1
|
Liu Y, Huang S, Liu WQ, Ba F, Liu Y, Ling S, Li J. An In Vitro Hybrid Biocatalytic System Enabled by a Combination of Surface-Displayed, Purified, and Cell-Free Expressed Enzymes. ACS Synth Biol 2024; 13:1434-1441. [PMID: 38695987 DOI: 10.1021/acssynbio.4c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Enzymatic cascades have become a green and sustainable approach for the synthesis of valuable chemicals and pharmaceuticals. Using sequential enzymes to construct a multienzyme complex is an effective way to enhance the overall performance of biosynthetic routes. Here we report the design of an efficient in vitro hybrid biocatalytic system by assembling three enzymes that can convert styrene to (S)-1-phenyl-1,2-ethanediol. Specifically, we prepared the three enzymes in different ways, which were cell surface-displayed, purified, and cell-free expressed. To assemble them, we fused two orthogonal peptide-protein pairs (i.e., SpyTag/SpyCatcher and SnoopTag/SnoopCatcher) to the three enzymes, allowing their spatial organization by covalent assembly. By doing this, we constructed a multienzyme complex, which could enhance the production of (S)-1-phenyl-1,2-ethanediol by 3 times compared to the free-floating enzyme system without assembly. After optimization of the reaction system, the final product yield reached 234.6 μM with a substrate conversion rate of 46.9% (based on 0.5 mM styrene). Taken together, our strategy integrates the merits of advanced biochemical engineering techniques, including cellular surface display, spatial enzyme organization, and cell-free expression, which offers a new solution for chemical biosynthesis by enzymatic cascade biotransformation. We, therefore, anticipate that our approach will hold great potential for designing and constructing highly efficient systems to synthesize chemicals of agricultural, industrial, and pharmaceutical significance.
Collapse
Affiliation(s)
- Ying Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| |
Collapse
|
2
|
Wang Y, Sun R, Chen P, Wang F. Catalytic Synthesis of (S)-CHBE by Directional Coupling and Immobilization of Carbonyl Reductase and Glucose Dehydrogenase. Biomolecules 2024; 14:504. [PMID: 38672520 PMCID: PMC11048691 DOI: 10.3390/biom14040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Ethyl (S)-4-chloro-3-hydroxybutyrate ((S)-CHBE) is an important chiral intermediate in the synthesis of the cholesterol-lowering drug atorvastatin. Studying the use of SpyTag/SpyCatcher and SnoopTag/SnoopCatcher systems for the asymmetric reduction reaction and directed coupling coenzyme regeneration is practical for efficiently synthesizing (S)-CHBE. In this study, Spy and Snoop systems were used to construct a double-enzyme directed fixation system of carbonyl reductase (BsCR) and glucose dehydrogenase (BsGDH) for converting 4-chloroacetoacetate (COBE) to (S)-CHBE and achieving coenzyme regeneration. We discussed the enzymatic properties of the immobilized enzyme and the optimal catalytic conditions and reusability of the double-enzyme immobilization system. Compared to the free enzyme, the immobilized enzyme showed an improved optimal pH and temperature, maintaining higher relative activity across a wider range. The double-enzyme immobilization system was applied to catalyze the asymmetric reduction reaction of COBE, and the yield of (S)-CHBE reached 60.1% at 30 °C and pH 8.0. In addition, the double-enzyme immobilization system possessed better operational stability than the free enzyme, and maintained about 50% of the initial yield after six cycles. In summary, we show a simple and effective strategy for self-assembling SpyCatcher/SnoopCatcher and SpyTag/SnoopTag fusion proteins, which inspires building more cascade systems at the interface. It provides a new method for facilitating the rapid construction of in vitro immobilized multi-enzyme complexes from crude cell lysate.
Collapse
Affiliation(s)
- Yadong Wang
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Technology and Business University (BTBU), Beijing 100048, China; (Y.W.); (R.S.); (P.C.)
- School of Light Industry Science and Engineering, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Ruiqi Sun
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Technology and Business University (BTBU), Beijing 100048, China; (Y.W.); (R.S.); (P.C.)
- School of Light Industry Science and Engineering, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Peng Chen
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Technology and Business University (BTBU), Beijing 100048, China; (Y.W.); (R.S.); (P.C.)
- School of Light Industry Science and Engineering, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Fenghuan Wang
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Technology and Business University (BTBU), Beijing 100048, China; (Y.W.); (R.S.); (P.C.)
- School of Light Industry Science and Engineering, Beijing Technology and Business University (BTBU), Beijing 100048, China
| |
Collapse
|
3
|
Wang D, Fu X, Gao J, Zhao X, Bai W. Enhancing Poly-γ-glutamic Acid Production in Bacillus tequilensis BL01 through a Multienzyme Assembly Strategy and Expression Features of Glutamate Synthesis from Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8674-8683. [PMID: 38569079 DOI: 10.1021/acs.jafc.4c00685] [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: 04/05/2024]
Abstract
The enhancement of intracellular glutamate synthesis in glutamate-independent poly-γ-glutamic acid (γ-PGA)-producing strains is an essential strategy for improving γ-PGA production. Bacillus tequilensis BL01ΔpgdSΔggtΔsucAΔgudB:P43-ppc-pyk-gdhA for the efficient synthesis of γ-PGA was constructed through expression of glutamate synthesis features of Corynebacterium glutamicum, which increased the titer of γ-PGA by 2.18-fold (3.24 ± 0.22 g/L) compared to that of B. tequilensis BL01ΔpgdSΔggtΔsucAΔgudB (1.02 ± 0.11 g/L). To further improve the titer of γ-PGA and decrease the production of byproducts, three enzymes (Ppc, Pyk, and AceE) were assembled to a complex using SpyTag/Catcher pairs. The results showed that the γ-PGA titer of the assembled strain was 31.31% higher than that of the unassembled strain. To further reduce the production cost, 25.73 ± 0.69 g/L γ-PGA with a productivity of 0.48 g/L/h was obtained from cheap molasses. This work provides new metabolic engineering strategies to improve the production of γ-PGA in B. tequilensis BL01. Furthermore, the engineered strain has great potential for the industrial production of γ-PGA from molasses.
Collapse
Affiliation(s)
- Dexin Wang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Xiaoping Fu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Jiaqi Gao
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xingya Zhao
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Wenqin Bai
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| |
Collapse
|
4
|
Cao N, Guo R, Song P, Wang S, Liu G, Shi J, Wang L, Li M, Zuo X, Yang X, Fan C, Li M, Zhang Y. DNA Framework-Programmed Nanoscale Enzyme Assemblies. NANO LETTERS 2024; 24:4682-4690. [PMID: 38563501 DOI: 10.1021/acs.nanolett.4c01137] [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: 04/04/2024]
Abstract
Multienzyme assemblies mediated by multivalent interaction play a crucial role in cellular processes. However, the three-dimensional (3D) programming of an enzyme complex with defined enzyme activity in vitro remains unexplored, primarily owing to limitations in precisely controlling the spatial topological configuration. Herein, we introduce a nanoscale 3D enzyme assembly using a tetrahedral DNA framework (TDF), enabling the replication of spatial topological configuration and maintenance of an identical edge-to-edge distance akin to natural enzymes. Our results demonstrate that 3D nanoscale enzyme assemblies in both two-enzyme systems (glucose oxidase (GOx)/horseradish peroxidase (HRP)) and three-enzyme systems (amylglucosidase (AGO)/GOx/HRP) lead to enhanced cascade catalytic activity compared to the low-dimensional structure, resulting in ∼5.9- and ∼7.7-fold enhancements over homogeneous diffusional mixtures of free enzymes, respectively. Furthermore, we demonstrate the enzyme assemblies for the detection of the metabolism biomarkers creatinine and creatine, achieving a low limit of detection, high sensitivity, and broad detection range.
