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Yang W, Sun H, Cui Z, Chen L, Ji Y, Lu F, Liu Y. Spatially sequential co-immobilization of phosphorylases in tiny environments and its application in the synthesis of glucosyl glycerol. Int J Biol Macromol 2024; 279:135139. [PMID: 39208907 DOI: 10.1016/j.ijbiomac.2024.135139] [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: 03/19/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
2-O-(α-d-glucopyranosyl)-sn-glycerol (2-αGG) has been applied in the food industry due to its numerous physiological benefits. The synthesis of 2-αGG can be achieved through a cascade catalytic reaction involving sucrose phosphorylase (SP) and 2-O-α-glucosylglycerol phosphorylase (GGP). However, the low substrate transfer rates between free enzymes have hindered the efficiency of 2-αGG synthesis. To address this issue, a novel technology was developed to prepare sequential multi-enzyme nanoflowers via chemical crosslinking and protein assembly, thus overcoming diffusion limitations. Specifically, spatially sequential co-immobilized enzymes, referred to as SP-GGP@Cap, were created through the targeted assembly of Bifidobacterium adolescentis SP and Marinobacter adhaerens GGP on Ca2+. This assembly was facilitated by the spontaneous protein reaction between SpyTag and SpyCatcher. Compared to free SP-GGP, SP-GGP@Cap demonstrated improved thermal and pH stability. Moreover, SP-GGP@Cap enhanced the biosynthesis of 2-αGG, achieving a relative concentration of 98 %. Additionally, it retained the ability to catalyze the substrate to yield 61 % relative concentration of 2-αGG even after ten cycles of recycling. This study presents a strategy for the spatially sequential co-immobilization of multiple enzymes in a confined environment and provides an exceptional biocatalyst for the potential industrial production of 2-αGG.
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Affiliation(s)
- Wenhua Yang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Hui Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zhihan Cui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Lei Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yuan Ji
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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2
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Mezgec K, Snoj J, Ulčakar L, Ljubetič A, Tušek Žnidarič M, Škarabot M, Jerala R. Coupling of Spectrin Repeat Modules for the Assembly of Nanorods and Presentation of Protein Domains. ACS NANO 2024. [PMID: 39392430 DOI: 10.1021/acsnano.4c07701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Modular protein engineering is a powerful approach for fabricating high-molecular-weight assemblies and biomaterials with nanoscale precision. Herein, we address the challenge of designing an extended nanoscale filamentous architecture inspired by the central rod domain of human dystrophin, which protects sarcolemma during muscle contraction and consists of spectrin repeats composed of three-helical bundles. A module of three tandem spectrin repeats was used as a rigid building block self-assembling via coiled-coil (CC) dimer-forming peptides. CC peptides were precisely integrated to maintain the spectrin α-helix continuity in an appropriate frame to form extended nanorods. An orthogonal set of customizable CC heterodimers was harnessed for modular rigid domain association, which could be additionally regulated by metal ions and chelators. We achieved a robust assembly of rigid rods several micrometers in length, determined by atomic force microscopy and negative stain transmission electron microscopy. Furthermore, these rigid rods can serve as a scaffold for the decoration of diverse proteins or biologically active peptides along their length with adjustable spacing up to tens of nanometers, as confirmed by the DNA-PAINT super-resolution microscopy. This demonstrates the potential of modular bottom-up protein engineering and tunable CCs for the fabrication of functionalized protein biomaterials.
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Affiliation(s)
- Klemen Mezgec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jaka Snoj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Liza Ulčakar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI-1000 Ljubljana, Slovenia
| | - Miha Škarabot
- Condensed Matter Department, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- CTGCT, Centre of Technology of Gene and Cell Therapy, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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3
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Johnson ER, Kennedy NW, Mills CE, Liang S, Chandrasekar S, Nichols TM, Rybnicky GA, Tullman-Ercek D. Signal sequences target enzymes and structural proteins to bacterial microcompartments and are critical for microcompartment formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.25.615066. [PMID: 39386669 PMCID: PMC11463388 DOI: 10.1101/2024.09.25.615066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Spatial organization of pathway enzymes has emerged as a promising tool to address several challenges in metabolic engineering, such as flux imbalances and off-target product formation. Bacterial microcompartments (MCPs) are a spatial organization strategy used natively by many bacteria to encapsulate metabolic pathways that produce toxic, volatile intermediates. Several recent studies have focused on engineering MCPs to encapsulate heterologous pathways of interest, but how this engineering affects MCP assembly and function is poorly understood. In this study, we investigated the role of signal sequences, short domains that target proteins to the MCP core, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterized two novel Pdu signal sequences on the structural proteins PduM and PduB, which constitutes the first report of metabolosome signal sequences on structural proteins rather than enzymes. We then explored the role of enzymatic and structural Pdu signal sequences on MCP assembly by deleting their encoding sequences from the genome alone and in combination. Deleting enzymatic signal sequences decreased MCP formation, but this defect could be recovered in some cases by overexpressing genes encoding the knocked-out signal sequence fused to a heterologous protein. By contrast, deleting structural signal sequences caused similar defects to knocking out the genes encoding the full length PduM and PduB proteins. Our results contribute to a growing understanding of how MCPs form and function in bacteria and provide strategies to mitigate assembly disruption when encapsulating heterologous pathways in MCPs.
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Affiliation(s)
- Elizabeth R. Johnson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Nolan W. Kennedy
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
| | - Carolyn. E. Mills
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Shiqi Liang
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
| | - Swetha Chandrasekar
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA
| | - Taylor M. Nichols
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Grant A Rybnicky
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
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4
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Wang BP, Yin X, Huang MY, Li TY, Long XF, Li Y, Niu FX. A Self-Assembling γPFD-SpyCatcher Hydrogel Scaffold for the Coimmobilization of SpyTag-Enzymes to Facilitate the Catalysis of Regulated Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19940-19947. [PMID: 39194331 DOI: 10.1021/acs.jafc.4c03403] [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: 08/29/2024]
Abstract
In this study, a γPFD-SpyCatcher hydrogel scaffold with the capacity for spontaneous assembly was established. With a maximum loading capacity of a 1:1 molar ratio with SpyTag-enzymes, the immobilized proteins can not only rapidly provide pure enzymes but also exhibit improved thermal and pH stability. The results of the transmission electron microscopic analysis and the traits they present indicated that SpyCatcher promotes the aggregation of γPFD and the formation of hydrogels. In the cell-free pyruvate synthesis system, the γPFD-SpyCatcher coimmobilized SpyTag-hexokinase (HK), SpyTag-phosphofructokinase (PFK) and SpyTag-pyruvate kinase (PK) were employed, and the production of pyruvate increased by 43, 78 and 47% respectively. In in vitro experiments, the oxidative deamination activity of glutamate dehydrogenase (GDH) coimmobilized with γPFD-SpyCatcher was 38% higher than that of purified enzymes. These findings indicate that the γPFD-SpyCatcher-based hydrogels play an important role in breaking the barrier of regulatory enzymes and will provide more strategies for the development of synthetic biology.
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Affiliation(s)
- Bei-Ping Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Xue Yin
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Ming-Yue Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Tian-Yan Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Xiu-Feng Long
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Ya Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Fu-Xing Niu
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
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5
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Wang R, Su Y, Yang W, Zhang H, Wang J, Gao W. Enhanced precision and efficiency in metabolic regulation: Compartmentalized metabolic engineering. BIORESOURCE TECHNOLOGY 2024; 402:130786. [PMID: 38703958 DOI: 10.1016/j.biortech.2024.130786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Metabolic engineering has witnessed remarkable advancements, enabling successful large-scale, cost-effective and efficient production of numerous compounds. However, the predominant expression of heterologous genes in the cytoplasm poses limitations, such as low substrate concentration, metabolic competition and product toxicity. To overcome these challenges, compartmentalized metabolic engineering allows the spatial separation of metabolic pathways for the efficient and precise production of target compounds. Compartmentalized metabolic engineering and its common strategies are comprehensively described in this study, where various membranous compartments and membraneless compartments have been used for compartmentalization and constructive progress has been made. Additionally, the challenges and future directions are discussed in depth. This review is dedicated to providing compartmentalized, precise and efficient methods for metabolic production, and provides valuable guidance for further development in the field of metabolic engineering.
