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Zhu Y, Zhou J, Gu X, Wang H, Han H, Ni Y. Engineering a newly identified alcohol dehydrogenase from Sphingobium Sp. for efficient utilization of nicotinamide cofactors biomimetics. BIORESOUR BIOPROCESS 2025; 12:41. [PMID: 40325297 PMCID: PMC12052742 DOI: 10.1186/s40643-025-00870-z] [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: 02/07/2025] [Accepted: 03/31/2025] [Indexed: 05/07/2025] Open
Abstract
Nicotinamide cofactor biomimetics (NCBs) serve as low-cost alternatives to the expensive NAD(P)+/NAD(P)H, holding significant potential for applications in oxidoreductases. In this study, an alcohol dehydrogenase (SpADH2) from Sphingobium sp. SYK-6 was identified for the utilization of synthetic NCBs. SpADH2 exhibited a catalytic activity of 11.55 U/g in oxidation of syringyl alcohol when utilizing para-3-carbamoyl-1-(4-carboxybenzyl)pyridin-1-ium (p-BANA+) as cofactor. Semi-rational engineering of SpADH2 led to identification of key variants (H43L, A290I, H43L/A290I) with enhanced catalytic efficiency and specificity using p-BANA+ as the cofactor. Compared with wild-type, variant H43L/A290I exhibited a 7-fold increase in activity and an astonishing 6750-fold improvement in cofactor specificity ratio. Enzymatic characterization reveals that the substrate spectrum of SpADH2 could change significantly when utilizing different totally synthetic NCBs (tsNCBs). Furthermore, interaction analysis demonstrates critical roles of residues 43 and 290 in anchoring and release of p-BANA+. This study identified a natural ADH capable of utilizing totally synthetic NCBs, which has never been reported. Importantly, our results provide valuable ADH candidates for potential synthetic biology and industrial developments, and offer valuable guidance for identification and engineering ADHs toward utilizing NCBs as cofactors with improved catalytic performance.
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Affiliation(s)
- Yichun Zhu
- Key laboratory of industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jieyu Zhou
- Key laboratory of industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Xiangyuan Gu
- Key laboratory of industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Huiru Wang
- Key laboratory of industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Hao Han
- Key laboratory of industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Ye Ni
- Key laboratory of industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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2
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Guo X, Wang X, Hu Y, Zhang L, Zhao ZK. Truncating the C terminus of formate dehydrogenase leads to improved preference to nicotinamide cytosine dinucleotide. Sci Rep 2024; 14:28701. [PMID: 39562703 PMCID: PMC11576888 DOI: 10.1038/s41598-024-79885-z] [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: 09/02/2024] [Accepted: 11/13/2024] [Indexed: 11/21/2024] Open
Abstract
Formate dehydrogenase (FDH) is widely applied in regeneration of redox cofactors. There are continuing interests to engineer FDH for improved catalytic activity and cofactor preference. In the crystal structure of FDH from Pseudomonas sp. 101 (pseFDH), the C terminus with 9 amino acid residues cannot be resolved. However, our earlier work showed mutations at C terminus led pseFDH variants to favor a non-natural cofactor nicotinamide cytosine dinucleotide (NCD). Here, we investigated the role of C-terminal residues on cofactor preference by truncating their corresponding C terminus of pseFDH variants. Sequence comparison analysis showed that C-terminal residues were barely conservative among different FDHs. pseFDH and mutants with their C termini truncated were constructed, and the resulted variants showed improved preference to NCD mainly because NAD-dependent activity dropped more substantially. Further structure analysis showed that these pseFDH variants had their cofactor binding domains reconstructed to favor molecular interactions with NCD. Our work indicated that C-terminal residues of pseFDH affected enzyme activity and cofactor preference, which provides a new approach for ameliorating the performance of redox enzymes.