Collapse
Affiliation(s)
- Nan Cao
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruiyan Guo
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Ping Song
- State Key Laboratory of Oncogenes and Related Genes School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shaopeng Wang
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Gang Liu
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Min Li
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiurong Yang
- Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yueyue Zhang
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| |
Collapse
|
5
|
Li W, Yan X, Xia W, Zhao L, Pei J. Enzymatic properties and immobilization of a thermostable prenyltransferase from Aspergillus fumigatiaffinis for the production of prenylated naringenin. Bioorg Chem 2024; 145:107183. [PMID: 38340474 DOI: 10.1016/j.bioorg.2024.107183] [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: 12/04/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Prenyltransferases catalyze the synthesis of prenylated flavonoids, providing these with greater lipid solubility, biological activity, and availability. In this study, a thermostable prenyltransferase (AfPT) from Aspergillus fumigatiaffinis was cloned and expressed in Escherichia coli. By optimizing induction conditions, the expression level of AfPT reached 39.3 mU/mL, which was approximately 200 % of that before optimization. Additionally, we determined the enzymatic properties of AfPT. Subsequently, AfPT was immobilized on carboxymethyl cellulose magnetic nanoparticles (CMN) at a maximum load of 0.6 mg/mg. Optimal activity of CMN-AfPT was achieved at pH 8.0 and 55 °C. Thermostability assays showed that the residual activity of CMN-AfPT was greater than 50 % after incubation at 55 °C for 4 h. Km and Vmax of CMN-AfPT for naringenin were 0.082 mM and 5.57 nmol/min/mg, respectively. The Kcat/Km ratio of CMN-AfPT was higher than that of AfPT. Residual prenyltransferase activity of CMN-AfPT remained higher than 70 % even after 30 days of storage. Further, CMN-AfPT retained 68 % of its original activity after 10 cycles of reuse. Compared with free AfPT, CMN-AfPT showed higher catalytic efficiency, thermostability, metal ion tolerance, substrate affinity, storage stability, and reusability. Our study presents a thermostable prenyltransferase and its immobilized form for the production of prenylated flavonoids in vitro.
Collapse
Affiliation(s)
- Wenbo Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Xin Yan
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Wenli Xia
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Linguo Zhao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China.
| | - Jianjun Pei
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China.
| |
Collapse
|
6
|
Lu Q, Xu Y, Poppleton E, Zhou K, Sulc P, Stephanopoulos N, Ke Y. DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes. NANO LETTERS 2024; 24:1703-1709. [PMID: 38278134 PMCID: PMC10853956 DOI: 10.1021/acs.nanolett.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
The development of methods to synthesize artificial protein complexes with precisely controlled configurations will enable diverse biological and medical applications. Using DNA to link proteins provides programmability that can be difficult to achieve with other methods. Here, we use DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures, including a dimer, two types of trimer structures, and three types of tetramer assemblies, on a DNA origami platform by using a C3-symmetric building block composed of a protein trimer modified with DNA handles. Our approach expands the scope for the precise assembly of protein-based nanostructures and will enable the formulation of functional protein complexes with stoichiometric and geometric control.
Collapse
Affiliation(s)
- Qinyi Lu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yang Xu
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Erik Poppleton
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Kun Zhou
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Petr Sulc
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Stephanopoulos
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yonggang Ke
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
7
|
Sun X, Zhang T, Liu Y, Chen P, Qin H, Yang J, Sun Y. Self-assembled multienzyme complex facilitates synthesis of glucosylglycerol from maltodextrin and glycerol. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:266-272. [PMID: 37551437 DOI: 10.1002/jsfa.12907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Compound 2-O-α-d-glucosylglycerol (2αGG) naturally serves as a compatible osmolyte in acclimation to environmental stresses, such as high osmolarity, dryness, and extreme temperature. It presents several bioactivities and has been used in the food, agriculture, and cosmetics areas. RESULTS In the present study, we attempted to synthesize the 2αGG from low-cost maltodextrin and glycerol by constructing an in vitro multi-enzyme system. The system contained two core enzymes, namely glucan phosphorylases (GPs) and glucosylglycerol phosphorylases (GGPs), and two auxiliary enzymes, namely isoamylase and 4-α-glucanotransferase. Several new GGPs from different organisms were characterized with the function of converting α-G1P and glycerol to sole stereo-configuration product 2αGG. Then, polypeptide SpyTag-SpyCatcher was employed to construct a self-assembled multienzyme complex, and different combinations between enzymes and peptides were constructed and tested. The best self-assembled multienzyme complex exhibited three-fold higher productivity compared to that of free enzyme. This reaction system also produced 240 mm (61 g L-1 ) 2αGG under high substrate concentration, with a conversion yield of 86%. CONCLUSION The present study provides an efficient approach for producing 2αGG. It also demonstrates that the SpyTag-SpyCatcher system could be applied to construct other multienzyme complexes for increased productivity and product titer. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Xinming Sun
- Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tong Zhang
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Medicine, Shandong University of Technology, Zibo, China
| | - Yinlu Liu
- Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Peng Chen
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Huimin Qin
- Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, China
| | - Jiangang Yang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yuanxia Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Yang L, Choi CHJ, Wang J, Xia J, Zhang L, Ngai T, Zi Y, Huang Z. Celebrating 60 Years of The Chinese University of Hong Kong: Research Highlights in Nanoscience and Nanotechnology. ACS NANO 2024; 18:4-13. [PMID: 38112319 DOI: 10.1021/acsnano.3c11732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Recent breakthroughs and advances in nanoscience and nanotechnology have profoundly impacted young-generation education, accelerated knowledge transfer to enhance the quality of life, and improved environmental and economic sustainability. The Chinese University of Hong Kong (CUHK), a globally recognized education and research institute, has played a crucial role in promoting major strategic research directions in nanoscience, including translational biomedicine and information and automation technology, as well as environment and sustainability. To celebrate the 60th Anniversary of CUHK, we present this Virtual Issue that showcases the cutting-edge research at CUHK published in ACS Nano.
Collapse
Affiliation(s)
- Lin Yang
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Chung Hang Jonathan Choi
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Jianfang Wang
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Jiang Xia
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Li Zhang
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - To Ngai
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Yunlong Zi
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| | - Zhifeng Huang
- The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, People's Republic of China
| |
Collapse
|
9
|
Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
Collapse
Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
| |
Collapse
|
10
|
Liu N, Dong W, Yang H, Li JH, Chiu TY. Application of artificial scaffold systems in microbial metabolic engineering. Front Bioeng Biotechnol 2023; 11:1328141. [PMID: 38188488 PMCID: PMC10771841 DOI: 10.3389/fbioe.2023.1328141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024] Open
Abstract
In nature, metabolic pathways are often organized into complex structures such as multienzyme complexes, enzyme molecular scaffolds, or reaction microcompartments. These structures help facilitate multi-step metabolic reactions. However, engineered metabolic pathways in microbial cell factories do not possess inherent metabolic regulatory mechanisms, which can result in metabolic imbalance. Taking inspiration from nature, scientists have successfully developed synthetic scaffolds to enhance the performance of engineered metabolic pathways in microbial cell factories. By recruiting enzymes, synthetic scaffolds facilitate the formation of multi-enzyme complexes, leading to the modulation of enzyme spatial distribution, increased enzyme activity, and a reduction in the loss of intermediate products and the toxicity associated with harmful intermediates within cells. In recent years, scaffolds based on proteins, nucleic acids, and various organelles have been developed and employed to facilitate multiple metabolic pathways. Despite varying degrees of success, synthetic scaffolds still encounter numerous challenges. The objective of this review is to provide a comprehensive introduction to these synthetic scaffolds and discuss their latest research advancements and challenges.