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Affiliation(s)
- Rubing Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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Luo Z, Qiao L, Chen H, Mao Z, Wu S, Ma B, Xie T, Wang A, Pei X, Sheldon RA. Precision Engineering of the Co-immobilization of Enzymes for Cascade Biocatalysis. Angew Chem Int Ed Engl 2024; 63:e202403539. [PMID: 38556813 DOI: 10.1002/anie.202403539] [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: 02/20/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
The design and orderly layered co-immobilization of multiple enzymes on resin particles remain challenging. In this study, the SpyTag/SpyCatcher binding pair was fused to the N-terminus of an alcohol dehydrogenase (ADH) and an aldo-keto reductase (AKR), respectively. A non-canonical amino acid (ncAA), p-azido-L-phenylalanine (p-AzF), as the anchor for covalent bonding enzymes, was genetically inserted into preselected sites in the AKR and ADH. Employing the two bioorthogonal counterparts of SpyTag/SpyCatcher and azide-alkyne cycloaddition for the immobilization of AKR and ADH enabled sequential dual-enzyme coating on porous microspheres. The ordered dual-enzyme reactor was subsequently used to synthesize (S)-1-(2-chlorophenyl)ethanol asymmetrically from the corresponding prochiral ketone, enabling the in situ regeneration of NADPH. The reactor exhibited a high catalytic conversion of 74 % and good reproducibility, retaining 80 % of its initial activity after six cycles. The product had 99.9 % ee, which that was maintained in each cycle. Additionally, the double-layer immobilization method significantly increased the enzyme loading capacity, which was approximately 1.7 times greater than that of traditional single-layer immobilization. More importantly, it simultaneously enabled both the purification and immobilization of multiple enzymes on carriers, thus providing a convenient approach to facilitate cascade biocatalysis.
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Affiliation(s)
- Zhiyuan Luo
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Li Qiao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Haomin Chen
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Zhili Mao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Shujiao Wu
- School of Pharmacy, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Bianqin Ma
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Anming Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, 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
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7
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Hua W, Liang B, Zhou S, Zhang Q, Xu S, Chen K, Wang X. An integrated cofactor and co-substrate recycling pathway for the biosynthesis of 1,5-pentanediol. Microb Cell Fact 2024; 23:132. [PMID: 38711050 DOI: 10.1186/s12934-024-02408-y] [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: 12/22/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND 1,5-pentanediol (1,5-PDO) is a linear diol with an odd number of methylene groups, which is an important raw material for polyurethane production. In recent years, the chemical methods have been predominantly employed for synthesizing 1,5-PDO. However, with the increasing emphasis on environmentally friendly production, it has been a growing interest in the biosynthesis of 1,5-PDO. Due to the limited availability of only three reported feasible biosynthesis pathways, we developed a new biosynthetic pathway to form a cell factory in Escherichia coli to produce 1,5-PDO. RESULTS In this study, we reported an artificial pathway for the synthesis of 1,5-PDO from lysine with an integrated cofactor and co-substrate recycling and also evaluated its feasibility in E.coli. To get through the pathway, we first screened aminotransferases originated from different organisms to identify the enzyme that could successfully transfer two amines from cadaverine, and thus GabT from E. coli was characterized. It was then cascaded with lysine decarboxylase and alcohol dehydrogenase from E. coli to achieve the whole-cell production of 1,5-PDO from lysine. To improve the whole-cell activity for 1,5-PDO production, we employed a protein scaffold of EutM for GabT assembly and glutamate dehydrogenase was also validated for the recycling of NADPH and α-ketoglutaric acid (α-KG). After optimizing the cultivation and bioconversion conditions, the titer of 1,5-PDO reached 4.03 mM. CONCLUSION We established a novel pathway for 1,5-PDO production through two consecutive transamination reaction from cadaverine, and also integrated cofactor and co-substrate recycling system, which provided an alternative option for the biosynthesis of 1,5-PDO.
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Affiliation(s)
| | - Bo Liang
- Nanjing Tech University, Nanjing, China
| | | | | | - Shuang Xu
- Nanjing Tech University, Nanjing, China
| | | | - Xin Wang
- Nanjing Tech University, Nanjing, China.
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8
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Ledesma‐Fernandez A, Velasco‐Lozano S, Campos‐Muelas P, Madrid R, López‐Gallego F, Cortajarena AL. Engineering bio-brick protein scaffolds for organizing enzyme assemblies. Protein Sci 2024; 33:e4984. [PMID: 38607190 PMCID: PMC11010954 DOI: 10.1002/pro.4984] [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: 01/10/2024] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/13/2024]
Abstract
Enzyme scaffolding is an emerging approach for enhancing the catalytic efficiency of multi-enzymatic cascades by controlling their spatial organization and stoichiometry. This study introduces a novel family of engineered SCAffolding Bricks, named SCABs, utilizing the consensus tetratricopeptide repeat (CTPR) domain for organized multi-enzyme systems. Two SCAB systems are developed, one employing head-to-tail interactions with reversible covalent disulfide bonds, the other relying on non-covalent metal-driven assembly via engineered metal coordinating interfaces. Enzymes are directly fused to SCAB modules, triggering assembly in a non-reducing environment or by metal presence. A proof-of-concept with formate dehydrogenase (FDH) and L-alanine dehydrogenase (AlaDH) shows enhanced specific productivity by 3.6-fold compared to free enzymes, with the covalent stapling outperforming the metal-driven assembly. This enhancement likely stems from higher-order supramolecular assembly and improved NADH cofactor regeneration, resulting in more efficient cascades. This study underscores the potential of protein engineering to tailor scaffolds, leveraging supramolecular spatial-organizing tools, for more efficient enzymatic cascade reactions.
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Affiliation(s)
- Alba Ledesma‐Fernandez
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- University of the Basque Country (UPV/EHU)LeioaSpain
| | - Susana Velasco‐Lozano
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH‐CSIC)University of ZaragozaZaragozaSpain
- Aragonese Foundation for Research and Development (ARAID)ZaragozaSpain
| | | | - Ricardo Madrid
- BioAssays S.L.MadridSpain
- Complutense University of MadridMadridSpain
| | - Fernando López‐Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
| | - Aitziber L. Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
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9
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Lim S, Clark DS. Phase-separated biomolecular condensates for biocatalysis. Trends Biotechnol 2024; 42:496-509. [PMID: 37925283 DOI: 10.1016/j.tibtech.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/06/2023]
Abstract
Nature often uses dynamically assembling multienzymatic complexes called metabolons to achieve spatiotemporal control of complex metabolic reactions. Researchers are aiming to mimic this strategy of organizing enzymes to enhance the performance of artificial biocatalytic systems. Biomolecular condensates formed through liquid-liquid phase separation (LLPS) can serve as a powerful tool to drive controlled assembly of enzymes. Diverse enzymatic pathways have been reconstituted within catalytic condensates in vitro as well as synthetic membraneless organelles in living cells. Furthermore, in vivo condensates have been engineered to regulate metabolic pathways by selectively sequestering enzymes. Thus, harnessing LLPS for controlled organization of enzymes provides an opportunity to dynamically regulate biocatalytic processes.
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Affiliation(s)
- Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA..
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10
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Feng J, Han Y, Xu S, Liao Y, Wang Y, Xu S, Li H, Wang X, Chen K. Engineering RuBisCO-based shunt for improved cadaverine production in Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 398:130529. [PMID: 38437969 DOI: 10.1016/j.biortech.2024.130529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
The process of biological fermentation is often accompanied by the release of CO2, resulting in low yield and environmental pollution. Refixing CO2 to the product synthesis pathway is an attractive approach to improve the product yield. Cadaverine is an important diamine used for the synthesis of bio-based polyurethane or polyamide. Here, aiming to increase its final production, a RuBisCO-based shunt consisting of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and phosphoribulate kinase (PRK) was expressed in cadaverine-producing E. coli. This shunt was calculated capable of increasing the maximum theoretical cadaverine yield based on flux model analysis. When a functional RuBisCO-based shunt was established and optimized in E. coli, the cadaverine production and yield of the final engineered strain reached the highest level, which were 84.1 g/L and 0.37 g/g Glucose, respectively. Thus, the design of in situ CO2 fixation provides a green and efficient industrial production process.
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Affiliation(s)
- Jia Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China
| | - Ye Han
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China
| | - Shuang Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China
| | - Yang Liao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China
| | - Yongtao Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China
| | - Hui Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China.
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, Jiangsu, China.
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11
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Liu ZX, Gao YD, Yang LC. Biocatalytic Hydrogen-Borrowing Cascade in Organic Synthesis. JACS AU 2024; 4:877-892. [PMID: 38559715 PMCID: PMC10976568 DOI: 10.1021/jacsau.4c00026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Biocatalytic hydrogen borrowing represents an environmentally friendly and highly efficient synthetic method. This innovative approach involves converting various substrates into high-value-added products, typically via a one-pot, two/three-step sequence encompassing dehydrogenation (intermediate transformation) and hydrogenation processes employing the hydride shuffling between NAD(P)+ and NAD(P)H. Represented key transformations in hydrogen borrowing include stereoisomer conversion within alcohols, conversion between alcohols and amines, conversion of allylic alcohols to saturated carbonyl counterparts, and α,β-unsaturated aldehydes to saturated carboxylic acids, etc. The direct transformation methodology and environmentally benign characteristics of hydrogen borrowing have contributed to its advancements in fine chemical synthesis or drug developments. Over the past decades, the hydrogen borrowing strategy in biocatalysis has led to the creation of diverse catalytic systems, demonstrating substantial potential for straightforward synthesis as well as asymmetric transformations. This perspective serves as a detailed exposition of the recent advancements in biocatalytic reactions employing the hydrogen borrowing strategy. It provides insights into the potential of this approach for future development, shedding light on its promising prospects in the field of biocatalysis.