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Affiliation(s)
- Xiaojia Guo
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xueying Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yinghan Hu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lingyun Zhang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zongbao K Zhao
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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3
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Aspacio D, Zhang Y, Cui Y, Luu E, King E, Black WB, Perea S, Zhu Q, Wu Y, Luo R, Siegel JB, Li H. Shifting redox reaction equilibria on demand using an orthogonal redox cofactor. Nat Chem Biol 2024; 20:1535-1546. [PMID: 39138383 DOI: 10.1038/s41589-024-01702-5] [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: 10/20/2023] [Accepted: 07/16/2024] [Indexed: 08/15/2024]
Abstract
Nature's two redox cofactors, nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), are held at different reduction potentials, driving catabolism and anabolism in opposite directions. In biomanufacturing, there is a need to flexibly control redox reaction direction decoupled from catabolism and anabolism. We established nicotinamide mononucleotide (NMN+) as a noncanonical cofactor orthogonal to NAD(P)+. Here we present the development of Nox Ortho, a reduced NMN+ (NMNH)-specific oxidase, that completes the toolkit to modulate NMNH:NMN+ ratio together with an NMN+-specific glucose dehydrogenase (GDH Ortho). The design principle discovered from Nox Ortho engineering and modeling is facilely translated onto six different enzymes to create NMN(H)-orthogonal biocatalysts with a consistent ~103-106-fold cofactor specificity switch from NAD(P)+ to NMN+. We assemble these enzymes to produce stereo-pure 2,3-butanediol in cell-free systems and in Escherichia coli, enabled by NMN(H)'s distinct redox ratio firmly set by its designated driving forces, decoupled from both NAD(H) and NADP(H).
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Affiliation(s)
- Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Yulai Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Emma Luu
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - William B Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Qiang Zhu
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Yongxian Wu
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Ray Luo
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Justin B Siegel
- Genome Center, University of California, Davis, Davis, CA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA.
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA.
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4
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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; 124:9081-9112. [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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5
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Bourgery C, Mendoza DJ, Garnier G, Mouterde LMM, Allais F. Immobilization of Adenosine Derivatives onto Cellulose Nanocrystals via Click Chemistry for Biocatalysis Applications. ACS APPLIED MATERIALS & INTERFACES 2024; 16:11315-11323. [PMID: 38394235 DOI: 10.1021/acsami.3c19025] [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: 02/25/2024]
Abstract
Adenosine triphosphate (ATP) is a central molecule of organisms and is involved in many biological processes. It is also widely used in biocatalytic processes, especially as a substrate and precursor of many cofactors─such as nicotinamide adenine dinucleotide phosphate (NADP(H)), coenzyme A (CoA), and S-adenosylmethionine (SAM). Despite its great scientific interest and pivotal role, its use in industrial processes is impeded by its prohibitory cost. To overcome this limitation, we developed a greener synthesis of adenosine derivatives and efficiently selectively grafted them onto organic nanoparticles. In this study, cellulose nanocrystals were used as a model combined with click chemistry via a copper-catalyzed azide/alkyne cycloaddition reaction (CuAAC). The grafted adenosine triphosphate derivative fully retains its biocatalytic capability, enabling heterobiocatalysis for modern biochemical processes.
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Affiliation(s)
- Célestin Bourgery
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle 51110, France
| | - David Joram Mendoza
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Gil Garnier
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle 51110, France
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Louis M M Mouterde
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle 51110, France
| | - Florent Allais
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle 51110, France
- Bioresource Processing Research Institute of Australia (BioPRIA), Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
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Xu H, Cheng Q, Qiu Y, Mao J, Ji Q, Zhu M, Zhang L, Wang Z, Li A, Xia Y. A Novel Strategy for Whole-Cell Biotransformation Enabling Simultaneous l-Phenyllactic Acid Production and Coenzyme Regeneration. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:20772-20781. [PMID: 37963219 DOI: 10.1021/acs.jafc.3c06387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
l-Phenyllactic acid (l-PLA) is a small molecular organic acid that exhibits a powerful capacity for inhibition against foodborne pathogens. In this work, we developed a new cost-effective and environmentally friendly process for the biosynthesis of l-PLA. This strategy designed a novel whole-cell biotransformation system employing two heterologous enzymes, namely, phenylalanine dehydrogenase (PheDH) and l-hydroxyisocaproate dehydrogenase (l-HicDH). The novelty of this strategy lies in the first-time utilization of these two enzymes, which not only enables cascade catalysis for the production of l-PLA but also facilitates the regeneration of the coenzymes (NAD+/NADH) using only two enzymes rather than introducing more heterologous enzymes to the system. Consequently, this strategy can effectively simplify the biosynthesis process of l-PLA and minimize production costs. The initial l-PLA yield using this process achieved 2.53 ± 0.07 g/L. Furthermore, through meticulous optimization of the parameters for inducible enzyme expression and l-PLA biosynthesis, the l-PLA yield was successfully increased to 4.68 ± 0.04 g/L with a yield rate of 64.54 ± 0.29%. Moreover, this novel strategy is versatile in the biosynthesis of other organic acids, which can be achieved by easily modulating the combinations of substrates and enzymes.