Collapse
Affiliation(s)
- Nana Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Wei Dong
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Huanming Yang
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Jing-Hua Li
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Tsan-Yu Chiu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| |
Collapse
|
11
|
Du B, Sun M, Hui W, Xie C, Xu X. Recent Advances on Key Enzymes of Microbial Origin in the Lycopene Biosynthesis Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12927-12942. [PMID: 37609695 DOI: 10.1021/acs.jafc.3c03942] [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: 08/24/2023]
Abstract
Lycopene is a common carotenoid found mainly in ripe red fruits and vegetables that is widely used in the food industry due to its characteristic color and health benefits. Microbial synthesis of lycopene is gradually replacing the traditional methods of plant extraction and chemical synthesis as a more economical and productive manufacturing strategy. The biosynthesis of lycopene is a typical multienzyme cascade reaction, and it is important to understand the characteristics of each key enzyme involved and how they are regulated. In this paper, the catalytic characteristics of the key enzymes involved in the lycopene biosynthesis pathway and related studies are first discussed in detail. Then, the strategies applied to the key enzymes of lycopene synthesis, including fusion proteins, enzyme screening, combinatorial engineering, CRISPR/Cas9-based gene editing, DNA assembly, and scaffolding technologies are purposefully illustrated and compared in terms of both traditional and emerging multienzyme regulatory strategies. Finally, future developments and regulatory options for multienzyme synthesis of lycopene and similar secondary metabolites are also discussed.
Collapse
Affiliation(s)
- Bangmian Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Mengjuan Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Wenyang Hui
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Chengjia Xie
- School of Chemical Engineering, Yangzhou Polytechnic Institute, Yangzhou 225127, Jiangsu Province, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| |
Collapse
|
12
|
Yang J, Zhang J, Yan P, Zhang Z, Gao W, Xu M, Xu X, Liu B, Chen Z. Asymmetric Assembly and Self-Adjuvanted Antigen Delivery Platform for Improved Antigen Uptake and Antitumor Effect. Bioconjug Chem 2023; 34:856-865. [PMID: 37083372 DOI: 10.1021/acs.bioconjchem.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The development of effective tumor vaccines is an important direction in the field of cancer prevention/immunotherapy. Efficient antigen delivery is essential for inducing effective antitumor responses for tumor vaccines. Lumazine synthase (BLS) from Brucella spp. is a decameric protein with delivery and adjuvant properties, but its application in tumor vaccines is limited. Here, we developed an antigen delivery platform by combining a BLS asymmetric assembly and the Plug-and-Display system of SpyCatcher/SpyTag. An asymmetric assembly system consisting of BLSke and BLSdr was developed to equally assemble two molecules. Then, the MHC-I-restricted ovalbumin peptide (OVA(257-264) SIINFEKL) was conjugated with BLSke, and a cell-penetrating peptide (CPP) KALA was conjugated with BLSdr using the SpyCatcher/SpyTag system. KALA modification enhanced internalization of OVA peptides by DCs as well as promoted the maturation of DCs and the cross-presentation of SIINFEKL. Moreover, the immunotherapy of a KALA-modified vaccine suppressed tumor growth and enhanced CD8+ T cell responses in E.G7-OVA tumor-bearing mice. In the prophylactic model, KALA-modified vaccination showed the most significant protective effect and significantly prolonged the survival period of tumor challenged mice. In conclusion, the asymmetric assembly platform equally assembles two proteins or peptides, avoiding their spatial or functional interference. This asymmetric assembly and Plug-and-Display technology provide a universal platform for rapid development of personalized tumor vaccines.
Collapse
Affiliation(s)
- Jianghua Yang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province 110866, P. R. China
| | - Jinsong Zhang
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Key Laboratory of Tropical Diseases Control, School of public health, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Ping Yan
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province 110866, P. R. China
| | - Zhao Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province 110866, P. R. China
| | - Weiyu Gao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province 110866, P. R. China
| | - Man Xu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province 110866, P. R. China
| | - Xinling Xu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province 110866, P. R. China
| | - Baoshan Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province 110866, P. R. China
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province 110866, P. R. China
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Key Laboratory of Tropical Diseases Control, School of public health, Sun Yat-sen University, Guangzhou 510275, P. R. China
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Innovative Institute of Zoonoses, Inner Mongolia Minzu University, Tongliao 028000, P. R. China
| |
Collapse
|
13
|
Xu S, Gao S, An Y. Research progress of engineering microbial cell factories for pigment production. Biotechnol Adv 2023; 65:108150. [PMID: 37044266 DOI: 10.1016/j.biotechadv.2023.108150] [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: 10/24/2022] [Revised: 03/14/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
Pigments are widely used in people's daily life, such as food additives, cosmetics, pharmaceuticals, textiles, etc. In recent years, the natural pigments produced by microorganisms have attracted increased attention because these processes cannot be affected by seasons like the plant extraction methods, and can also avoid the environmental pollution problems caused by chemical synthesis. Synthetic biology and metabolic engineering have been used to construct and optimize metabolic pathways for production of natural pigments in cellular factories. Building microbial cell factories for synthesis of natural pigments has many advantages, including well-defined genetic background of the strains, high-density and rapid culture of cells, etc. Until now, the technical means about engineering microbial cell factories for pigment production and metabolic regulation processes have not been systematically analyzed and summarized. Therefore, the studies about construction, modification and regulation of synthetic pathways for microbial synthesis of pigments in recent years have been reviewed, aiming to provide an up-to-date summary of engineering strategies for microbial synthesis of natural pigments including carotenoids, melanins, riboflavins, azomycetes and quinones. This review should provide new ideas for further improving microbial production of natural pigments in the future.
Collapse
Affiliation(s)
- Shumin Xu
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China; College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China; College of Food Science, Shenyang Agricultural University, Shenyang, China; Shenyang Key Laboratory of Microbial Resources Mining and Molecular Breeding, Shenyang, China; Liaoning Provincial Key Laboratory of Agricultural Biotechnology, Shenyang, China.
| |
Collapse
|
14
|
Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
Collapse
Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| |
Collapse
|
15
|
Huang S, Ba F, Liu WQ, Li J. Stapled NRPS enhances the production of valinomycin in Escherichia coli. Biotechnol Bioeng 2023; 120:793-802. [PMID: 36510694 DOI: 10.1002/bit.28303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
Nonribosomal peptides (NRPs) are a large family of secondary metabolites with notable bioactivities, which distribute widely in natural resources across microbes and plants. To obtain these molecules, heterologous production of NRPs in robust surrogate hosts like Escherichia coli represent a feasible approach. However, reconstitution of the full biosynthetic pathway in a host often leads to low productivity, which is at least in part due to the low efficiency of enzyme interaction in vivo except for the well-known reasons of metabolic burden (e.g., expression of large NRP synthetases-NRPSs with molecular weights of >100 kDa) and cellular toxicity on host cells. To enhance the catalytic efficiency of large NRPSs in vivo, here we propose to staple NRPS enzymes by using short peptide/protein pairs (e.g., SpyTag/SpyCatcher) for enhanced NRP production. We achieve this goal by introducing a stapled NRPS system for the biosynthesis of the antibiotic NRP valinomycin in E. coli. The results indicate that stapled valinomycin synthetase (Vlm1 and Vlm2) enables higher product accumulation than those two free enzymes (e.g., the maximum improvement is nearly fourfold). After further optimization by strain and bioprocess engineering, the final valinomycin titer maximally reaches about 2800 µg/L, which is 73 times higher than the initial titer of 38 µg/L. We expect that stapling NRPS enzymes will be a promising catalytic strategy for high-level biosynthesis of NRP natural products.
