targeting one-carbon metabolism for cancer immunotherapy. Clin Transl Med 2024; 14:e1521. [PMID: 38279895 PMCID: PMC10819114 DOI: 10.1002/ctm2.1521] [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: 08/01/2023] [Revised: 11/15/2023] [Accepted: 12/10/2023] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND One-carbon (1C) metabolism is a metabolic network that plays essential roles in biological reactions. In 1C metabolism, a series of nutrients are used to fuel metabolic pathways, including nucleotide metabolism, amino acid metabolism, cellular redox defence and epigenetic maintenance. At present, 1C metabolism is considered the hallmark of cancer. The 1C units obtained from the metabolic pathways increase the proliferation rate of cancer cells. In addition, anticancer drugs, such as methotrexate, which target 1C metabolism, have long been used in the clinic. In terms of immunotherapy, 1C metabolism has been used to explore biomarkers connected with immunotherapy response and immune-related adverse events in patients. METHODS We collected numerous literatures to explain the roles of one-carbon metabolism in cancer immunotherapy. RESULTS In this review, we focus on the important pathways in 1C metabolism and the function of 1C metabolism enzymes in cancer immunotherapy. Then, we summarise the inhibitors acting on 1C metabolism and their potential application on cancer immunotherapy. Finally, we provide a viewpoint and conclusion regarding the opportunities and challenges of targeting 1C metabolism for cancer immunotherapy in clinical practicability in the future. CONCLUSION Targeting one-carbon metabolism is useful for cancer immunotherapy.
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Affiliation(s)
- Xinxin Ren
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
- Department of PathologyCancer CenterZhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiang Wang
- Department of PharmacyAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouZhejiangChina
| | - Guowan Zheng
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Shanshan Wang
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Qiyue Wang
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Mengnan Yuan
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Tong Xu
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Jiajie Xu
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Ping Huang
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Minghua Ge
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
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5
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Wu T, Gómez-Coronado PA, Kubis A, Lindner SN, Marlière P, Erb TJ, Bar-Even A, He H. Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli. Nat Commun 2023; 14:8490. [PMID: 38123535 PMCID: PMC10733421 DOI: 10.1038/s41467-023-44247-2] [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: 11/12/2022] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
One-carbon (C1) substrates, such as methanol or formate, are attractive feedstocks for circular bioeconomy. These substrates are typically converted into formaldehyde, serving as the entry point into metabolism. Here, we design an erythrulose monophosphate (EuMP) cycle for formaldehyde assimilation, leveraging a promiscuous dihydroxyacetone phosphate dependent aldolase as key enzyme. In silico modeling reveals that the cycle is highly energy-efficient, holding the potential for high bioproduct yields. Dissecting the EuMP into four modules, we use a stepwise strategy to demonstrate in vivo feasibility of the modules in E. coli sensor strains with sarcosine as formaldehyde source. From adaptive laboratory evolution for module integration, we identify key mutations enabling the accommodation of the EuMP reactions with endogenous metabolism. Overall, our study demonstrates the proof-of-concept for a highly efficient, new-to-nature formaldehyde assimilation pathway, opening a way for the development of a methylotrophic platform for a C1-fueled bioeconomy in the future.
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Affiliation(s)
- Tong Wu
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117, Berlin, Germany
| | - Paul A Gómez-Coronado
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Armin Kubis
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117, Berlin, Germany
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 81 rue Réaumur, 75002, Paris, France
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Hai He
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
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6
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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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7
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Black WB, Perea S, Li H. Design, construction, and application of noncanonical redox cofactor infrastructures. Curr Opin Biotechnol 2023; 84:103019. [PMID: 37939631 DOI: 10.1016/j.copbio.2023.103019] [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: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Controlling the flow of carbon and reducing power in biological systems is a central theme in metabolic engineering. Often, trade-offs in pushing carbon flux through targeted pathways while operating in conditions agreeable to the host are required due to the central pools of the shared native redox cofactors NAD(P)/H. Noncanonical redox cofactors (NRCs) have emerged as promising tools to transform how engineers develop biotransformation systems. These new-to-Nature redox cofactors have been demonstrated to function orthogonally to the endogenous cofactors, support pathway thermodynamics optimization, and achieve product scopes previously difficult to reach due to endogenous pathway crosstalk. This review will discuss the development of NRC infrastructures, comprising NRC pools, cofactor reduction sources, and cofactor oxidation sinks, the (pool-source-sink) infrastructure.