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Affiliation(s)
- Huidong Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qianqian Cheng
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yangyu Qiu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jingjing Mao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qinyi Ji
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mulan Zhu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Lili Zhang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Aitao Li
- School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yu Xia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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7
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Wang S, Jiang W, Jin X, Qi Q, Liang Q. Genetically encoded ATP and NAD(P)H biosensors: potential tools in metabolic engineering. Crit Rev Biotechnol 2023; 43:1211-1225. [PMID: 36130803 DOI: 10.1080/07388551.2022.2103394] [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: 12/08/2021] [Accepted: 05/08/2022] [Indexed: 11/03/2022]
Abstract
To date, many metabolic engineering tools and strategies have been developed, including tools for cofactor engineering, which is a common strategy for bioproduct synthesis. Cofactor engineering is used for the regulation of pyridine nucleotides, including NADH/NAD+ and NADPH/NADP+, and adenosine triphosphate/adenosine diphosphate (ATP/ADP), which is crucial for maintaining redox and energy balance. However, the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP cannot be monitored in real time using traditional methods. Recently, many biosensors for detecting, monitoring, and regulating the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP have been developed. Although cofactor biosensors have been mainly developed for use in mammalian cells, the potential application of cofactor biosensors in metabolic engineering in bacterial and yeast cells has received recent attention. Coupling cofactor biosensors with genetic circuits is a promising strategy in metabolic engineering for optimizing the production of biochemicals. In this review, we focus on the development of biosensors for NADH/NAD+, NADPH/NADP+, and ATP/ADP and the potential application of these biosensors in metabolic engineering. We also provide critical perspectives, identify current research challenges, and provide guidance for future research in this promising field.
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Affiliation(s)
- Sumeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xin Jin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Chen N, Du N, Shen R, He T, Xi J, Tan J, Bian G, Yang Y, Liu T, Tan W, Yu L, Yuan Q. Redox signaling-driven modulation of microbial biosynthesis and biocatalysis. Nat Commun 2023; 14:6800. [PMID: 37884498 PMCID: PMC10603113 DOI: 10.1038/s41467-023-42561-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Microbial communication can drive coordinated functions through sensing, analyzing and processing signal information, playing critical roles in biomanufacturing and life evolution. However, it is still a great challenge to develop effective methods to construct a microbial communication system with coordinated behaviors. Here, we report an electron transfer triggered redox communication network consisting of three building blocks including signal router, optical verifier and bio-actuator for microbial metabolism regulation and coordination. In the redox communication network, the Fe3+/Fe2+ redox signal can be dynamically and reversibly transduced, channeling electrons directly and specifically into bio-actuator cells through iron oxidation pathway. The redox communication network drives gene expression of electron transfer proteins and simultaneously facilitates the critical reducing power regeneration in the bio-actuator, thus enabling regulation of microbial metabolism. In this way, the redox communication system efficiently promotes the biomanufacturing yield and CO2 fixation rate of bio-actuator. Furthermore, the results demonstrate that this redox communication strategy is applicable both in co-culture and microbial consortia. The proposed electron transfer triggered redox communication strategy in this work could provide an approach for reducing power regeneration and metabolic optimization and could offer insights into improving biomanufacturing efficiency.