Collapse
Affiliation(s)
- Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| |
Collapse
|
16
|
Chen R, Wan L, Zhu Y, Liu Y, Zhang W, Mu W. Spatial organization of pathway enzymes via self-assembly to improve 2'-fucosyllactose biosynthesis in engineered Escherichia coli. Biotechnol Bioeng 2023; 120:524-535. [PMID: 36326175 DOI: 10.1002/bit.28279] [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: 04/24/2022] [Revised: 10/22/2022] [Accepted: 10/30/2022] [Indexed: 11/05/2022]
Abstract
As one of the most abundant components in human milk oligosaccharides, 2'-fucosyllactose (2'-FL) possesses versatile beneficial health effects. Although most studies focused on overexpressing or fine-tuning the expression of pathway enzymes and achieved a striking increase of 2'-FL production, directly facilitating the metabolic flux toward the key intermediate GDP-l-fucose seems to be ignored. Here, multienzyme complexes consisting of sequential pathway enzymes were constructed by using specific peptide interaction motifs in recombinant Escherichia coli to achieve a higher titer of 2'-FL. Specifically, we first fine-tuned the expression level of pathway enzymes and balanced the metabolic flux toward 2'-FL synthesis. Then, two key enzymes (GDP-mannose 4,6-dehydratase and GDP- l-fucose synthase) were self-assembled into enzyme complexes in vivo via a short peptide interaction pair RIAD-RIDD (RI anchoring disruptor-RI dimer D/D domains), resulting in noticeable improvement of 2'-FL production. Next, to further strengthen the metabolic flux toward 2'-FL, three pathway enzymes were further aggregated into multienzyme assemblies by using another orthogonal protein interaction motif (Spycatcher-SpyTag or PDZ-PDZlig). Intracellular multienzyme assemblies remarkably enlarged the flux toward 2'-FL biosynthesis and showed a 2.1-fold increase of 2'-FL production compared with a strain expressing free-floating and unassembled enzymes. The optimally engineered strain EZJ23 accumulated 4.8 g/L 2'-FL in shake flask fermentation and was capable of producing 25.1 g/L 2'-FL by fed-batch cultivation. This work provides novel approaches for further improvement and large-scale production of 2'-FL and demonstrates the effectiveness of spatial assembly of pathway enzymes to improve the production of valuable products in the engineered host strain.
Collapse
Affiliation(s)
- Roulin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Li Wan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yuanlin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| |
Collapse
|
17
|
Kang W, Ma X, Kakarla D, Zhang H, Fang Y, Chen B, Zhu K, Zheng D, Wu Z, Li B, Xue C. Organizing Enzymes on Self-Assembled Protein Cages for Cascade Reactions. Angew Chem Int Ed Engl 2022; 61:e202214001. [PMID: 36288455 DOI: 10.1002/anie.202214001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Indexed: 11/06/2022]
Abstract
Cells use self-assembled biomaterials such as lipid membranes or proteinaceous shells to coordinate thousands of reactions that simultaneously take place within crowded spaces. However, mimicking such spatial organization for synthetic applications in engineered systems remains a challenge, resulting in inferior catalytic efficiency. In this work, we show that protein cages as an ideal scaffold to organize enzymes to enhance cascade reactions both in vitro and in living cells. We demonstrate that not only enzyme-enzyme distance but also the improved Km value contribute to the enhanced reaction rate of cascade reactions. Three sequential enzymes for lycopene biosynthesis have been co-localized on the exterior of the engineered protein cages in Escherichia coli, leading to an 8.5-fold increase of lycopene production by streamlining metabolic flux towards its biosynthesis. This versatile system offers a powerful tool to achieve enzyme spatial organization for broad applications in biocatalysis.
Collapse
Affiliation(s)
- Wei Kang
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ningbo Institute of Dalian University of Technology, Ningbo, 315016, China
| | - Xiao Ma
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Deepika Kakarla
- Department of Mechanical Engineering, Kennesaw State University, GA 0060, Marietta, USA
| | - Huawei Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yunming Fang
- National Energy Research Centre for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Baizhu Chen
- School of Biomedical Engineering, SUN YAT-SEN University, Shenzhen, 518000, China
| | - Kongfu Zhu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Danni Zheng
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ningbo Institute of Dalian University of Technology, Ningbo, 315016, China
| | - Zhiyue Wu
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Bo Li
- Department of Mechanical Engineering, Kennesaw State University, GA 0060, Marietta, USA
| | - Chuang Xue
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ningbo Institute of Dalian University of Technology, Ningbo, 315016, China
| |
Collapse
|
18
|
Wan L, Chen R, Zhu Y, Zhang W, Mu W. Interaction between the Anchoring Domain of A-Kinase Anchoring Proteins and the Dimerization and Docking Domain of Protein Kinase A: A Potent Tool for Synthetic Biology. ACS Synth Biol 2022; 11:3154-3162. [PMID: 36197832 DOI: 10.1021/acssynbio.2c00443] [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] [Indexed: 01/24/2023]
Abstract
Nature is enriched with specific interactions between receptor proteins and their cognate ligands. These interacting pairs can be exploited and applied for the construction of well-ordered multicomponent assemblies with multivalency and multifunctionality. One of the research hotspots of this area is the formation of multienzyme complexes with stable and tunable architectures, which may bear the potential to facilitate cascade biocatalysis and/or strengthen metabolic fluxes. Here we focus on a special interacting pair, the anchoring domain (AD) derived from A-kinase anchoring protein and its interacting dimerization and docking domain (DDD) derived from cyclic AMP-dependent protein kinase, which has potential to be an effective and powerful synthetic biology tool for the construction of multienzyme assemblies. We review the origin and interaction mechanism of AD-DDD, followed by the application of this so-called dock-and-lock pair to form various bioconjugates with multivalency and multispecificity. Then several recent studies related to the construction of multienzyme complexes using AD-DDD, and more specifically, the RIAD-RIDD interacting pair, are presented. Finally, we also discuss the great biotechnology potential and perspectives of AD-DDD as a potent synthetic biology tool for post-translational modifications.
Collapse
Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Roulin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
| |
Collapse
|
19
|
Yang Z, Leero DD, Yin C, Yang L, Zhu L, Zhu Z, Jiang L. Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks. BIORESOURCE TECHNOLOGY 2022; 361:127656. [PMID: 35872277 DOI: 10.1016/j.biortech.2022.127656] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.
Collapse
Affiliation(s)
- Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Donald Delano Leero
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Chengtai Yin
- College of Overseas Education, Nanjing Tech University, Nanjing 211816, China
| | - Lei Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| |
Collapse
|
20
|
Metabolic pathway assembly using docking domains from type I cis-AT polyketide synthases. Nat Commun 2022; 13:5541. [PMID: 36130947 PMCID: PMC9492657 DOI: 10.1038/s41467-022-33272-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Engineered metabolic pathways in microbial cell factories often have no natural organization and have challenging flux imbalances, leading to low biocatalytic efficiency. Modular polyketide synthases (PKSs) are multienzyme complexes that synthesize polyketide products via an assembly line thiotemplate mechanism. Here, we develop a strategy named mimic PKS enzyme assembly line (mPKSeal) that assembles key cascade enzymes to enhance biocatalytic efficiency and increase target production by recruiting cascade enzymes tagged with docking domains from type I cis-AT PKS. We apply this strategy to the astaxanthin biosynthetic pathway in engineered Escherichia coli for multienzyme assembly to increase astaxanthin production by 2.4-fold. The docking pairs, from the same PKSs or those from different cis-AT PKSs evidently belonging to distinct classes, are effective enzyme assembly tools for increasing astaxanthin production. This study addresses the challenge of cascade catalytic efficiency and highlights the potential for engineering enzyme assembly. Assembly artificial pathway in design connecting media can increase biosynthetic efficiency, but the choice of connecting media is limited. Here, the authors develop a new protein assembly strategy using a pool of docking peptides from polyketide synthase and show its application in astaxanthin biosynthesis in E. coli.
Collapse
|
21
|
Chen Y, Ming D, Zhu L, Huang H, Jiang L. Tailoring the Tag/Catcher System by Integrating Covalent Bonds and Noncovalent Interactions for Highly Efficient Protein Self-Assembly. Biomacromolecules 2022; 23:3936-3947. [PMID: 35998650 DOI: 10.1021/acs.biomac.2c00765] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Covalent bonds and noncovalent interactions play crucial roles in enzyme self-assembly. Here, we designed a Tag/Catcher system named NGTag/NGCatcher in which the Catcher is a highly charged protein that can bind proteins with positively charged tails and rapidly form a stable isopeptide bond with NGTag. In this study, we present a multienzyme strategy based on covalent bonds and noncovalent interactions. In vitro, mCherry, YFP, and GFP can form protein-rich three-dimensional networks based on NGCatcher, NGTag, and RK (Arginine/Lysine) tails, respectively. Furthermore, this technology was applied to improve lycopene production in Escherichia coli. Three key enzymes were involved in lycopene production variants from Deinococcus wulumuqiensis R12 of NGCatcher_CrtE, NGTag_Idi, and RKIspARK, where the multienzyme complexes were clearly observed in vivo and in vitro, and the lycopene production in vivo was 17.8-fold higher than that in the control group. The NGTag/NGCatcher system will provide new opportunities for in vivo and in vitro multienzyme catalysis.