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Affiliation(s)
- William B Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America; Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-3900, United States of America.
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8
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Kurt E, Qin J, Williams A, Zhao Y, Xie D. Perspectives for Using CO 2 as a Feedstock for Biomanufacturing of Fuels and Chemicals. Bioengineering (Basel) 2023; 10:1357. [PMID: 38135948 PMCID: PMC10740661 DOI: 10.3390/bioengineering10121357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.
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Affiliation(s)
- Elif Kurt
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Alexandria Williams
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
| | - Youbo Zhao
- Physical Sciences Inc., 20 New England Business Ctr., Andover, MA 01810, USA;
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA 01854, USA; (E.K.); (J.Q.); (A.W.)
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9
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Sarwar A, Lee EY. Methanol-based biomanufacturing of fuels and chemicals using native and synthetic methylotrophs. Synth Syst Biotechnol 2023; 8:396-415. [PMID: 37384124 PMCID: PMC10293595 DOI: 10.1016/j.synbio.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/03/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023] Open
Abstract
Methanol has recently gained significant attention as a potential carbon substrate for the production of fuels and chemicals, owing to its high degree of reduction, abundance, and low price. Native methylotrophic yeasts and bacteria have been investigated for the production of fuels and chemicals. Alternatively, synthetic methylotrophic strains are also being developed by reconstructing methanol utilization pathways in model microorganisms, such as Escherichia coli. Owing to the complex metabolic pathways, limited availability of genetic tools, and methanol/formaldehyde toxicity, the high-level production of target products for industrial applications are still under development to satisfy commercial feasibility. This article reviews the production of biofuels and chemicals by native and synthetic methylotrophic microorganisms. It also highlights the advantages and limitations of both types of methylotrophs and provides an overview of ways to improve their efficiency for the production of fuels and chemicals from methanol.
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10
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Wood JC, Gonzalez-Garcia RA, Daygon D, Talbo G, Plan MR, Marcellin E, Virdis B. Characterisation of acetogen formatotrophic potential using Eubacterium limosum. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12600-6. [PMID: 37272938 DOI: 10.1007/s00253-023-12600-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 06/06/2023]
Abstract
Formate is a promising energy carrier that could be used to transport renewable electricity. Some acetogenic bacteria, such as Eubacterium limosum, have the native ability to utilise formate as a sole substrate for growth, which has sparked interest in the biotechnology industry. However, formatotrophic metabolism in E. limosum is poorly understood, and a system-level characterisation in continuous cultures is yet to be reported. Here, we present the first steady-state dataset for E. limosum formatotrophic growth. At a defined dilution rate of 0.4 d-1, there was a high specific uptake rate of formate (280 ± 56 mmol/gDCW/d; gDCW = gramme dry cell weight); however, most carbon went to CO2 (150 ± 11 mmol/gDCW/d). Compared to methylotrophic growth, protein differential expression data and intracellular metabolomics revealed several key features of formate metabolism. Upregulation of phosphotransacetylase (Pta) appears to be a futile attempt of cells to produce acetate as the major product. Instead, a cellular energy limitation resulted in the accumulation of intracellular pyruvate and upregulation of pyruvate formate ligase (Pfl) to convert formate to pyruvate. Therefore, metabolism is controlled, at least partially, at the protein expression level, an unusual feature for an acetogen. We anticipate that formate could be an important one-carbon substrate for acetogens to produce chemicals rich in pyruvate, a metabolite generally in low abundance during syngas growth. KEY POINTS: First Eubacterium limosum steady-state formatotrophic growth omics dataset High formate specific uptake rate, however carbon dioxide was the major product Formate may be the cause of intracellular stress and biofilm formation.
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Affiliation(s)
- Jamin C Wood
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - R Axayacatl Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Dara Daygon
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Gert Talbo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Manuel R Plan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD, Brisbane, 4072, Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, Brisbane, 4072, Australia
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, QLD, Brisbane, 4072, Australia.
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11
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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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12
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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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13
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Bannister KR, Prather KL. Engineering polyester monomer diversity through novel pathway design. Curr Opin Biotechnol 2023; 79:102852. [PMID: 36481340 DOI: 10.1016/j.copbio.2022.102852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022]
Abstract
Polyesters composed of hydroxy acids (HAs) and diols serve many material niches and are invaluable to our daily lives. However, their traditional synthesis from petrochemicals creates many environmental concerns. Metabolically engineered microorganisms have been leveraged for the industrially competitive production of a few polyesters with properties that limit their application. Designing new metabolic pathways to polyester building blocks is essential to broadening material property diversity and improving carbon and energy usage of current bioproduction schemes. This review focuses on recently developed pathways to HAs and diols. Specifically, new pathways to 2,3- and ω-Hydroxy acids, as well as C3-C4 and medium-chain-length diols, are discussed. Pathways to the same compound are compared on the basis of criteria such as energy usage, number of pathway steps, and titer. Finally, suggestions for improvements and next steps for each pathway are also discussed.