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Affiliation(s)
- Na Chen
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Na Du
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Ruichen Shen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Tianpei He
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jing Xi
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Guangkai Bian
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, 518055, Shenzhen, P. R. China
| | - Yanbing Yang
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Tiangang Liu
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Lilei Yu
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China.
| | - Quan Yuan
- Renmin Hospital of Wuhan University, College of Chemistry and Molecular Sciences, Institute of Molecular Medicine, School of Microelectronics, School of Pharmaceutical Sciences, Wuhan University, 430072, Wuhan, P. R. China.
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China.
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9
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Aspacio D, Zhang Y, Cui Y, King E, Black WB, Perea S, Luu E, Siegel JB, Li H. Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555398. [PMID: 37693387 PMCID: PMC10491207 DOI: 10.1101/2023.08.29.555398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Natural metabolism relies on chemical compartmentalization of two redox cofactors, NAD+ and NADP+, to orchestrate life-essential redox reaction directions. However, in whole cells the reliance on these canonical cofactors limits flexible control of redox reaction direction as these reactions are permanently tied to catabolism or anabolism. In cell-free systems, NADP+ is too expensive in large scale. We have previously reported the use of nicotinamide mononucleotide, (NMN+) as a low-cost, noncanonical redox cofactor capable of specific electron delivery to diverse chemistries. Here, we present Nox Ortho, an NMNH-specific water-forming oxidase, that completes the toolkit to modulate NMNH/NMN+ ratio. This work uncovers an enzyme design principle that succeeds in parallel engineering of six butanediol dehydrogenases as NMN(H)-orthogonal biocatalysts consistently with a 103 - 106 -fold cofactor specificity switch from NAD(P)+ to NMN+. We combine these to produce chiral-pure 2,3-butanediol (Bdo) isomers without interference from NAD(H) or NADP(H) in vitro and in E. coli cells. We establish that NMN(H) can be held at a distinct redox ratio on demand, decoupled from both NAD(H) and NADP(H) redox ratios in vitro and in vivo.
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Affiliation(s)
- Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Yulai Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - William B. Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Emma Luu
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Genome Center, University of California, Davis, Davis, California 95616, United States
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
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10
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Liu F, He L, Dong S, Xuan J, Cui Q, Feng Y. Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges. Molecules 2023; 28:5850. [PMID: 37570818 PMCID: PMC10421094 DOI: 10.3390/molecules28155850] [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: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Enzymes are essential catalysts for various chemical reactions in biological systems and often rely on metal ions or cofactors to stabilize their structure or perform functions. Improving enzyme performance has always been an important direction of protein engineering. In recent years, various artificial small molecules have been successfully used in enzyme engineering. The types of enzymatic reactions and metabolic pathways in cells can be expanded by the incorporation of these artificial small molecules either as cofactors or as building blocks of proteins and nucleic acids, which greatly promotes the development and application of biotechnology. In this review, we summarized research on artificial small molecules including biological metal cluster mimics, coenzyme analogs (mNADs), designer cofactors, non-natural nucleotides (XNAs), and non-natural amino acids (nnAAs), focusing on their design, synthesis, and applications as well as the current challenges in synthetic biology.
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Affiliation(s)
- Fenghua Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingling He
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Xuan
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Sun Y, Zhang T, Lu B, Li X, Jiang L. Application of cofactors in the regulation of microbial metabolism: A state of the art review. Front Microbiol 2023; 14:1145784. [PMID: 37113222 PMCID: PMC10126289 DOI: 10.3389/fmicb.2023.1145784] [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: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Cofactors are crucial chemicals that maintain cellular redox balance and drive the cell to do synthetic and catabolic reactions. They are involved in practically all enzymatic activities that occur in live cells. It has been a hot research topic in recent years to manage their concentrations and forms in microbial cells by using appropriate techniques to obtain more high-quality target products. In this review, we first summarize the physiological functions of common cofactors, and give a brief overview of common cofactors acetyl coenzyme A, NAD(P)H/NAD(P)+, and ATP/ADP; then we provide a detailed introduction of intracellular cofactor regeneration pathways, review the regulation of cofactor forms and concentrations by molecular biological means, and review the existing regulatory strategies of microbial cellular cofactors and their application progress, to maximize and rapidly direct the metabolic flux to target metabolites. Finally, we speculate on the future of cofactor engineering applications in cell factories. Graphical Abstract.