Collapse
Affiliation(s)
- Yao Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Dengming Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - He Huang
- College of Pharmaceutical Science, Nanjing Tech University, Nanjing 211816, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| |
Collapse
|
22
|
Ouyang Y, Zhang P, Willner I. Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures. Bioconjug Chem 2022; 34:51-69. [PMID: 35973134 PMCID: PMC9853509 DOI: 10.1021/acs.bioconjchem.2c00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.
Collapse
|
23
|
Pei X, Luo Z, Qiao L, Xiao Q, Zhang P, Wang A, Sheldon RA. Putting precision and elegance in enzyme immobilisation with bio-orthogonal chemistry. Chem Soc Rev 2022; 51:7281-7304. [PMID: 35920313 DOI: 10.1039/d1cs01004b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The covalent immobilisation of enzymes generally involves the use of highly reactive crosslinkers, such as glutaraldehyde, to couple enzyme molecules to each other or to carriers through, for example, the free amino groups of lysine residues, on the enzyme surface. Unfortunately, such methods suffer from a lack of precision. Random formation of covalent linkages with reactive functional groups in the enzyme leads to disruption of the three dimensional structure and accompanying activity losses. This review focuses on recent advances in the use of bio-orthogonal chemistry in conjunction with rec-DNA to affect highly precise immobilisation of enzymes. In this way, cost-effective combination of production, purification and immobilisation of an enzyme is achieved, in a single unit operation with a high degree of precision. Various bio-orthogonal techniques for putting this precision and elegance into enzyme immobilisation are elaborated. These include, for example, fusing (grafting) peptide or protein tags to the target enzyme that enable its immobilisation in cell lysate or incorporating non-standard amino acids that enable the application of bio-orthogonal chemistry.
Collapse
Affiliation(s)
- Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Zhiyuan Luo
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Li Qiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Qinjie Xiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Pengfei Zhang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, 2050, Johannesburg, South Africa. .,Department of Biotechnology, Section BOC, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
24
|
Li M, Zhou P, Chen M, Yu H, Ye L. Spatiotemporal Regulation of Astaxanthin Synthesis in S. cerevisiae. ACS Synth Biol 2022; 11:2636-2649. [PMID: 35914247 DOI: 10.1021/acssynbio.2c00044] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As a high-valued antioxidant, astaxanthin biosynthesis using microbial cell factories has attracted increasing attention. However, its lipophilic nature conflicts with the limited storage capacity for lipophilic substances of model microorganisms such as Saccharomyces cerevisiae. Expansion of lipid droplets by enhancing lipid synthesis provides more storage room while diverting the metabolic flux from the target pathway. Therefore, proper spatial regulation is required. In this study, a library of genes related to lipid metabolism were screened using the trifunctional CRISPR system, identifying opi3 and hrd1 as new engineering targets to promote astaxanthin synthesis by moderately rather than excessively upregulating lipid synthesis. The astaxanthin yield reached 9.79 mg/g DCW after lipid engineering and was further improved to 10.21 mg/g DCW by balancing the expression of β-carotene hydroxylase and ketolase. Finally, by combining spatial regulation through lipid droplet engineering and temporal regulation via temperature-responsive pathway expression, 446.4 mg/L astaxanthin was produced in fed-batch fermentation.
Collapse
Affiliation(s)
- Min Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Pingping Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.,College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Mingkai Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| |
Collapse
|
25
|
Jia M, Luo Z, Chen H, Ma B, Qiao L, Xiao Q, Zhang P, Wang A. Programmable Polyproteams of Tyrosine Ammonia Lyases as Cross-Linked Enzymes for Synthesizing p-Coumaric Acid. Biomolecules 2022; 12:biom12070997. [PMID: 35883553 PMCID: PMC9313006 DOI: 10.3390/biom12070997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 12/20/2022] Open
Abstract
Ideal immobilization with enhanced biocatalyst activity and thermostability enables natural enzymes to serve as a powerful tool to yield synthetically useful chemicals in industry. Such an enzymatic method strategy becomes easier and more convenient with the use of genetic and protein engineering. Here, we developed a covalent programmable polyproteam of tyrosine ammonia lyases (TAL-CLEs) by fusing SpyTag and SpyCatcher peptides into the N-terminal and C-terminal of the TAL, respectively. The resulting circular enzymes were clear after the spontaneous isopeptide bonds formed between the SpyTag and SpyCatcher. Furthermore, the catalytic performance of the TAL-CLEs was measured via a synthesis sample of p-Coumaric acid. Our TAL-CLEs showed excellent catalytic efficiency, with 98.31 ± 1.14% yield of the target product—which is 4.15 ± 0.08 times higher than that of traditional glutaraldehyde-mediated enzyme aggregates. They also showed over four times as much enzyme-activity as wild-type TAL does and demonstrated good reusability, and so may become a good candidate for industrial enzymes.
Collapse
Affiliation(s)
| | | | | | | | - Li Qiao
- Correspondence: (L.Q.); (A.W.)
| | | | | | | |
Collapse
|
26
|
Wang Y, Liu M, Wei Q, Wu W, He Y, Gao J, Zhou R, Jiang L, Qu J, Xia J. Phase-Separated Multienzyme Compartmentalization for Terpene Biosynthesis in a Prokaryote. Angew Chem Int Ed Engl 2022; 61:e202203909. [PMID: 35562330 DOI: 10.1002/anie.202203909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Indexed: 01/18/2023]
Abstract
Liquid-liquid phase separation (LLPS) forms biomolecular condensates or coacervates in cells. Metabolic enzymes can form phase-separated subcellular compartments that enrich enzymes, cofactors, and substrates. Herein, we report the construction of synthetic multienzyme condensates that catalyze the biosynthesis of a terpene, α-farnesene, in the prokaryote E. coli. RGGRGG derived from LAF-1 was used as the scaffold protein to form the condensates by LLPS. Multienzyme condensates were then formed by assembling two enzymes Idi and IspA through an RIAD/RIDD interaction. Multienzyme condensates constructed inside E. coli cells compartmentalized the cytosolic space into regions of high and low enzyme density and led to a significant enhancement of α-farnesene production. This work demonstrates LLPS-driven compartmentalization of the cytosolic space of prokaryotic cells, condensation of a biosynthetic pathway, and enhancement of the biosynthesis of α-farnesene.