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Affiliation(s)
- K'yal R Bannister
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kristala Lj Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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14
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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: 24] [Impact Index Per Article: 24.0] [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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15
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Scown CD. Prospects for carbon-negative biomanufacturing. Trends Biotechnol 2022; 40:1415-1424. [PMID: 36192249 DOI: 10.1016/j.tibtech.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 01/21/2023]
Abstract
Biomanufacturing has the potential to reduce demand for petrochemicals and mitigate climate change. Recent studies have also suggested that some of these products can be net carbon negative, effectively removing CO2 from the atmosphere and locking it up in products. This review explores the magnitude of carbon removal achievable through biomanufacturing and discusses the likely fate of carbon in a range of target molecules. Solvents, cleaning agents, or food and pharmaceutical additives will likely re-release their carbon as CO2 at the end of their functional lives, while carbon incorporated into non-compostable polymers can result in long-term sequestration. Future research can maximize its impact by focusing on reducing emissions, achieving performance advantages, and enabling a more circular carbon economy.
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Affiliation(s)
- Corinne D Scown
- Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Life-Cycle, Economics and Agronomy Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Energy and Biosciences Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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16
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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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17
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Methanol biotransformation toward high-level production of fatty acid derivatives by engineering the industrial yeast Pichia pastoris. Proc Natl Acad Sci U S A 2022; 119:e2201711119. [PMID: 35858340 PMCID: PMC9303929 DOI: 10.1073/pnas.2201711119] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Methanol-based biorefinery is a promising strategy to achieve carbon neutrality goals by linking CO2 capture and solar energy storage. As a typical methylotroph, Pichia pastoris shows great potential in methanol biotransformation. However, challenges still remain in engineering methanol metabolism for chemical overproduction. Here, we present the global rewiring of the central metabolism for efficient production of free fatty acids (FFAs; 23.4 g/L) from methanol, with an enhanced supply of precursors and cofactors, as well as decreased accumulation of formaldehyde. Finally, metabolic transforming of the fatty acid cell factory enabled overproduction of fatty alcohols (2.0 g/L) from methanol. This study demonstrated that global metabolic rewiring released the great potential of P. pastoris for methanol biotransformation toward chemical overproduction.
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18
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Gao J, Li Y, Yu W, Zhou YJ. Rescuing yeast from cell death enables overproduction of fatty acids from sole methanol. Nat Metab 2022; 4:932-943. [PMID: 35817856 DOI: 10.1038/s42255-022-00601-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
Abstract
Methanol is an ideal feedstock for biomanufacturing that can be beneficial for global carbon neutrality; however, the toxicity of methanol limits the efficiency of methanol metabolism toward biochemical production. We here show that engineering production of free fatty acids from sole methanol results in cell death with decreased cellular levels of phospholipids in the methylotrophic yeast Ogataea polymorpha, and cell growth is restored by adaptive laboratory evolution. Whole-genome sequencing of the adapted strains reveals that inactivation of LPL1 (encoding a putative lipase) and IZH3 (encoding a membrane protein related to zinc metabolism) preserve cell survival by restoring phospholipid metabolism. Engineering the pentose phosphate pathway and gluconeogenesis enables high-level production of free fatty acid (15.9 g l-1) from sole methanol. Preventing methanol-associated toxicity underscores the link between lipid metabolism and methanol tolerance, which should contribute to enhancing methanol-based biomanufacturing.