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Affiliation(s)
- Zong-Xiao Liu
- State Key Laboratory of Bioactive Substance
and Function of Natural Medicines, Institute
of Materia Medica, Chinese Academy of Medical Sciences & Peking
Union Medical College, 100050 Beijing, P. R. China
| | - Ya-Dong Gao
- State Key Laboratory of Bioactive Substance
and Function of Natural Medicines, Institute
of Materia Medica, Chinese Academy of Medical Sciences & Peking
Union Medical College, 100050 Beijing, P. R. China
| | - Li-Cheng Yang
- State Key Laboratory of Bioactive Substance
and Function of Natural Medicines, Institute
of Materia Medica, Chinese Academy of Medical Sciences & Peking
Union Medical College, 100050 Beijing, P. R. China
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12
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Li T, Chang P, Chen W, Shi Z, Xue C, Dykes GF, Huang F, Wang Q, Liu LN. Nanoengineering Carboxysome Shells for Protein Cages with Programmable Cargo Targeting. ACS NANO 2024; 18:7473-7484. [PMID: 38326220 PMCID: PMC10938918 DOI: 10.1021/acsnano.3c11559] [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: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Protein nanocages have emerged as promising candidates for enzyme immobilization and cargo delivery in biotechnology and nanotechnology. Carboxysomes are natural proteinaceous organelles in cyanobacteria and proteobacteria and have exhibited great potential in creating versatile nanocages for a wide range of applications given their intrinsic characteristics of self-assembly, cargo encapsulation, permeability, and modularity. However, how to program intact carboxysome shells with specific docking sites for tunable and efficient cargo loading is a key question in the rational design and engineering of carboxysome-based nanostructures. Here, we generate a range of synthetically engineered nanocages with site-directed cargo loading based on an α-carboxysome shell in conjunction with SpyTag/SpyCatcher and Coiled-coil protein coupling systems. The systematic analysis demonstrates that the cargo-docking sites and capacities of the carboxysome shell-based protein nanocages could be precisely modulated by selecting specific anchoring systems and shell protein domains. Our study provides insights into the encapsulation principles of the α-carboxysome and establishes a solid foundation for the bioengineering and manipulation of nanostructures capable of capturing cargos and molecules with exceptional efficiency and programmability, thereby enabling applications in catalysis, delivery, and medicine.
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Affiliation(s)
- Tianpei Li
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Ping Chang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Weixian Chen
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Zhaoyang Shi
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Chunling Xue
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Gregory F. Dykes
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Fang Huang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Qiang Wang
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Lu-Ning Liu
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
- MOE
Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science
Center for Deep Ocean Multispheres and Earth System & College
of Marine Life Sciences, Ocean University
of China, Qingdao 266003, China
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13
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Shinde YD, Chowdhury C. Potential utility of bacterial protein nanoreactor for sustainable in-situ biocatalysis in wide range of bioprocess conditions. Enzyme Microb Technol 2024; 173:110354. [PMID: 37988973 DOI: 10.1016/j.enzmictec.2023.110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/30/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles that natively encapsulates the enzymes, substrates, and cofactors within a protein shell. They optimize the reaction rates by enriching the substrate in the vicinity of enzymes to increase the yields of the product and mitigate the outward diffusion of the toxic or volatile intermediates. The shell protein subunits of MCP shell are selectively permeable and have specialized pores for the selective inward diffusion of substrates and products release. Given their attributes, MCPs have been recently explored as potential candidates as subcellular nano-bioreactor for the enhanced production of industrially important molecules by exercising pathway encapsulation. In the current study, MCPs have been shown to sustain enzyme activity for extended periods, emphasizing their durability against a range of physical challenges such as temperature, pH and organic solvents. The significance of an intact shell in conferring maximum protection is highlighted by analyzing the differences in enzyme activities inside the intact and broken shell. Moreover, a minimal synthetic shell was designed with recruitment of a heterologous enzyme cargo to demonstrate the improved durability of the enzyme. The encapsulated enzyme was shown to be more stable than its free counterpart under the aforementioned conditions. Bacterial MCP-mediated encapsulation can serve as a potential strategy to shield the enzymes used under extreme conditions by maintaining the internal microenvironment and enhancing their cycle life, thereby opening new means for stabilizing, and reutilizing the enzymes in several bioprocess industries.
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Affiliation(s)
- Yashodhara D Shinde
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH 411008, India
| | - Chiranjit Chowdhury
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, MH 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP 201002, India.
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14
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Ma W, Li F, Li L, Li B, Niu K, Liu Q, Han L, Han L, Fang X. Production of D -tagatose, bioethanol, and microbial protein from the dairy industry by-product whey powder using an integrated bioprocess. Biotechnol J 2024; 19:e2300415. [PMID: 38375553 DOI: 10.1002/biot.202300415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
We designed and constructed a green and sustainable bioprocess to efficiently coproduce D -tagatose, bioethanol, and microbial protein from whey powder. First, a one-pot biosynthesis process involving lactose hydrolysis and D -galactose redox reactions for D -tagatose production was established in vitro via a three-enzyme cascade. Second, a nicotinamide adenine dinucleotide phosphate-dependent galactitol dehydrogenase mutant, D36A/I37R, based on the nicotinamide adenine dinucleotide-dependent polyol dehydrogenase from Paracoccus denitrificans was created through rational design and screening. Moreover, an NADPH recycling module was created in the oxidoreductive pathway, and the tagatose yield increased by 3.35-fold compared with that achieved through the pathway without the cofactor cycle. The reaction process was accelerated using an enzyme assembly with a glycine-serine linker, and the tagatose production rate was 9.28-fold higher than the initial yield. Finally, Saccharomyces cerevisiae was introduced into the reaction solution, and 266.5 g of D -tagatose, 162.6 g of bioethanol, and 215.4 g of dry yeast (including 38% protein) were obtained from 1 kg of whey powder (including 810 g lactose). This study provides a promising sustainable process for functional food (D -tagatose) production. Moreover, this process fully utilized whey powder, demonstrating good atom economy.
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Affiliation(s)
- Wei Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Fengyi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Longyue Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Bin Li
- Shandong Henglu Biotechnology Co., Ltd., Jinan, Shandong, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qinghua Liu
- Shandong Henglu Biotechnology Co., Ltd., Jinan, Shandong, China
| | - Laichuang Han
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Lijuan Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
- Rongcheng Huihai Chuangda Biotechnology Co., Ltd., Weihai, Shandong, China
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15
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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.
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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.
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16
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Priyanka, Maiti S. Co-assembly-mediated biosupramolecular catalysis: thermodynamic insights into nucleobase specific (oligo)nucleotide attachment and cleavage. J Mater Chem B 2023; 11:10383-10394. [PMID: 37874292 DOI: 10.1039/d3tb01747h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Gaining control over the stability and cleavage of phosphoester and phosphodiester remains a matter of interest for their application in biotechnology to oligonucleotide-based therapeutics. Herein, we report an efficient unactivated phosphoester hydrolysis (stable mono/di/tri/cyclic nucleotide to nucleoside conversion) via a biosupramolecular system comprising of a non-covalent complex of enzyme, alkaline phosphatase (ALP), and Zn(II)-metallosurfactant. We also demonstrate the nucleobase selective activation or inhibition of ALP-mediated oligonucleotide digestion process using that complex. The higher binding affinity of Zn(II)-containing headgroup with phosphate-containing substrate enhanced the effective substrate concentration surrounding the enzyme, which, in turn, results in a drastic decrease in the Michaelis constant (KM), along with an increase in the turnover (kcat). The catalytic activation or inhibition of nucleobase-specific oligonucleotide digestion depends on the hydration, localization of the substrates, and viscosity of the resultant co-assembly upon substrate binding with the enzyme-metallosurfactant complex. Additionally, through isothermal titration calorimetry experiment, we demonstrate enthalpy-entropy change during both the supramolecular binding of (oligo)nucleotides and simultaneous activation/inhibition in catalytic cleavage. Overall, it showed the possible modularity of Zn(II)-mediated biosupramolecular interaction, describing intrinsic thermodynamic aspects in developing complex biocatalytic circuits with nucleobase-specific oligonucleotides inputs, which are relevant in designing nucleic acid-based cargo for drug delivery and bioimaging.