Collapse
Affiliation(s)
- Yue Wang
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Min Liu
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qixin Wei
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wanjie Wu
- Departments of Electronic and Computer Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yanping He
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiayang Gao
- Center for Cell & Developmental Biology, School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Renjie Zhou
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Liwen Jiang
- Center for Cell & Developmental Biology, School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jianan Qu
- Departments of Electronic and Computer Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| |
Collapse
|
27
|
Wei Q, Wang Y, Liu Z, Liu M, Cao S, Jiang H, Xia J. Multienzyme Assembly on Caveolar Membranes In Cellulo. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qixin Wei
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhenjun Liu
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Min Liu
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sheng Cao
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| |
Collapse
|
28
|
Zhai H, Cui L, Xiong Z, Qi Q, Hou J. CRISPR-mediated protein-tagging signal amplification systems for efficient transcriptional activation and repression in Saccharomyces cerevisiae. Nucleic Acids Res 2022; 50:5988-6000. [PMID: 35641106 PMCID: PMC9178002 DOI: 10.1093/nar/gkac463] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/24/2022] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Saccharomyces cerevisiae is an important model eukaryotic microorganism and widely applied in fundamental research and the production of various chemicals. Its ability to efficiently and precisely control the expression of multiple genes is valuable for metabolic engineering. The clustered regularly interspaced short palindromic repeats (CRISPR)-mediated regulation enables complex gene expression programming; however, the regulation efficiency is often limited by the efficiency of pertinent regulators. Here, we developed CRISPR-mediated protein-tagging signal amplification system for simultaneous multiplexed gene activation and repression in S. cerevisiae. By introducing protein scaffolds (SPY and SunTag systems) to recruit multiple copies of regulators to different nuclease-deficient CRISPR proteins and design optimization, our system amplified gene regulation efficiency significantly. The gene activation and repression efficiencies reached as high as 34.9-fold and 95%, respectively, being 3.8- and 8.6-fold higher than those observed on the direct fusion of regulators with nuclease-deficient CRISPR proteins, respectively. We then applied the orthogonal bifunctional CRISPR-mediated transcriptional regulation system to regulate the expression of genes associated with 3-hydroxypropanoic acid production to deduce that CRISPR-associated regulator recruiting systems represent a robust method for simultaneously regulating multiple genes and rewiring metabolic pathways.
Collapse
Affiliation(s)
- Haotian Zhai
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P.R. China
| | - Li Cui
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P.R. China
| | - Zhen Xiong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P.R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P.R. China
| | - Jin Hou
- To whom correspondence should be addressed. Tel: +86 532 5863 2401;
| |
Collapse
|
29
|
Wang Y, Liu M, Wei Q, Wu W, He Y, Gao J, Zhou R, Jiang L, Qu J, Xia J. Phase‐Separated Multienzyme Compartmentalization for Terpene Biosynthesis in a Prokaryote. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yue Wang
- Chinese University of Hong Kong Shaw College: The Chinese University of Hong Kong Chemistry HONG KONG
| | - Min Liu
- The Chinese University of Hong Kong Chemistry HONG KONG
| | - Qixin Wei
- The Chinese University of Hong Kong Chemistry HONG KONG
| | - Wanjie Wu
- Hong Kong University of Science and Technology School of Engineering Engineering HONG KONG
| | - Yanping He
- The Chinese University of Hong Kong Department of Biomedical Engineering HONG KONG
| | - Jiayang Gao
- The Chinese University of Hong Kong School of Life Sciences HONG KONG
| | - Renjie Zhou
- The Chinese University of Hong Kong Department of Biomedical Engineering HONG KONG
| | - Liwen Jiang
- The Chinese University of Hong Kong School of Life Sciences HONG KONG
| | - Jianan Qu
- Hong Kong University of Science and Technology School of Engineering Engineering HONG KONG
| | - Jiang Xia
- The Chinese University of Hong Kong Department of Chemistry SC G59, Department of ChemistryThe Chinese University of Hong Kong 00000 Shatin HONG KONG
| |
Collapse
|
30
|
Sun Q, Heater BS, Li TL, Ye W, Guo Z, Chan MK. Cry3Aa*SpyCatcher Fusion Crystals Produced in Bacteria as Scaffolds for Multienzyme Coimmobilization. Bioconjug Chem 2022; 33:386-396. [PMID: 35100510 DOI: 10.1021/acs.bioconjchem.2c00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The production of Cry3Aa enzyme fusion crystals in Bacillus thuringiensis provides a direct method to immobilize individual enzymes and thereby improve their stability and recyclability. Nevertheless, many reactions require multiple enzymes to produce a desired product; thus a general strategy was developed to extend our Cry3Aa technology to multienzyme coimmobilization. Here, we report the direct production of particles comprising a modified Cry3Aa (Cry3Aa*) fused to SpyCatcher002 (Cry3Aa*SpyCat2) for coimmobilization of model enzymes MenF, MenD, and MenH associated with the biosynthesis of menaquinone. The resultant coimmobilized particles showed improved reaction rates compared to free enzymes presumably due to the higher local enzyme substrate concentrations and enhanced enzyme coupling made possible by colocalization. Furthermore, coimmobilization of these enzymes on Cry3Aa*SpyCat2 led to increased thermal stability and recyclability of the overall multienzyme system. These characteristics together with its overall simplicity of production highlight the benefits of Cry3Aa*SpyCat2 crystals as a platform for enzyme coimmobilization.
Collapse
Affiliation(s)
- Qian Sun
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Bradley S Heater
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Tin Lok Li
- Hong Kong Branch of Guangdong Southern Marine Science and Engineering Laboratory (Guangzhou), Shenzhen Research Institute and Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Weijian Ye
- Hong Kong Branch of Guangdong Southern Marine Science and Engineering Laboratory (Guangzhou), Shenzhen Research Institute and Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Zhihong Guo
- Hong Kong Branch of Guangdong Southern Marine Science and Engineering Laboratory (Guangzhou), Shenzhen Research Institute and Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Michael K Chan
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| |
Collapse
|
31
|
Lyu X, Lyu Y, Yu H, Chen W, Ye L, Yang R. Biotechnological advances for improving natural pigment production: a state-of-the-art review. BIORESOUR BIOPROCESS 2022; 9:8. [PMID: 38647847 PMCID: PMC10992905 DOI: 10.1186/s40643-022-00497-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
In current years, natural pigments are facing a fast-growing global market due to the increase of people's awareness of health and the discovery of novel pharmacological effects of various natural pigments, e.g., carotenoids, flavonoids, and curcuminoids. However, the traditional production approaches are source-dependent and generally subject to the low contents of target pigment compounds. In order to scale-up industrial production, many efforts have been devoted to increasing pigment production from natural producers, via development of both in vitro plant cell/tissue culture systems, as well as optimization of microbial cultivation approaches. Moreover, synthetic biology has opened the door for heterologous biosynthesis of pigments via design and re-construction of novel biological modules as well as biological systems in bio-platforms. In this review, the innovative methods and strategies for optimization and engineering of both native and heterologous producers of natural pigments are comprehensively summarized. Current progress in the production of several representative high-value natural pigments is also presented; and the remaining challenges and future perspectives are discussed.
Collapse
Affiliation(s)
- Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - WeiNing Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China.
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
| |
Collapse
|
32
|
Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
Collapse
Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| |
Collapse
|
33
|
Sun Q, Raeeszadeh-Sarmazdeh M, Tsai SL, Chen W. Strategies for Multienzyme Assemblies. Methods Mol Biol 2022; 2487:113-131. [PMID: 35687232 DOI: 10.1007/978-1-0716-2269-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to co-localize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.
Collapse
Affiliation(s)
- Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, Taiwan
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
| |
Collapse
|
34
|
Zhang P, Fischer A, Ouyang Y, Wang J, Sohn YS, Karmi O, Nechushtai R, Willner I. Biocatalytic cascades and intercommunicated biocatalytic cascades in microcapsule systems. Chem Sci 2022; 13:7437-7448. [PMID: 35872834 PMCID: PMC9241983 DOI: 10.1039/d2sc01542k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022] Open
Abstract
Dynamic dimerization of GOx-loaded microcapsules with β-gal//hemin/G-quadruplex-bridged T1/T2-loaded microcapsules guides the bi-directional intercommunication of the three catalysts cascade.
Collapse
Affiliation(s)
- Pu Zhang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Amit Fischer
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yu Ouyang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ola Karmi
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rachel Nechushtai
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
35
|
Wei Q, Xia J. Self-Assembled Multienzyme Nanostructures for Biocatalysis in Cellulo. Methods Mol Biol 2022; 2487:197-204. [PMID: 35687238 DOI: 10.1007/978-1-0716-2269-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Multienzyme complexes naturally exist in cells to catalyze cascade reactions in metabolic pathways. By clustering the enzymes in close proximity, these nanomachineries achieve effective conversion of metabolites. Bioengineers are working on the development of synthetic versions of multienzyme complexes in cells to synergize heterologous biosynthesis. Assembling enzymes on protein scaffolds through protein-protein interactions is a viable and facile way to form synthetic multienzyme complexes. Here, we describe the general methods to construct self-assembled multienzyme nanostructures in Escherichia coli for biosynthesis of valuable chemicals.