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Affiliation(s)
- Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Yunxia Li
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
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19
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Affiliation(s)
- Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Republic of Korea.
| | - Arslan Sarwar
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Republic of Korea
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20
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Peiro C, Vicente CM, Jallet D, Heux S. From a Hetero- to a Methylotrophic Lifestyle: Flash Back on the Engineering Strategies to Create Synthetic Methanol-User Strains. Front Bioeng Biotechnol 2022; 10:907861. [PMID: 35757790 PMCID: PMC9214030 DOI: 10.3389/fbioe.2022.907861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/16/2022] [Indexed: 12/31/2022] Open
Abstract
Engineering microorganisms to grow on alternative feedstocks is crucial not just because of the indisputable biotechnological applications but also to deepen our understanding of microbial metabolism. One-carbon (C1) substrate metabolism has been the focus of extensive research for the prominent role of C1 compounds in establishing a circular bioeconomy. Methanol in particular holds great promise as it can be produced directly from greenhouse gases methane and carbon dioxide using renewable resources. Synthetic methylotrophy, i.e. introducing a non-native methanol utilization pathway into a model host, has therefore been the focus of long-time efforts and is perhaps the pinnacle of metabolic engineering. It entails completely changing a microorganism's lifestyle, from breaking up multi-carbon nutrients for growth to building C-C bonds from a single-carbon molecule to obtain all metabolites necessary to biomass formation as well as energy. The frontiers of synthetic methylotrophy have been pushed further than ever before and in this review, we outline the advances that paved the way for the more recent accomplishments. These include optimizing the host's metabolism, "copy and pasting" naturally existing methylotrophic pathways, "mixing and matching" enzymes to build new pathways, and even creating novel enzymatic functions to obtain strains that are able to grow solely on methanol. Finally, new approaches are contemplated to further advance the field and succeed in obtaining a strain that efficiently grows on methanol and allows C1-based production of added-value compounds.
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Affiliation(s)
- Camille Peiro
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Denis Jallet
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Stephanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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21
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Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria. Nat Commun 2022; 13:3058. [PMID: 35650184 PMCID: PMC9160091 DOI: 10.1038/s41467-022-30571-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
Carbon-negative synthesis of biochemical products has the potential to mitigate global CO2 emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimize and implement r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into Escherichia coli generates designer strains for the selective production of butanoic acid (4.9 ± 0.1 gL−1), as well as hexanoic acid (3.06 ± 0.03 gL−1) and 1-hexanol (1.0 ± 0.1 gL−1) at the best performance reported to date in this bacterium. We also generate Clostridium autoethanogenum strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL−1 in a 1.5 L continuous fermentation. Our strategy enables optimization of r-BOX derived products for biomanufacturing and industrial biotechnology. An attractive route for carbon-negative synthesis of biochemical products is the reverse β-oxidation pathway coupled to the Wood-Ljungdahl pathway. Here the authors use a high-throughput in vitro prototyping workflow to screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity.
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22
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Zhang C, Ottenheim C, Weingarten M, Ji L. Microbial Utilization of Next-Generation Feedstocks for the Biomanufacturing of Value-Added Chemicals and Food Ingredients. Front Bioeng Biotechnol 2022; 10:874612. [PMID: 35480982 PMCID: PMC9035589 DOI: 10.3389/fbioe.2022.874612] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Global shift to sustainability has driven the exploration of alternative feedstocks beyond sugars for biomanufacturing. Recently, C1 (CO2, CO, methane, formate and methanol) and C2 (acetate and ethanol) substrates are drawing great attention due to their natural abundance and low production cost. The advances in metabolic engineering, synthetic biology and industrial process design have greatly enhanced the efficiency that microbes use these next-generation feedstocks. The metabolic pathways to use C1 and C2 feedstocks have been introduced or enhanced into industrial workhorses, such as Escherichia coli and yeasts, by genetic rewiring and laboratory evolution strategies. Furthermore, microbes are engineered to convert these low-cost feedstocks to various high-value products, ranging from food ingredients to chemicals. This review highlights the recent development in metabolic engineering, the challenges in strain engineering and bioprocess design, and the perspectives of microbial utilization of C1 and C2 feedstocks for the biomanufacturing of value-added products.
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Affiliation(s)
- Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Congqiang Zhang, ,
| | - Christoph Ottenheim
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Melanie Weingarten
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - LiangHui Ji
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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23
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Tarasava K, Lee SH, Chen J, Köpke M, Jewett MC, Gonzalez R. Reverse β-oxidation pathways for efficient chemical production. J Ind Microbiol Biotechnol 2022; 49:6537408. [PMID: 35218187 PMCID: PMC9118988 DOI: 10.1093/jimb/kuac003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022]
Abstract
Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.