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Affiliation(s)
- Yang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ting Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Bingqian Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xiangfei Li
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, Wuhu, China
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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12
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Li N, Li L, Yu S, Zhou J. Dual-channel glycolysis balances cofactor supply for l-homoserine biosynthesis in Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2023; 369:128473. [PMID: 36509305 DOI: 10.1016/j.biortech.2022.128473] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
l-Homoserine is an important platform compound that is widely used to produce many valuable bio-based products, but production of l-homoserine in Corynebacterium glutamicum remains low. In this study, an efficient l-homoserine-producing strain was constructed. Native pentose phosphate pathway (PPP) was enhanced and heterologous Entner-Doudoroff (ED) pathway was carefully introduced into l-homoserine-producing strain, which increased the l-homoserine titer. Coexpression of NADH-dependent aspartate-4-semialdehyde dehydrogenase and aspartate dehydrogenase could increase the titer from 11.3 to 13.3 g/L. Next, NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase (NADP-GPD) was coexpressed with that of NAD+-dependent (NAD-GPD) to construct dual-channel glycolysis for balance of intracellular cofactors, which increased the l-homoserine titer by 48.6 % to 16.8 g/L. Finally, engineered strain Cg18-1 accumulated 63.5 g/L l-homoserine after 96 h in a 5 L bioreactor, the highest titer reported to date for C. glutamicum. This dual-channel glycolysis strategy provides a reference for automatic cofactor regulation to promote efficient biosynthesis of other target products.
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Affiliation(s)
- Ning Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lihong Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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13
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Vainstein S, Banta S. Engineering Candida boidinii formate dehydrogenase for activity with the non-canonical cofactor 3'-NADP(H). Protein Eng Des Sel 2023; 36:gzad009. [PMID: 37658768 DOI: 10.1093/protein/gzad009] [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: 07/07/2023] [Revised: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Oxidoreductases catalyze essential redox reactions, and many require a diffusible cofactor for electron transport, such as NAD(H). Non-canonical cofactor analogs have been explored as a means to create enzymatic reactions that operate orthogonally to existing metabolism. Here, we aimed to engineer the formate dehydrogenase from Candid boidinii (CbFDH) for activity with the non-canonical cofactor nicotinamide adenine dinucleotide 3'-phosphate (3'-NADP(H)). We used PyRosetta, the Cofactor Specificity Reversal Structural Analysis and Library Design (CSR-SALAD), and structure-guided saturation mutagenesis to identify mutations that enable CbFDH to use 3'-NADP+. Two single mutants, D195A and D195G, had the highest activities with 3'-NADP+, while the double mutant D195G/Y196S exhibited the highest cofactor selectivity reversal behavior. Steady state kinetic analyses were performed; the D195A mutant exhibited the highest KTS value with 3'-NADP+. This work compares the utility of computational approaches for cofactor specificity engineering while demonstrating the engineering of an important enzyme for novel non-canonical cofactor selectivity.
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Affiliation(s)
- Salomon Vainstein
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
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14
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Meng D, Liu M, Su H, Song H, Chen L, Li Q, Liu YN, Zhu Z, Liu W, Sheng X, You C, Zhang YHPJ. Coenzyme Engineering of Glucose-6-phosphate Dehydrogenase on a Nicotinamide-Based Biomimic and Its Application as a Glucose Biosensor. ACS Catal 2023. [DOI: 10.1021/acscatal.2c04707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Dongdong Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Meixia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Hao Su
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, People’s Republic of China
| | - Haiyan Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Lijie Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Bioengineering, Tianjin University of Science and Technology, Tianjin 300453, People’s Republic of China
| | - Qiangzi Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - Ya-nan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, People’s Republic of China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, People’s Republic of China
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
- in vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, People’s Republic of China
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15
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King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nat Commun 2022; 13:7282. [PMID: 36435948 PMCID: PMC9701214 DOI: 10.1038/s41467-022-35021-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN+) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN+-based reducing power. This is based on an orthogonal, NMN+-dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN+. With a throughput of >106 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme's global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme's access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Sarah Maxel
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
| | - Yulai Zhang
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
| | - Karissa C Kenney
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Youtian Cui
- Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Emma Luu
- Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Justin B Siegel
- Genome Center, University of California Davis, Davis, CA, 95616, USA
- Department of Chemistry, Molecular Medicine University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine University of California, Davis, Davis, CA, USA
| | - Gregory A Weiss
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
- Department Materials Science and Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Han Li
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA.