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Affiliation(s)
- Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
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17
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Kang Q, Fang H, Xiang M, Xiao K, Jiang P, You C, Lee SY, Zhang D. A synthetic cell-free 36-enzyme reaction system for vitamin B 12 production. Nat Commun 2023; 14:5177. [PMID: 37620358 PMCID: PMC10449867 DOI: 10.1038/s41467-023-40932-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Adenosylcobalamin (AdoCbl), a biologically active form of vitamin B12 (coenzyme B12), is one of the most complex metal-containing natural compounds and an essential vitamin for animals. However, AdoCbl can only be de novo synthesized by prokaryotes, and its industrial manufacturing to date was limited to bacterial fermentation. Here, we report a method for the synthesis of AdoCbl based on a cell-free reaction system performing a cascade of catalytic reactions from 5-aminolevulinic acid (5-ALA), an inexpensive compound. More than 30 biocatalytic reactions are integrated and optimized to achieve the complete cell-free synthesis of AdoCbl, after overcoming feedback inhibition, the complicated detection, instability of intermediate products, as well as imbalance and competition of cofactors. In the end, this cell-free system produces 417.41 μg/L and 5.78 mg/L of AdoCbl using 5-ALA and the purified intermediate product hydrogenobyrate as substrates, respectively. The strategies of coordinating synthetic modules of complex cell-free system describe here will be generally useful for developing cell-free platforms to produce complex natural compounds with long and complicated biosynthetic pathways.
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Affiliation(s)
- Qian Kang
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Huan Fang
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Mengjie Xiang
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
| | - Kaixing Xiao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Pingtao Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Chun You
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 four program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Dawei Zhang
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China.
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.
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18
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Ledesma-Fernandez A, Velasco-Lozano S, Santiago-Arcos J, López-Gallego F, Cortajarena AL. Engineered repeat proteins as scaffolds to assemble multi-enzyme systems for efficient cell-free biosynthesis. Nat Commun 2023; 14:2587. [PMID: 37142589 PMCID: PMC10160029 DOI: 10.1038/s41467-023-38304-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Multi-enzymatic cascades with enzymes arranged in close-proximity through a protein scaffold can trigger a substrate channeling effect, allowing for efficient cofactor reuse with industrial potential. However, precise nanometric organization of enzymes challenges the design of scaffolds. In this study, we create a nanometrically organized multi-enzymatic system exploiting engineered Tetrapeptide Repeat Affinity Proteins (TRAPs) as scaffolding for biocatalysis. We genetically fuse TRAP domains and program them to selectively and orthogonally recognize peptide-tags fused to enzymes, which upon binding form spatially organized metabolomes. In addition, the scaffold encodes binding sites to selectively and reversibly sequester reaction intermediates like cofactors via electrostatic interactions, increasing their local concentration and, consequently, the catalytic efficiency. This concept is demonstrated for the biosynthesis of amino acids and amines using up to three enzymes. Scaffolded multi-enzyme systems present up to 5-fold higher specific productivity than the non-scaffolded ones. In-depth analysis suggests that channeling of NADH cofactor between the assembled enzymes enhances the overall cascade throughput and the product yield. Moreover, we immobilize this biomolecular scaffold on solid supports, creating reusable heterogeneous multi-functional biocatalysts for consecutive operational batch cycles. Our results demonstrate the potential of TRAP-scaffolding systems as spatial-organizing tools to increase the efficiency of cell-free biosynthetic pathways.
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Affiliation(s)
- Alba Ledesma-Fernandez
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Susana Velasco-Lozano
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
- Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH-CSIC), University of Zaragoza, C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain
- Aragonese Foundation for Research and Development (ARAID), Zaragoza, Spain
| | - Javier Santiago-Arcos
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
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19
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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.
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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
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20
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Qiu Y, Lin Y, Zeng B, Qin P, Yi Z, Zhang G. Revealing the role of tunable amino acid residues in elastin-like polypeptides (ELPs)-mediated biomimetic silicification. Int J Biol Macromol 2023; 227:105-112. [PMID: 36539170 DOI: 10.1016/j.ijbiomac.2022.12.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Elastin-like polypeptides (ELPs) are attractive materials for the green preparation of silica nanoparticles via biomimetic silicification. However, the critical factors affecting the ELP-mediated silicification remain unclear. Herein, the role of tunable amino acid residues of ELPs in silicification was studied using three ELPs (ELPs[V9F-40], ELPs[KV8F-40], and ELPs[K5V4F-40]) and their fusion proteins (ELPs[V9F-40]-SpyCatcher, ELPs[KV8F-40]-SpyCatcher, and ELPs[K5V4F-40]-SpyCatcher) with different contents of lysine residues. Bioinformatics methods were employed for the first time to reveal the key physicochemical parameters correlated with silicification. The specific activity of ELPs was increased with the promotion of lysine content with a high correlation coefficient (R = 0.899). Furthermore, exogenous acidic protein SpyCatcher would hinder the interactions between the silica precursors and ELPs, leading to the significantly decrease in specific activity. The isoelectric point (pI) of ELPs presented the highest correlation to silicification with a coefficient of 0.963. The charges of the ELPs [K5V4F-40] at different pH were calculated based on the sequence or structure. Interestingly, the excellent correlation between charges based on structure and specific activity was obtained. Collectively, the novel methods developed here may pave a new way for rational design of ELPs or other peptides for efficient and green preparation of silica nanomaterials for biomedicine, biocatalysis, and biosensor.
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Affiliation(s)
- Yue Qiu
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou 215008, Jiangsu, China; Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China
| | - Yuanqing Lin
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen 361024, Fujian, China.
| | - Bo Zeng
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Peiliang Qin
- Department of Science and Technology Industry Division, Suzhou Polytechnical Institute of Agriculture, Suzhou, Jiangsu 215008, China
| | - Zhiwei Yi
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China; Technology Innovation Center for Exploitation of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China.
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21
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Construction of Bi-Enzyme Self-Assembly Clusters Based on SpyCatcher/SpyTag for the Efficient Biosynthesis of (R)-Ethyl 2-hydroxy-4-phenylbutyrate. Biomolecules 2023; 13:biom13010091. [PMID: 36671476 PMCID: PMC9855569 DOI: 10.3390/biom13010091] [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: 12/13/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Cascade reactions catalyzed by multi-enzyme systems are important in science and industry and can be used to synthesize drugs and nutrients. In this study, two types of macromolecules of bi-enzyme self-assembly clusters (BESCs) consisting of carbonyl reductase (CpCR) and glucose dehydrogenase (GDH) were examined. Stereoselective CpCR and GDH were successfully fused with SpyCatcher and SpyTag, respectively, to obtain four enzyme modules, namely: SpyCatcher-CpCR, SpyCatcher-GDH, SpyTag-CpCR, and SpyTag-GDH, which were covalently coupled in vitro to form two types of hydrogel-like BESCs: CpCR-SpyCatcher-SpyTag-GDH and GDH-SpyCatcher-SpyTag-CpCR. CpCR-SpyCatcher-SpyTag-GDH showed a better activity and efficiently converted ethyl 2-oxo-4-phenylbutyrate (OPBE) to ethyl(R)2-hydroxy-4-phenylbutanoate ((R)-HPBE), while regenerating NADPH. At 30 °C and pH 7, the conversion rate of OPBE with CpCR-SpyCatcher-SpyTag-GDH as a catalyst reached 99.9%, with the ee% of (R)-HPBE reaching above 99.9%. This conversion rate was 2.4 times higher than that obtained with the free bi-enzyme. The pH tolerance and temperature stability of the BESCs were also improved compared with those of the free enzymes. In conclusion, bi-enzyme assemblies were docked using SpyCatcher/SpyTag to produce BESCs with a special structure and excellent catalytic activity, improving the catalytic efficiency of the enzyme.
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22
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Bitterwolf P, Zoheir AE, Hertel J, Kröll S, Rabe KS, Niemeyer CM. Intracellular Assembly of Interacting Enzymes Yields Highly-Active Nanoparticles for Flow Biocatalysis. Chemistry 2022; 28:e202202157. [PMID: 36000795 PMCID: PMC9828753 DOI: 10.1002/chem.202202157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Indexed: 01/12/2023]
Abstract
All-enzyme hydrogel (AEH) particles with a hydrodynamic diameter of up to 120 nm were produced intracellularly with an Escherichia coli-based in vivo system. The inCell-AEH nanoparticles were generated from polycistronic vectors enabling simultaneous expression of two interacting enzymes, the Lactobacillus brevis alcohol dehydrogenase (ADH) and the Bacillus subtilis glucose-1-dehydrogenase (GDH), fused with a SpyCatcher or SpyTag, respectively. Formation of inCell-AEH was analyzed by dynamic light scattering and atomic force microscopy. Using the stereoselective two-step reduction of a prochiral diketone substrate, we show that the inCell-AEH approach can be advantageously used in whole-cell flow biocatalysis, by which flow reactors could be operated for >4 days under constant substrate perfusion. More importantly, the inCell-AEH concept enables the recovery of efficient catalyst materials for stable flow bioreactors in a simple and economical one-step procedure from crude bacterial lysates. We believe that our method will contribute to further optimization of sustainable biocatalytic processes.