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Affiliation(s)
- Katia Tarasava
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Seung Hwan Lee
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Jing Chen
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | | | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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24
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Zhuang X, Zhang Y, Xiao AF, Zhang A, Fang B. Applications of Synthetic Biotechnology on Carbon Neutrality Research: A Review on Electrically Driven Microbial and Enzyme Engineering. Front Bioeng Biotechnol 2022; 10:826008. [PMID: 35145960 PMCID: PMC8822124 DOI: 10.3389/fbioe.2022.826008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
With the advancement of science, technology, and productivity, the rapid development of industrial production, transportation, and the exploitation of fossil fuels has gradually led to the accumulation of greenhouse gases and deterioration of global warming. Carbon neutrality is a balance between absorption and emissions achieved by minimizing carbon dioxide (CO2) emissions from human social productive activity through a series of initiatives, including energy substitution and energy efficiency improvement. Then CO2 was offset through forest carbon sequestration and captured at last. Therefore, efficiently reducing CO2 emissions and enhancing CO2 capture are a matter of great urgency. Because many species have the natural CO2 capture properties, more and more scientists focus their attention on developing the biological carbon sequestration technique and further combine with synthetic biotechnology and electricity. In this article, the advances of the synthetic biotechnology method for the most promising organisms were reviewed, such as cyanobacteria, Escherichia coli, and yeast, in which the metabolic pathways were reconstructed to enhance the efficiency of CO2 capture and product synthesis. Furthermore, the electrically driven microbial and enzyme engineering processes are also summarized, in which the critical role and principle of electricity in the process of CO2 capture are canvassed. This review provides detailed summary and analysis of CO2 capture through synthetic biotechnology, which also pave the way for implementing electrically driven combined strategies.
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Affiliation(s)
- Xiaoyan Zhuang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - Yonghui Zhang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - An-Feng Xiao
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - Aihui Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- *Correspondence: Aihui Zhang, ; Baishan Fang,
| | - Baishan Fang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- *Correspondence: Aihui Zhang, ; Baishan Fang,
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25
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Zahn M, König G, Cuong Pham HV, Seroka B, Lazny R, Yang G, Ouerfelli O, Lotowski Z, Rohwerder T. Mechanistic details of the actinobacterial lyase-catalyzed degradation reaction of 2-hydroxyisobutyryl-CoA. J Biol Chem 2021; 298:101522. [PMID: 34952003 PMCID: PMC8760513 DOI: 10.1016/j.jbc.2021.101522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 11/28/2022] Open
Abstract
Actinobacterial 2-hydroxyacyl-CoA lyase reversibly catalyzes the thiamine diphosphate-dependent cleavage of 2-hydroxyisobutyryl-CoA to formyl-CoA and acetone. This enzyme has great potential for use in synthetic one-carbon assimilation pathways for sustainable production of chemicals, but lacks details of substrate binding and reaction mechanism for biochemical reengineering. We determined crystal structures of the tetrameric enzyme in the closed conformation with bound substrate, covalent postcleavage intermediate, and products, shedding light on active site architecture and substrate interactions. Together with molecular dynamics simulations of the covalent precleavage complex, the complete catalytic cycle is structurally portrayed, revealing a proton transfer from the substrate acyl Cβ hydroxyl to residue E493 that returns it subsequently to the postcleavage Cα-carbanion intermediate. Kinetic parameters obtained for mutants E493A, E493Q, and E493K confirm the catalytic role of E493 in the WT enzyme. However, the 10- and 50-fold reduction in lyase activity in the E493A and E493Q mutants, respectively, compared with WT suggests that water molecules may contribute to proton transfer. The putative catalytic glutamate is located on a short α-helix close to the active site. This structural feature appears to be conserved in related lyases, such as human 2-hydroxyacyl-CoA lyase 2. Interestingly, a unique feature of the actinobacterial 2-hydroxyacyl-CoA lyase is a large C-terminal lid domain that, together with active site residues L127 and I492, restricts substrate size to ≤C5 2-hydroxyacyl residues. These details about the catalytic mechanism and determinants of substrate specificity pave the ground for designing tailored catalysts for acyloin condensations for one-carbon and short-chain substrates in biotechnological applications.
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Affiliation(s)
- Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom.
| | - Gerhard König
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Huy Viet Cuong Pham
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Barbara Seroka
- Faculty of Chemistry, University of Bialystok, K. Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Ryszard Lazny
- Faculty of Chemistry, University of Bialystok, K. Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Guangli Yang
- Organic Synthesis Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Zenon Lotowski
- Faculty of Chemistry, University of Bialystok, K. Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Thore Rohwerder
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
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Singer SW. A new path for one-carbon conversion. Nat Metab 2021; 3:1286-1287. [PMID: 34675441 DOI: 10.1038/s42255-021-00461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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