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16
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Metabolic engineering of Escherichia coli for improved D-pantothenic acid biosynthesis by enhancing NADPH availability. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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A phosphite-based screening platform for identification of enzymes favoring nonnatural cofactors. Sci Rep 2022; 12:12484. [PMID: 35864126 PMCID: PMC9304416 DOI: 10.1038/s41598-022-16599-0] [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: 01/23/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Enzymes with dedicated cofactor preference are essential for advanced biocatalysis and biomanufacturing, especially when employing nonnatural nicotinamide cofactors in redox reactions. However, directed evolution of an enzyme to switch its cofactor preference is often hindered by the lack of efficient and affordable method for screening as the cofactor per se or the substrate can be prohibitively expensive. Here, we developed a growth-based selection platform to identify nonnatural cofactor-dependent oxidoreductase mutants. The growth of bacteria depended on the nicotinamide cytosine dinucleotide (NCD) mediated conversion of non-metabolizable phosphite into phosphate. The strain BW14329 lacking the ability to oxidize phosphite was suitable as host, and NCD-dependent phosphite dehydrogenase (Pdh*) is essential to the selection platform. Previously confirmed NCD synthetase with NCD synthesis capacity and NCD-dependent malic enzyme were successfully identified by using the platform. The feasibility of this strategy was successfully demonstrated using derived NCD-active malic enzyme as well as for the directed evolution of NCD synthetase in Escherichia coli. A phosphite-based screening platform was built for identification of enzymes favoring nonnatural cofactor NCD. In the future, once Pdh variants favoring other biomimetic or nonnatural cofactors are available this selection platform may be readily redesigned to attain new enzyme variants with anticipated cofactor preference, providing opportunities to further expand the chemical space of redox cofactors in chemical biology and synthetic biology.
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18
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Liu H, Arbing MA, Bowie JU. Expanding the use of ethanol as a feedstock for cell-free synthetic biochemistry by implementing acetyl-CoA and ATP generating pathways. Sci Rep 2022; 12:7700. [PMID: 35546163 PMCID: PMC9095697 DOI: 10.1038/s41598-022-11653-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/20/2022] [Indexed: 12/01/2022] Open
Abstract
Ethanol is a widely available carbon compound that can be increasingly produced with a net negative carbon balance. Carbon-negative ethanol might therefore provide a feedstock for building a wider range of sustainable chemicals. Here we show how ethanol can be converted with a cell free system into acetyl-CoA, a central precursor for myriad biochemicals, and how we can use the energy stored in ethanol to generate ATP, another key molecule important for powering biochemical pathways. The ATP generator produces acetone as a value-added side product. Our ATP generator reached titers of 27 ± 6 mM ATP and 59 ± 15 mM acetone with maximum ATP synthesis rate of 2.8 ± 0.6 mM/h and acetone of 7.8 ± 0.8 mM/h. We illustrated how the ATP generating module can power cell-free biochemical pathways by converting mevalonate into isoprenol at a titer of 12.5 ± 0.8 mM and a maximum productivity of 1.0 ± 0.05 mM/h. These proof-of-principle demonstrations may ultimately find their way to the manufacture of diverse chemicals from ethanol and other simple carbon compounds.
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Affiliation(s)
- Hongjiang Liu
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles, Boyer Hall, 611 Charles E. Young Dr. E, Los Angeles, CA, 90095-1570, USA
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles, Boyer Hall, 611 Charles E. Young Dr. E, Los Angeles, CA, 90095-1570, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles, Boyer Hall, 611 Charles E. Young Dr. E, Los Angeles, CA, 90095-1570, USA.