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Affiliation(s)
- Patrick Bitterwolf
- Institute for Biological Interfaces (IBG1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 1Karlsruhe76344Germany
| | - Ahmed E. Zoheir
- Department of Genetics and CytologyNational Research Centre (NRC)33 El Buhouth St.Cairo12622Egypt
| | - Julian Hertel
- Institute for Biological Interfaces (IBG1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 1Karlsruhe76344Germany
| | - Sandra Kröll
- Institute for Biological Interfaces (IBG1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 1Karlsruhe76344Germany
| | - Kersten S. Rabe
- Institute for Biological Interfaces (IBG1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 1Karlsruhe76344Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG1)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 1Karlsruhe76344Germany
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23
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Winegar PH, Figg CA, Teplensky MH, Ramani N, Mirkin CA. Modular Nucleic Acid Scaffolds for Synthesizing Monodisperse and Sequence-Encoded Antibody Oligomers. Chem 2022; 8:3018-3030. [PMID: 36405374 PMCID: PMC9674055 DOI: 10.1016/j.chempr.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesizing protein oligomers that contain exact numbers of multiple different proteins in defined architectures is challenging. DNA-DNA interactions can be used to program protein assembly into oligomers; however, existing methods require changes to DNA design to achieve different numbers and oligomeric sequences of proteins. Herein, we develop a modular DNA scaffold that uses only six synthetic oligonucleotides to organize proteins into defined oligomers. As a proof-of-concept, model proteins (antibodies) are oligomerized into dimers and trimers, where antibody function is retained. Illustrating the modularity of this technique, dimer and trimer building blocks are then assembled into pentamers containing three different antibodies in an exact stoichiometry and oligomeric sequence. In sum, this report describes a generalizable method for organizing proteins into monodisperse, sequence-encoded oligomers using DNA. This advance will enable studies into how oligomeric protein sequences affect material properties in areas spanning pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.
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Affiliation(s)
- Peter H. Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - C. Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - Michelle H. Teplensky
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Namrata Ramani
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Lead contact
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24
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Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
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25
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Chen K, Dong X, Sun Y. Sequentially co-immobilized PET and MHET hydrolases via Spy chemistry in calcium phosphate nanocrystals present high-performance PET degradation. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129517. [PMID: 35809363 DOI: 10.1016/j.jhazmat.2022.129517] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Accumulation of polyethylene terephthalate (PET) has brought an enormous threat to the ecosystem. The recently reported PET hydrolase (DuraPETase) and MHET hydrolase (MHETase) can synergistically catalyze the complete PET degradation. Hence, this work was designed to develop a bienzymatic cascade catalysis by co-immobilizing the two enzymes for PET biodegradation. DuraPETase and MHETase were sequentially co-immobilized in calcium phosphate nanocrystals (CaP) through SpyTag/SpyCatcher system. MHETase-SpyCatcher was first embedded inside the nanocrystals via biomimetic mineralization, and DuraPETase-SpyTag was then conjugated on the outlayer (~1.5 µm). The bienzyme compartmentalization facilitated DuraPETase interaction with the solid substrate, and the layered structures of the nanocrystals protected the enzymes, thus enhancing their stability. The high specific surface area of the nanocrystals and the proximity effects from the bienzymatic cascade were beneficial to the improved enzyme activity. Experimental data and molecular dynamics simulations revealed the activation effect of Ca2+ on DuraPETase. Taken together, the final results indicate that the PET degradation efficiency of DuraPETase-MHETase@CaP increased by 6.1 and 1.5 times over the free bienzyme system within 10 d at 40 °C and 50 °C, with weight losses at 32.2% and 50.3%, respectively. The bienzymatic cascade with DuraPETase-MHETase@CaP can completely degrade PET, contributing to the recycling of PET.
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Affiliation(s)
- Kun Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
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26
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Xiong Y, Tsitkov S, Hess H, Gang O, Zhang Y. Microscale Colocalization of Cascade Enzymes Yields Activity Enhancement. ACS NANO 2022; 16:10383-10391. [PMID: 35549238 DOI: 10.1021/acsnano.2c00475] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Colocalization of cascade enzymes is broadly discussed as a phenomenon that can boost the cascade reaction throughput, although a direct experimental verification is often challenging. This is mainly due to difficulties in establishing proper size regimes and in the analytical quantification of colocalization effect with adequate experimental systems and simulations. In this study, by taking advantage of reversible DNA-directed colocalization of enzymes on microspheres, we established a cascade system that can be used to directly evaluate the colocalization effect with exactly the same experimental settings except for the state of enzyme dispersion. In the regime of highly dilute microspheres of particular sizes, the colocalized cascade shows enhanced activity compared with the freely diffusing cascade, as evidenced by a shortened lag phase in the time-course production. Reaction-diffusion modeling reveals that the enhancement can be ascribed to the initial accumulation of intermediate substrate around the colocalized enzymes and is found to be carrier-size-dependent. This work demonstrates the dependence of the colocalization effect of enzyme cascades on an interplay of nano- and microscales, lending theoretical support to the rational design of highly efficient multienzyme catalysts.
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Affiliation(s)
- Yan Xiong
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Stanislav Tsitkov
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yifei Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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27
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Mittmann E, Mickoleit F, Maier DS, Stäbler SY, Klein MA, Niemeyer CM, Rabe KS, Schüler D. A Magnetosome-Based Platform for Flow Biocatalysis. ACS APPLIED MATERIALS & INTERFACES 2022; 14:22138-22150. [PMID: 35508355 PMCID: PMC9121345 DOI: 10.1021/acsami.2c03337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Biocatalysis in flow reactor systems is of increasing importance for the transformation of the chemical industry. However, the necessary immobilization of biocatalysts remains a challenge. We here demonstrate that biogenic magnetic nanoparticles, so-called magnetosomes, represent an attractive alternative for the development of nanoscale particle formulations to enable high and stable conversion rates in biocatalytic flow processes. In addition to their intriguing material characteristics, such as high crystallinity, stable magnetic moments, and narrow particle size distribution, magnetosomes offer the unbeatable advantage over chemically synthesized nanoparticles that foreign protein "cargo" can be immobilized on the enveloping membrane via genetic engineering and thus, stably presented on the particle surface. To exploit these advantages, we develop a modular connector system in which abundant magnetosome membrane anchors are genetically fused with SpyCatcher coupling groups, allowing efficient covalent coupling with complementary SpyTag-functionalized proteins. The versatility of this approach is demonstrated by immobilizing a dimeric phenolic acid decarboxylase to SpyCatcher magnetosomes. The functionalized magnetosomes outperform similarly functionalized commercial particles by exhibiting stable substrate conversion during a 60 h period, with an average space-time yield of 49.2 mmol L-1 h-1. Overall, our results demonstrate that SpyCatcher magnetosomes significantly expand the genetic toolbox for particle surface functionalization and increase their application potential as nano-biocatalysts.
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Affiliation(s)
- Esther Mittmann
- Institute
for Biological Interfaces 1, Karlsruhe Institute
of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Frank Mickoleit
- Department
of Microbiology, University of Bayreuth, Universitätsstraße 30, D-95447 Bayreuth, Germany
| | - Denis S. Maier
- Department
of Microbiology, University of Bayreuth, Universitätsstraße 30, D-95447 Bayreuth, Germany
| | - Sabrina Y. Stäbler
- Department
of Microbiology, University of Bayreuth, Universitätsstraße 30, D-95447 Bayreuth, Germany
| | - Marius A. Klein
- Department
of Microbiology, University of Bayreuth, Universitätsstraße 30, D-95447 Bayreuth, Germany
| | - Christof M. Niemeyer
- Institute
for Biological Interfaces 1, Karlsruhe Institute
of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Kersten S. Rabe
- Institute
for Biological Interfaces 1, Karlsruhe Institute
of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Dirk Schüler
- Department
of Microbiology, University of Bayreuth, Universitätsstraße 30, D-95447 Bayreuth, Germany
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28
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Chen X, Chen X, Zhu L, Liu W, Jiang L. Efficient production of inulo-oligosaccharides from inulin by exo- and endo-inulinase co-immobilized onto a self-assembling protein scaffold. Int J Biol Macromol 2022; 210:588-599. [PMID: 35513090 DOI: 10.1016/j.ijbiomac.2022.04.213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 11/19/2022]
Abstract
Inulin can be hydrolyzed by inulinases to yield inulo-oligosaccharides (IOSs), which have great application potential in the food and nutraceutical industries. However, conventional enzymatic production of IOSs is limited by long hydrolysis times and poor thermo-stability of inulinases. Here, the self-assembling protein scaffold EutM was engineered to co-immobilize exo-inulinase (EXINU) and endo-inulinase (ENINU) for synergistic hydrolysis of inulin to produce IOSs with 3 to 5 monosaccharide units (DP3-5 IOSs). The immobilization of EXINU/ENINU onto the EutM scaffold resulted in an increase of catalytic efficiency, a 65% increase of the Vmax of ENINU, as well as an increase of thermo-stability, with 4.26-fold higher residual activity of EXINU after 22 h-incubation at 50 °C. After optimization, two efficient production protocols were obtained, in which the yield and productivity of DP3-5 IOSs reached 80.38% and 70.86 g·(L·h)-1, respectively, which were at a high level in similar studies. Overall, this study provides an attractive self-assembling protein platform for the co-immobilization of inulinases, as well as optimized bioprocesses with great promise for the industrial production of DP3-5 IOSs.