Collapse
Affiliation(s)
- Qixin Wei
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, SAR, China.
| |
Collapse
|
36
|
Hossain MS, Ji J, Lynch CJ, Guzman M, Nangia S, Mozhdehi D. Adaptive Recombinant Nanoworms from Genetically Encodable Star Amphiphiles. Biomacromolecules 2021; 23:863-876. [PMID: 34942072 PMCID: PMC8924867 DOI: 10.1021/acs.biomac.1c01314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recombinant nanoworms are promising candidates for materials and biomedical applications ranging from the templated synthesis of nanomaterials to multivalent display of bioactive peptides and targeted delivery of theranostic agents. However, molecular design principles to synthesize these assemblies (which are thermodynamically favorable only in a narrow region of the phase diagram) remain unclear. To advance the identification of design principles for the programmable assembly of proteins into well-defined nanoworms and to broaden their stability regimes, we were inspired by the ability of topologically engineered synthetic macromolecules to acess rare mesophases. To test this design principle in biomacromolecular assemblies, we used post-translational modifications (PTMs) to generate lipidated proteins with precise topological and compositional asymmetry. Using an integrated experimental and computational approach, we show that the material properties (thermoresponse and nanoscale assembly) of these hybrid amphiphiles are modulated by their amphiphilic architecture. Importantly, we demonstrate that the judicious choice of amphiphilic architecture can be used to program the assembly of proteins into adaptive nanoworms, which undergo a morphological transition (sphere-to-nanoworms) in response to temperature stimuli.
Collapse
Affiliation(s)
- Md Shahadat Hossain
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, 111 College Place, Syracuse, New York 13244, United States
| | - Jingjing Ji
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Christopher J Lynch
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, 111 College Place, Syracuse, New York 13244, United States
| | - Miguel Guzman
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, 111 College Place, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States.,BioInspired Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
| | - Davoud Mozhdehi
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, 111 College Place, Syracuse, New York 13244, United States.,BioInspired Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
| |
Collapse
|
37
|
Li D, Xiong Q, Liang L, Duan H. Multienzyme nanoassemblies: from rational design to biomedical applications. Biomater Sci 2021; 9:7323-7342. [PMID: 34647942 DOI: 10.1039/d1bm01106e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multienzyme nanoassemblies (MENAs) that combine the functions of several enzymes into one entity have attracted widespread research interest due to their improved enzymatic performance and great potential for multiple applications. Considerable progress has been made to design and fabricate MENAs in recent years. This review begins with an introduction of the up-to-date strategies in designing MENAs, mainly including substrate channeling, compartmentalization and control of enzyme stoichiometry. The desirable properties that endow MENAs with important applications are also discussed in detail. Then, the recent advances in utilizing MENAs in the biomedical field are reviewed, with a particular focus on biosensing, tumor therapy, antioxidant and drug delivery. Finally, the challenges and perspectives for development of versatile MENAs are summarized.
Collapse
Affiliation(s)
- Di Li
- State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. .,School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qirong Xiong
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
| | - Li Liang
- State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hongwei Duan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
| |
Collapse
|
38
|
Wan L, Zhu Y, Chen G, Luo G, Zhang W, Mu W. Efficient Production of 2'-Fucosyllactose from l-Fucose via Self-Assembling Multienzyme Complexes in Engineered Escherichia coli. ACS Synth Biol 2021; 10:2488-2498. [PMID: 34415729 DOI: 10.1021/acssynbio.1c00102] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
2'-Fucosyllactose (2'-FL) has been widely used as a nutritional additive in infant formula due to its multifarious nutraceutical and pharmaceutical functions in neonate health. As such, it is essential to develop an efficient and extensive microbial fermentation platform to cater to the needs of the 2'-FL market. In this study, a spatial synthetic biology strategy was employed to promote 2'-FL biosynthesis in recombinant Escherichia coli. First, the salvage pathway for 2'-FL production from l-fucose and lactose was constructed by introducing a bifunctional enzyme l-fucokinase/GDP-l-fucose pyrophosphorylase (Fkp) derived from Bacteroides fragilis and an α-1,2-fucosyltransferase (FutC) derived from Helicobacter pylori into engineered E. coli BL21(DE3). Next, the endogenous genes involved in the degradation and shunting of the substrate and key intermediate were inactivated to improve the availability of precursors for 2'-FL biosynthesis. Moreover, to further improve the yield and titer of 2'-FL, a short peptide pair (RIAD-RIDD) was used to form self-assembling multienzyme complexes in vivo. The spatial localization of peptides and stoichiometry of enzyme assemblies were subsequently optimized to further improve 2'-FL production. Finally, cofactor regeneration was also considered to alleviate the potential cofactor deficiency and redox flux imbalance in the biocatalysis process. Fed-batch fermentation of the final WLS20 strain accumulated 30.5 g/L extracellular 2'-FL with the yield and productivity of 0.661 mol/mol fucose and 0.48 g/L/h, respectively. This research has demonstrated that the application of spatial synthetic biology and metabolic engineering strategies can dramatically enlarge the titer and yield of 2'-FL biosynthesis in engineered E. coli.
Collapse
Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Geng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Guocong Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
39
|
Zhang X, Zhang S, Yang Z, Wang Z, Tian X, Zhou R. Self-cascade MoS 2 nanozymes for efficient intracellular antioxidation and hepatic fibrosis therapy. NANOSCALE 2021; 13:12613-12622. [PMID: 34264260 DOI: 10.1039/d1nr02366g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Cascade biocatalytic reactions involving multiple antioxidative enzymes are necessary in living cells to regulate cellular metabolism and redox homeostasis. Substantial efforts have been made to construct cascade reactions through engineered enzyme mimics to improve intracellular metabolic flux, especially under pathophysiological conditions. Here, we show that MoS2 nanozymes exhibit activities of four major cellular cascade antioxidant enzymes, including superoxide dismutase, catalase, peroxidase, and glutathione peroxidase. Meanwhile, MoS2 nanozymes attenuate electron transfer in cytochrome c/H2O2 to ameliorate the inherent antioxidant defense system under stress conditions. Thus, MoS2 nanozymes function as a self-cascade platform to inhibit intracellular reactive oxygen species (ROS) production by modulating mitochondrial function and scavenging abundant ROS through their intrinsic antioxidant capacity. Density functional theory calculations reveal the underlying mechanisms of the intracellular environment-dependent catalase-like activity of MoS2 nanozymes. Furthermore, we find that the MoS2 nanozymes play a cytoprotective role in cells and significantly improve the treatment outcomes in a hepatic fibrosis mouse model. These results demonstrate the ROS-scavenging capacity of a single-component MoS2 nanozyme-based cascade reaction system and reveal the in-depth mechanism, which may advance the development of nanozyme-based antioxidative agents.