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19
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Odoh CK, Guo X, Arnone JT, Wang X, Zhao ZK. The role of NAD and NAD precursors on longevity and lifespan modulation in the budding yeast, Saccharomyces cerevisiae. Biogerontology 2022; 23:169-199. [PMID: 35260986 PMCID: PMC8904166 DOI: 10.1007/s10522-022-09958-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 11/26/2022]
Abstract
Molecular causes of aging and longevity interventions have witnessed an upsurge in the last decade. The resurgent interests in the application of small molecules as potential geroprotectors and/or pharmacogenomics point to nicotinamide adenine dinucleotide (NAD) and its precursors, nicotinamide riboside, nicotinamide mononucleotide, nicotinamide, and nicotinic acid as potentially intriguing molecules. Upon supplementation, these compounds have shown to ameliorate aging related conditions and possibly prevent death in model organisms. Besides being a molecule essential in all living cells, our understanding of the mechanism of NAD metabolism and its regulation remain incomplete owing to its omnipresent nature. Here we discuss recent advances and techniques in the study of chronological lifespan (CLS) and replicative lifespan (RLS) in the model unicellular organism Saccharomyces cerevisiae. We then follow with the mechanism and biology of NAD precursors and their roles in aging and longevity. Finally, we review potential biotechnological applications through engineering of microbial lifespan, and laid perspective on the promising candidature of alternative redox compounds for extending lifespan.
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Affiliation(s)
- Chuks Kenneth Odoh
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaojia Guo
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
| | - James T Arnone
- Department of Biology, William Paterson University, Wayne, NJ, 07470, USA
| | - Xueying Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
| | - Zongbao K Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
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20
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Wang J, Guo X, Wan L, Liu Y, Xue H, Zhao ZK. Engineering formaldehyde dehydrogenase from Pseudomonas putida to favor nicotinamide cytosine dinucleotide. Chembiochem 2022; 23:e202100697. [PMID: 35146861 DOI: 10.1002/cbic.202100697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/09/2022] [Indexed: 11/05/2022]
Abstract
The enzyme formaldehyde dehydrogenase (FalDH) from Pseudomonas putida is of particular interest for biotechnological applications as it catalyses the oxidation of formaldehyde independent of glutathione. However, the consumption of a stoichiometric amount of nicotinamide adenine dinucleotide (NAD) can be challenging at the metabolic level as this may affect many other NAD-linked processes. A potential solution is to engineer FalDH to utilize non-natural cofactors. Here we devised FalDH variants to favor nicotinamide cytosine dinucleotide (NCD) by structure-guided modification of the binding pocket for the adenine moiety of NAD. Several mutants were obtained and the best one FalDH 9B2 had over 150-fold higher preference for NCD than NAD. Molecular docking analysis indicated that the cofactor binding pocket shrinked to better fit NCD, a smaller-sized cofactor. FalDH 9B2 together with other NCD-linked enzymes offer opportunities to assemble orthogonal pathways for biological conversion of C1 molecules.
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Affiliation(s)
- Junting Wang
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Xiaojia Guo
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Li Wan
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Yuxue Liu
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Haizhao Xue
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Zongbao Kent Zhao
- Dalian Institute of Chemical Physics, Division of Biotechnology, 457 Zhongshan Road, 116023, Dalian, CHINA
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21
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Zhou C, Feng J, Wang J, Hao N, Wang X, Chen K. Design of an in vitro multienzyme cascade system for the biosynthesis of nicotinamide mononucleotide. Catal Sci Technol 2022. [DOI: 10.1039/d1cy01798e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Design the adenosine phosphate hydrolysis (APH) pathway multienzyme cascade system for the biosynthesis of nicotinamide mononucleotide (NMN) in vitro.
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Affiliation(s)
- Cailian Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Jiao Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Jing Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Ning Hao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People's Republic of China
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22
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Wan L, Wang X, Hu Y, Li Q, Zhao ZK. Gram-scale biocatalytic preparation of the non-natural cofactor nicotinamide cytosine dinucleotide. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2021.153568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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