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Affiliation(s)
- Xinyi Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xianhan Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, Jiangsu, 210009, China
| | - Wei Liu
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China..
| | - Ling Jiang
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China..
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29
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Caparco AA, Dautel DR, Champion JA. Protein Mediated Enzyme Immobilization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106425. [PMID: 35182030 DOI: 10.1002/smll.202106425] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Enzyme immobilization is an essential technology for commercializing biocatalysis. It imparts stability, recoverability, and other valuable features that improve the effectiveness of biocatalysts. While many avenues to join an enzyme to solid phases exist, protein-mediated immobilization is rapidly developing and has many advantages. Protein-mediated immobilization allows for the binding interaction to be genetically coded, can be used to create artificial multienzyme cascades, and enables modular designs that expand the variety of enzymes immobilized. By designing around binding interactions between protein domains, they can be integrated into functional materials for protein immobilization. These materials are framed within the context of biocatalytic performance, immobilization efficiency, and stability of the materials. In this review, supports composed entirely of protein are discussed first, with systems such as cellulosomes and protein cages being discussed alongside newer technologies like spore-based biocatalysts and forizymes. Protein-composite materials such as polymersomes and protein-inorganic supraparticles are then discussed to demonstrate how protein-mediated strategies are applied to many classes of solid materials. Critical analysis and future directions of protein-based immobilization are then discussed, with a particular focus on both computational and design strategies to advance this area of research and make it more broadly applicable to many classes of enzymes.
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Affiliation(s)
- Adam A Caparco
- Department of Nanoengineering, University of California, San Diego, MC 0448, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Dylan R Dautel
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA, 30332, USA
| | - Julie A Champion
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA, 30332, USA
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30
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Wang R, Zhang J, Luo Z, Xie T, Xiao Q, Pei X, Wang A. Controllably crosslinked dual enzymes enabled by genetic-encoded non-standard amino acid for efficiently enantioselective hydrogenation. Int J Biol Macromol 2022; 205:682-691. [PMID: 35247424 DOI: 10.1016/j.ijbiomac.2022.02.171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/30/2022] [Accepted: 02/26/2022] [Indexed: 12/17/2022]
Abstract
In traditional method for preparing crosslinked enzymes aggregates using glutaraldehyde, random linkage is inevitable, which often destroys the enzyme active sites and severely decreases the activity. To address this issue, using genetic encode expanding, nonstandard amino acids (NSAAs) were inserted into enzyme proteins at the preselected sites for crosslinking. When aldehyde ketone reductase (AKR), alcohol dehydrogenase (ADH) and glucose dehydrogenase (GDH) were utilized as model enzymes, their mutants containing p-azido-L-phenylalanine were bio-orthogonally crosslinked with diyne to form crosslinked dual enzymes (CLDEs) acting as a cascade biological oxidation and reduction system. Then, the resultant self-purified CLDEs were characterized using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM), etc. In the asymmetric synthesis of (S)-1-(2,6-dichloro-3-fluorophenyl) ethanol using CLDEs, high product yield (76.08%), ee value (99.99%) and reuse stability were achieved. The yield and ee value were 12.05 times and 1.39 times higher than those using traditional crosslinked enzyme aggregates, respectively. Thus, controllable insertion NSAAs in number and location can engender reasonable linkage and metal-free self-purification for target enzyme proteins. This facile and sustainable method could be further expanded to other dual and multienzyme systems for cascade biocatalysis.
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Affiliation(s)
- Ru Wang
- College of Medicine, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Jing Zhang
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Zhiyuan Luo
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Tian Xie
- College of Medicine, Hangzhou Normal University, Hangzhou 311121, PR China.
| | - Qinjie Xiao
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China.
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, PR China.
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31
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Chen X, Chen X, Zhu L, Liu W, Jiang L. Programming an Orthogonal Self-Assembling Protein Cascade Based on Reactive Peptide-Protein Pairs for In Vitro Enzymatic Trehalose Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4690-4700. [PMID: 35404598 DOI: 10.1021/acs.jafc.2c01118] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Trehalose is an important rare sugar that protects biomolecules against environmental stress. We herein introduce a dual enzyme cascade strategy that regulates the proportion of cargos and scaffolds, to maximize the benefits of enzyme immobilization. Based upon the self-assembling properties of the shell protein (EutM) from the ethanolamine utilization (Eut) bacterial microcompartment, we implemented the catalytic synthesis of trehalose from soluble starch with the coimmobilization of α-amylase and trehalose synthase. This strategy improved enzymatic cascade activity and operational stability. The cascade system enabled the efficient production of trehalose with a yield of ∼3.44 g/(L U), 1.5 times that of the free system. Moreover, its activity was maintained over 12 h, while the free system was almost completely inactivated after 4 h, demonstrating significantly enhanced thermostability. In conclusion, an attractive self-assembly coimmobilization platform was developed, which provides an effective biological process for the enzymatic synthesis of trehalose in vitro.
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Affiliation(s)
- Xianhan Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
| | - Xinyi Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, Jiangsu 210009, People's Republic of China
| | - Wei Liu
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
| | - Ling Jiang
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
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32
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Peng M, Siebert DL, Engqvist MKM, Niemeyer CM, Rabe KS. Modeling-Assisted Design of Thermostable Benzaldehyde Lyases from Rhodococcus erythropolis for Continuous Production of α-Hydroxy Ketones. Chembiochem 2022; 23:e202100468. [PMID: 34558792 PMCID: PMC9293332 DOI: 10.1002/cbic.202100468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Indexed: 12/18/2022]
Abstract
Enantiopure α-hydroxy ketones are important building blocks of active pharmaceutical ingredients (APIs), which can be produced by thiamine-diphosphate-dependent lyases, such as benzaldehyde lyase. Here we report the discovery of a novel thermostable benzaldehyde lyase from Rhodococcus erythropolis R138 (ReBAL). While the overall sequence identity to the only experimentally confirmed benzaldehyde lyase from Pseudomonas fluorescens Biovar I (PfBAL) was only 65 %, comparison of a structural model of ReBAL with the crystal structure of PfBAL revealed only four divergent amino acids in the substrate binding cavity. Based on rational design, we generated two ReBAL variants, which were characterized along with the wild-type enzyme in terms of their substrate spectrum, thermostability and biocatalytic performance in the presence of different co-solvents. We found that the new enzyme variants have a significantly higher thermostability (up to 22 °C increase in T50 ) and a different co-solvent-dependent activity. Using the most stable variant immobilized in packed-bed reactors via the SpyCatcher/SpyTag system, (R)-benzoin was synthesized from benzaldehyde over a period of seven days with a stable space-time-yield of 9.3 mmol ⋅ L-1 ⋅ d-1 . Our work expands the important class of benzaldehyde lyases and therefore contributes to the development of continuous biocatalytic processes for the production of α-hydroxy ketones and APIs.
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Affiliation(s)
- Martin Peng
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Dominik L. Siebert
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Martin K. M. Engqvist
- Chalmers University of TechnologyDepartment of Biology and Biological EngineeringDivision of Systems and Synthetic BiologyKemivägen 10412 96GothenburgSweden
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Kersten S. Rabe
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
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Lukasak B, Thompson RE, Mitchener MM, Feng VJ, Bagert JD, Muir TW. A Genetically Encoded Approach for Breaking Chromatin Symmetry. ACS CENTRAL SCIENCE 2022; 8:176-183. [PMID: 35233450 PMCID: PMC8875426 DOI: 10.1021/acscentsci.1c01332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 05/03/2023]
Abstract
Nucleosomes frequently exist as asymmetric species in native chromatin contexts. Current methods for the traceless generation of these heterotypic chromatin substrates are inefficient and/or difficult to implement. Here, we report an application of the SpyCatcher/SpyTag system as a convenient route to assemble desymmetrized nucleoprotein complexes. This genetically encoded covalent tethering system serves as an internal chaperone, maintained through the assembly process, affording traceless asymmetric nucleosomes following proteolytic removal of the tethers. The strategy allows for generation of nucleosomes containing asymmetric modifications on single or multiple histones, thereby providing facile access to a range of substrates. Herein, we use such constructs to interrogate how nucleosome desymmetrization caused by the incorporation of cancer-associated histone mutations alters chromatin remodeling processes. We also establish that our system provides access to asymmetric dinucleosomes, which allowed us to query the geometric/symmetry constraints of the unmodified histone H3 tail in stimulating the activity of the histone lysine demethylase, KDM5B. By providing a streamlined approach to generate these sophisticated substrates, our method expands the chemical biology toolbox available for interrogating the consequences of asymmetry on chromatin structure and function.