Collapse
Affiliation(s)
- Xinyu Zhang
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China.
| | | | | | | | | | | |
Collapse
|
40
|
Keeble AH, Yadav VK, Ferla MP, Bauer CC, Chuntharpursat-Bon E, Huang J, Bon RS, Howarth M. DogCatcher allows loop-friendly protein-protein ligation. Cell Chem Biol 2021; 29:339-350.e10. [PMID: 34324879 PMCID: PMC8878318 DOI: 10.1016/j.chembiol.2021.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/09/2021] [Accepted: 07/02/2021] [Indexed: 12/14/2022]
Abstract
There are many efficient ways to connect proteins at termini. However, connecting at a loop is difficult because of lower flexibility and variable environment. Here, we have developed DogCatcher, a protein that forms a spontaneous isopeptide bond with DogTag peptide. DogTag/DogCatcher was generated initially by splitting a Streptococcus pneumoniae adhesin. We optimized DogTag/DogCatcher through rational design and evolution, increasing reaction rate by 250-fold and establishing millimolar solubility of DogCatcher. When fused to a protein terminus, DogTag/DogCatcher reacts slower than SpyTag003/SpyCatcher003. However, inserted in loops of a fluorescent protein or enzyme, DogTag reacts much faster than SpyTag003. Like many membrane proteins, the ion channel TRPC5 has no surface-exposed termini. DogTag in a TRPC5 extracellular loop allowed normal calcium flux and specific covalent labeling on cells in 1 min. DogTag/DogCatcher reacts under diverse conditions, at nanomolar concentrations, and to 98% conversion. Loop-friendly ligation should expand the toolbox for creating protein architectures. Spontaneous transamidation at internal sites harnessing a DogTag/DogCatcher pair DogCatcher is designed and bred for high solubility and rapid reaction Within protein loops DogTag can clamp on its partner faster than SpyTag003 Fast and faithful fluorescent labeling of an ion channel at the cell surface via DogTag
Collapse
Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Vikash K Yadav
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matteo P Ferla
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Claudia C Bauer
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Eulashini Chuntharpursat-Bon
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Jin Huang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Robin S Bon
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
41
|
Sequential co-immobilization of multienzyme nanodevices based on SpyCatcher and SpyTag for robust biocatalysis. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
42
|
Sajid M, Channakesavula CN, Stone SR, Kaur P. Synthetic Biology towards Improved Flavonoid Pharmacokinetics. Biomolecules 2021; 11:biom11050754. [PMID: 34069975 PMCID: PMC8157843 DOI: 10.3390/biom11050754] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
Flavonoids are a structurally diverse class of natural products that have been found to have a range of beneficial activities in humans. However, the clinical utilisation of these molecules has been limited due to their low solubility, chemical stability, bioavailability and extensive intestinal metabolism in vivo. Recently, the view has been formed that site-specific modification of flavonoids by methylation and/or glycosylation, processes that occur in plants endogenously, can be used to improve and adapt their biophysical and pharmacokinetic properties. The traditional source of flavonoids and their modified forms is from plants and is limited due to the low amounts present in biomass, intrinsic to the nature of secondary metabolite biosynthesis. Access to greater amounts of flavonoids, and understanding of the impact of modifications, requires a rethink in terms of production, more specifically towards the adoption of plant biosynthetic pathways into ex planta synthesis approaches. Advances in synthetic biology and metabolic engineering, aided by protein engineering and machine learning methods, offer attractive and exciting avenues for ex planta flavonoid synthesis. This review seeks to explore the applications of synthetic biology towards the ex planta biosynthesis of flavonoids, and how the natural plant methylation and glycosylation pathways can be harnessed to produce modified flavonoids with more favourable biophysical and pharmacokinetic properties for clinical use. It is envisaged that the development of viable alternative production systems for the synthesis of flavonoids and their methylated and glycosylated forms will help facilitate their greater clinical application.
Collapse
|
43
|
Cui X, Wang Z, Li Z, Zhang X, Li Z. Programming Integrative Multienzyme Systems and Ionic Strength For Recyclable Synthesis of Glutathione. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3887-3894. [PMID: 33764060 DOI: 10.1021/acs.jafc.1c00158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the enzymatic cascade catalysis, it is a big challenge to construct a stable and reusable catalyst with targeted enzymes. The artificial multienzyme reactor has attracted great attention due to its potential for facilitating the performance of enzyme catalysis. In this study, we set up a reliable system that could assemble polyphosphate kinase (PPK) with bifunctional glutathione synthetase (GshF) via SpyCatcher/SpyTag to form multienzyme systems (MESs). Furthermore, MESs could assemble into nanoaggregates by altering the ionic strength, and the larger nanoaggregates could be applied in robust and reusable synthesis of glutathione (GSH). To enhance MES levels in vivo, gene duplication and different coexpression modes were performed. Finally, the optimized production of GSH and oxidized glutathione (GSSG) reached 102.6 and 6.7 mM within 2 h. Compared with the first round, the total yield only decreased by 9.4% after five continuous rounds of biocatalysis.
Collapse
Affiliation(s)
- Xiangwei Cui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zeyuan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zonglin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
44
|
Abstract
Significant advances in enzyme discovery, protein and reaction engineering have transformed biocatalysis into a viable technology for the industrial scale manufacturing of chemicals. Multi-enzyme catalysis has emerged as a new frontier for the synthesis of complex chemicals. However, the in vitro operation of multiple enzymes simultaneously in one vessel poses challenges that require new strategies for increasing the operational performance of enzymatic cascade reactions. Chief among those strategies is enzyme co-immobilization. This review will explore how advances in synthetic biology and protein engineering have led to bioinspired co-localization strategies for the scaffolding and compartmentalization of enzymes. Emphasis will be placed on genetically encoded co-localization mechanisms as platforms for future autonomously self-organizing biocatalytic systems. Such genetically programmable systems could be produced by cell factories or emerging cell-free systems. Challenges and opportunities towards self-assembling, multifunctional biocatalytic materials will be discussed.
Collapse
|
45
|
Dubey NC, Tripathi BP. Nature Inspired Multienzyme Immobilization: Strategies and Concepts. ACS APPLIED BIO MATERIALS 2021; 4:1077-1114. [PMID: 35014469 DOI: 10.1021/acsabm.0c01293] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.
Collapse
Affiliation(s)
- Nidhi C Dubey
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science and Engineering, Indian institute of Technology Delhi, New Delhi 110016, India
| |
Collapse
|
46
|
Su D, Li H, Yan X, Lin Y, Lu G. Biosensors based on fluorescence carbon nanomaterials for detection of pesticides. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116126] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
47
|
|
48
|
Engineered biosynthetic pathways and biocatalytic cascades for sustainable synthesis. Curr Opin Chem Biol 2020; 58:146-154. [PMID: 33152607 DOI: 10.1016/j.cbpa.2020.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 10/23/2022]
Abstract
Nature exploits biosynthetic cascades to construct numerous molecules from a limited set of starting materials. A deeper understanding of biosynthesis and extraordinary developments in gene technology has allowed the manipulation of natural pathways and construction of artificial cascades for the preparation of a range of molecules, which would be challenging to access using traditional synthetic chemical approaches. Alongside these metabolic engineering strategies, there has been continued interest in developing in vivo and in vitro biocatalytic cascades. Advancements in both metabolic engineering and biocatalysis are complementary, and this article aims to highlight some of the most exciting developments in these two areas with a particular focus on exploring those that have the potential to advance both pathway engineering and more traditional biocatalytic cascade development.
Collapse
|
49
|
|
50
|
Li L, Liu Z, Jiang H, Mao X. Biotechnological production of lycopene by microorganisms. Appl Microbiol Biotechnol 2020; 104:10307-10324. [PMID: 33097966 DOI: 10.1007/s00253-020-10967-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 12/16/2022]
Abstract
Lycopene is a dark red carotenoid belonging to C40 terpenoids and is widely found in a variety of plants, especially ripe red fruits and vegetables. Lycopene has been shown to reduce the risk of prostate cancer, other cancers, and cardiovascular disease. It is one of the most widely used carotenoids in the healthcare product market. Currently, commercially available lycopene is mainly extracted from tomatoes. However, production of lycopene from plants is costly and environmentally unfriendly. To date, there have been many reports on the biosynthesis of lycopene by microorganisms, providing another route for lycopene production. This review discusses the lycopene biosynthetic pathway and natural and engineered lycopene-accumulating microorganisms, as well as their production of lycopene. The effects of different metabolic engineering strategies on lycopene accumulation are also considered. Furthermore, this work presents perspectives concerning the microbial production of lycopene, especially trends to construct microbial cell factories for lycopene production. KEY POINTS: • Recent achievements in the lycopene biosynthesis in microorganisms. • Review of lycopene biosynthetic metabolism engineering strategy. • Discuss the current challenges and prospects of using microorganisms to produce lycopene.
Collapse
Affiliation(s)
- Lei Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Zhen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Hong Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|