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Rocha RA, Speight RE, Scott C. Engineering Enzyme Properties for Improved Biocatalytic Processes in Batch and Continuous Flow. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Raquel A. Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E. Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
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35
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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.
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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
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36
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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.
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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
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37
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Liu S, Wang Z, Chen K, Yu L, Shi Q, Dong X, Sun Y. Cascade chiral amine synthesis catalyzed by site-specifically co-immobilized alcohol and amine dehydrogenases. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00514j] [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
Sustainable and efficient production of chiral amines was realized with an oriented co-immobilized dual-enzyme system via SiBP-tag.
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Affiliation(s)
- Si Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Zhenfu Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Kun Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Linling Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Qinghong Shi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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38
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Giannakopoulou A, Chatzikonstantinou AV, Tsakni A, Chochos CL, Houhoula D, Stamatis H. A Bi-enzymatic Immobilized Nanobiocatalyst for the Biotransformation of Oleuropein to Hydroxytyrosol. Methods Mol Biol 2022; 2487:279-296. [PMID: 35687242 DOI: 10.1007/978-1-0716-2269-8_17] [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
Multi-enzymatic assemblies offer the opportunity of bringing in proximity several enzymes that are enabled to work together for the catalysis of multi-step reactions. Especially, the development of robust nanobiocatalytic systems comprising of several enzymes has gained considerable attention over the last few years for the catalysis of complex reactions and the production of high added-value products. In the present chapter, we describe the methodology for the development of a bi-enzymatic nanobiocatalyst consisting of the enzymes β-glucosidase from Thermotoga maritima and lipase A from Candida antarctica (CalA) co-immobilized on chitosan-coated magnetic nanoparticles. This nanobiocatalyst can be efficiently applied for the biotransformation of oleuropein to hydroxytyrosol, a reaction of increased biotechnological interest. Several techniques, as well as methodologies that are required for the characterization of the structure and the activity of such systems are also comprehensively described.
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Affiliation(s)
- Archontoula Giannakopoulou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, Ioannina, Greece.
| | - Alexandra V Chatzikonstantinou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, Ioannina, Greece
| | - Aliki Tsakni
- Department of Food Science and Technology, Faculty of Food Sciences, University of West Attica, Athens, Greece
| | - Christos L Chochos
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Dimitra Houhoula
- Department of Food Science and Technology, Faculty of Food Sciences, University of West Attica, Athens, Greece
| | - Haralambos Stamatis
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, Ioannina, Greece.
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Cox N, Charlier C, Vijayaraj R, De La Mare M, Barbe S, André I, Lippens G, Montanier CY. The covalent complex of Jo-In results from a long-lived, non-covalent intermediate state with near-native structure. Biochem Biophys Res Commun 2021; 589:223-228. [PMID: 34929445 DOI: 10.1016/j.bbrc.2021.12.028] [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: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Covalent protein complexes have been used to assemble enzymes in large scaffolds for biotechnology purposes. Although the catalytic mechanism of the covalent linking of such proteins is well known, the recognition and overall structural mechanisms driving the association are far less understood but could help further functional engineering of these complexes. Here, we study the Jo-In complex by NMR spectroscopy and molecular modelling. We characterize a transient non-covalent complex, with structural elements close to those in the final covalent complex. Using site specific mutagenesis, we further show that this non-covalent association is essential for the covalent complex to form.
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Affiliation(s)
- Neil Cox
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Cyril Charlier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Ramadoss Vijayaraj
- Toulouse White Biotechnology, UMS INRA 1337, UMS CNRS 3582, Institut National des Sciences Appliquées de Toulouse, 31077, Toulouse, France
| | - Marion De La Mare
- Toulouse White Biotechnology, UMS INRA 1337, UMS CNRS 3582, Institut National des Sciences Appliquées de Toulouse, 31077, Toulouse, France
| | - Sophie Barbe
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Isabelle André
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Guy Lippens
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France.
| | - Cédric Y Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France.
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40
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Kang SY, Pokhrel A, Bratsch S, Benson JJ, Seo SO, Quin MB, Aksan A, Schmidt-Dannert C. Engineering Bacillus subtilis for the formation of a durable living biocomposite material. Nat Commun 2021; 12:7133. [PMID: 34880257 PMCID: PMC8654922 DOI: 10.1038/s41467-021-27467-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/17/2021] [Indexed: 01/23/2023] Open
Abstract
Engineered living materials (ELMs) are a fast-growing area of research that combine approaches in synthetic biology and material science. Here, we engineer B. subtilis to become a living component of a silica material composed of self-assembling protein scaffolds for functionalization and cross-linking of cells. B. subtilis is engineered to display SpyTags on polar flagella for cell attachment to SpyCatcher modified secreted scaffolds. We engineer endospore limited B. subtilis cells to become a structural component of the material with spores for long-term storage of genetic programming. Silica biomineralization peptides are screened and scaffolds designed for silica polymerization to fabricate biocomposite materials with enhanced mechanical properties. We show that the resulting ELM can be regenerated from a piece of cell containing silica material and that new functions can be incorporated by co-cultivation of engineered B. subtilis strains. We believe that this work will serve as a framework for the future design of resilient ELMs.
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Affiliation(s)
- Sun-Young Kang
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Anaya Pokhrel
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Sara Bratsch
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Joey J. Benson
- grid.17635.360000000419368657Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Seung-Oh Seo
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Maureen B. Quin
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Alptekin Aksan
- grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA ,grid.17635.360000000419368657Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN, 55455, USA. .,BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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41
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Ding Q, Liu Y, Hu G, Guo L, Gao C, Chen X, Chen W, Chen J, Liu L. Engineering Escherichia coli biofilm to increase contact surface for shikimate and L-malate production. BIORESOUR BIOPROCESS 2021; 8:118. [PMID: 38650289 PMCID: PMC10992329 DOI: 10.1186/s40643-021-00470-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/22/2021] [Indexed: 11/10/2022] Open
Abstract
Microbial organelles are a promising model to promote cellular functions for the production of high-value chemicals. However, the concentrations of enzymes and nanoparticles are limited by the contact surface in single Escherichia coli cells. Herein, the definition of contact surface is to improve the amylase and CdS nanoparticles concentration for enhancing the substrate starch and cofactor NADH utilization. In this study, two biofilm-based strategies were developed to improve the contact surface for the production of shikimate and L-malate. First, the contact surface of E. coli was improved by amylase self-assembly with a blue light-inducible biofilm-based SpyTag/SpyCatcher system. This system increased the glucose concentration by 20.7% and the starch-based shikimate titer to 50.96 g L-1, which showed the highest titer with starch as substrate. Then, the contact surface of E. coli was improved using a biofilm-based CdS-biohybrid system by light-driven system, which improved the NADH concentration by 83.3% and increased the NADH-dependent L-malate titer to 45.93 g L-1. Thus, the biofilm-based strategies can regulate cellular functions to increase the efficiency of microbial cell factories based on the optogenetics, light-driven, and metabolic engineering.
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Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
- International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China.
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42
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Lv X, Jin K, Sun G, Ledesma-Amaro R, Liu L. Microscopy imaging of living cells in metabolic engineering. Trends Biotechnol 2021; 40:752-765. [PMID: 34799183 DOI: 10.1016/j.tibtech.2021.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 01/23/2023]
Abstract
Microscopy imaging of living cells is becoming a pivotal, noninvasive, and highly specific tool in metabolic engineering to visualize molecular dynamics in industrial microorganisms. This review describes the different microscopy methods, from fluorescence to super resolution, with application in microbial bioengineering. Firstly, the role and importance of microscopy imaging is analyzed in the context of strain design. Then, the advantages and disadvantages of different microscopy technologies are discussed, including confocal laser scanning microscopy (CLSM), spatial light interference microscopy (SLIM), and super-resolution microscopy, followed by their applications in synthetic biology. Finally, the future perspectives of live-cell imaging and their potential to transform microbial systems are analyzed. This review provides theoretical guidance and highlights the importance of microscopy in understanding and engineering microbial metabolism.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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43
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Zeng R, Lv C, Wang C, Zhao G. Bionanomaterials based on protein self-assembly: Design and applications in biotechnology. Biotechnol Adv 2021; 52:107835. [PMID: 34520791 DOI: 10.1016/j.biotechadv.2021.107835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023]
Abstract
Elegant protein assembly to generate new biomaterials undergoes extremely rapid development for wide extension of biotechnology applications, which can be a powerful tool not only for creating nanomaterials but also for advancing understanding of the structure of life. Unique biological properties of proteins bestow these artificial biomaterials diverse functions that can permit them to be applied in encapsulation, bioimaging, biocatalysis, biosensors, photosynthetic apparatus, electron transport, magnetogenetic applications, vaccine development and antibodies design. This review gives a perspective view of the latest advances in the construction of protein-based nanomaterials. We initially start with distinguishable, specific interactions to construct sundry nanomaterials through protein self-assembly and concisely expound the assembly mechanism from the design strategy. And then, the design and construction of 0D, 1D, 2D, 3D protein assembled nanomaterials are especially highlighted. Furthermore, the potential applications have been discussed in detail. Overall, this review will illustrate how to fabricate highly sophisticated nanomaterials oriented toward applications in biotechnology based on the rules of supramolecular chemistry.
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Affiliation(s)
- Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
| | - Chengtao Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China.
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44
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Gallus S, Mittmann E, Rabe KS. A Modular System for the Rapid Comparison of Different Membrane Anchors for Surface Display on Escherichia coli. Chembiochem 2021; 23:e202100472. [PMID: 34767678 PMCID: PMC9298812 DOI: 10.1002/cbic.202100472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/04/2021] [Indexed: 12/13/2022]
Abstract
Comparison of different membrane anchor motifs for the surface display of a protein of interest (passenger) is crucial for achieving the best possible performance. However, generating genetic fusions of the passenger to various membrane anchors is time-consuming. We herein employ a recently developed modular display system, in which the membrane anchor and the passenger are expressed separately and assembled in situ via SpyCatcher and SpyTag interaction, to readily combine a model passenger cytochrome P450 BM3 (BM3) with four different membrane anchors (Lpp-OmpA, PgsA, INP and AIDA-I). This approach has the significant advantage that passengers and membrane anchors can be freely combined in a modular fashion without the need to generate direct genetic fusion constructs in each case. We demonstrate that the membrane anchors impact not only cell growth and membrane integrity, but also the BM3 surface display capacity and whole-cell biocatalytic activity. The previously used Lpp-OmpA as well as PgsA were found to be efficient for the display of BM3 via SpyCatcher/SpyTag interaction. Our strategy can be transferred to other user-defined anchor and passenger combinations and could thus be used for acceleration and improvement of various applications involving cell surface display.
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Affiliation(s)
- Sabrina Gallus
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Esther Mittmann
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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Zhang YQ, Feng TT, Cao YF, Zhang XY, Wang T, Huanca Nina MR, Wang LC, Yu HL, Xu JH, Ge J, Bai YP. Confining Enzyme Clusters in Bacteriophage P22 Enhances Cofactor Recycling and Stereoselectivity for Chiral Alcohol Synthesis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yan-Qing Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Tao-Tao Feng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Yu-Fei Cao
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xiao-Yan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Tao Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Mario Roque Huanca Nina
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Li-Cheng Wang
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Jun Ge
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Yun-Peng Bai
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
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Liu H, Nidetzky B. Leloir glycosyltransferases enabled to flow synthesis: Continuous production of the natural C-glycoside nothofagin. Biotechnol Bioeng 2021; 118:4402-4413. [PMID: 34355386 PMCID: PMC9291316 DOI: 10.1002/bit.27908] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 01/12/2023]
Abstract
C‐glycosyltransferase (CGT) and sucrose synthase (SuSy), each fused to the cationic binding module Zbasic2, were co‐immobilized on anionic carrier (ReliSorb SP400) and assessed for continuous production of the natural C‐glycoside nothofagin. The overall reaction was 3ʹ‐C‐β‐glycosylation of the polyphenol phloretin from uridine 5ʹ‐diphosphate (UDP)‐glucose that was released in situ from sucrose and UDP. Using solid catalyst optimized for total (∼28 mg/g) as well as relative protein loading (CGT/SuSy = ∼1) and assembled into a packed bed (1 ml), we demonstrate flow synthesis of nothofagin (up to 52 mg/ml; 120 mM) from phloretin (≥95% conversion) solubilized by inclusion complexation in hydroxypropyl β‐cyclodextrin. About 1.8 g nothofagin (90 ml; 12–26 mg/ml) were produced continuously over 90 reactor cycles (2.3 h/cycle) with a space‐time yield of approximately 11 mg/(ml h) and a total enzyme turnover number of up to 2.9 × 103 mg/mg (=3.8 × 105 mol/mol). The co‐immobilized enzymes exhibited useful effectiveness (∼40% of the enzymes in solution), with limitations on the conversion rate arising partly from external liquid–solid mass transfer of UDP under packed‐bed flow conditions. The operational half‐life of the catalyst (∼200 h; 30°C) was governed by the binding stability of the glycosyltransferases (≤35% loss of activity) on the solid carrier. Collectively, the current study shows integrated process technology for flow synthesis with co‐immobilized sugar nucleotide‐dependent glycosyltransferases, using efficient glycosylation from sucrose via the internally recycled UDP‐glucose. This provides a basis from engineering science to promote glycosyltransferase applications for natural product glycosides and oligosaccharides.
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Affiliation(s)
- Hui Liu
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
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Berckman EA, Chen W. Self-assembling protein nanocages for modular enzyme assembly by orthogonal bioconjugation. Biotechnol Prog 2021; 37:e3190. [PMID: 34173352 DOI: 10.1002/btpr.3190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/24/2021] [Indexed: 11/06/2022]
Abstract
The wide variety of enzymatic pathways that can benefit from enzyme scaffolding is astronomical. While enzyme co-localization based on protein, DNA, and RNA scaffolds has been reported, we still lack scaffolds that offer well-defined and uniform three-dimensional structures for enzyme organization. Here we reported a new approach for protein co-localization using naturally occurring protein nanocages as a scaffold. Two different nanocages, the 25 nm E2 and the 34 nm heptatitis B virus, were used to demonstrate the successfully co-localization of the endoglucanase CelA and cellulose binding domain using the robust SpyTag/SpyCatcher bioconjugation chemistry. Because of the simplicity of the assembly, this strategy is useful not only for in vivo enzyme cascading but also the potential for in vivo applications as well.
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Affiliation(s)
- Emily A Berckman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA.,Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
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Kennedy NW, Mills CE, Nichols TM, Abrahamson CH, Tullman-Ercek D. Bacterial microcompartments: tiny organelles with big potential. Curr Opin Microbiol 2021; 63:36-42. [PMID: 34126434 DOI: 10.1016/j.mib.2021.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/13/2021] [Accepted: 05/17/2021] [Indexed: 11/28/2022]
Abstract
Organization of metabolic processes within the space of a cell is critical for the survival of many organisms. In bacteria, spatial organization is achieved via proteinaceous organelles called bacterial microcompartments, which encapsulate pathway enzymes, substrates, and co-factors to drive the safe and efficient metabolism of niche carbon sources. Microcompartments are self-assembled from shell proteins that encapsulate a core comprising various enzymes. This review discusses how recent advances in understanding microcompartment structure and assembly have informed engineering efforts to repurpose compartments and compartment-based structures for non-native functions. These advances, both in understanding of the native structure and function of compartments, as well as in the engineering of new functions, will pave the way for the use of these structures in bacterial cell factories.
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Affiliation(s)
- Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, 2-100 Hogan Hall, Evanston, IL, 60208, USA
| | - Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Taylor M Nichols
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Charlotte H Abrahamson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute B486, Evanston, IL, 60208, USA.
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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]
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Pokhrel A, Kang SY, Schmidt-Dannert C. Ethanolamine bacterial microcompartments: from structure, function studies to bioengineering applications. Curr Opin Microbiol 2021; 62:28-37. [PMID: 34034083 DOI: 10.1016/j.mib.2021.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022]
Abstract
Two decades of structural and functional studies have revealed functions, structures and diversity of bacterial microcompartments. The protein-based organelles encapsulate diverse metabolic pathways in semipermeable, icosahedral or pseudo-icosahedral shells. One of the first discovered and characterized microcompartments are those involved in ethanolamine degradation. This review will summarize their function and assembly along with shared and unique characteristics with other microcompartment types. The modularity and self-assembling properties of their shell proteins make them valuable targets for bioengineering. Advances and prospects for shell protein engineering in vivo and in vitro for synthetic biology and biotechnology applications will be discussed.
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Affiliation(s)
- Anaya Pokhrel
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Sun-Young Kang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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