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Fu C, Xu X, Xie Y, Liu Y, Liu M, Chen A, Blamey JM, Shi J, Zhao S, Sun J. Rational design of GDP‑D‑mannose mannosyl hydrolase for microbial L‑fucose production. Microb Cell Fact 2023; 22:56. [PMID: 36964553 PMCID: PMC10037897 DOI: 10.1186/s12934-023-02060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/11/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND L‑Fucose is a rare sugar that has beneficial biological activities, and its industrial production is mainly achieved with brown algae through acidic/enzymatic fucoidan hydrolysis and a cumbersome purification process. Fucoidan is synthesized through the condensation of a key substance, guanosine 5'‑diphosphate (GDP)‑L‑fucose. Therefore, a more direct approach for biomanufacturing L‑fucose could be the enzymatic degradation of GDP‑L‑fucose. However, no native enzyme is known to efficiently catalyze this reaction. Therefore, it would be a feasible solution to engineering an enzyme with similar function to hydrolyze GDP‑L‑fucose. RESULTS Herein, we constructed a de novo L‑fucose synthetic route in Bacillus subtilis by introducing heterologous GDP‑L‑fucose synthesis pathway and engineering GDP‑mannose mannosyl hydrolase (WcaH). WcaH displays a high binding affinity but low catalytic activity for GDP‑L‑fucose, therefore, a substrate simulation‑based structural analysis of the catalytic center was employed for the rational design and mutagenesis of selected positions on WcaH to enhance its GDP‑L‑fucose‑splitting efficiency. Enzyme mutants were evaluated in vivo by inserting them into an artificial metabolic pathway that enabled B. subtilis to yield L‑fucose. WcaHR36Y/N38R was found to produce 1.6 g/L L‑fucose during shake‑flask growth, which was 67.3% higher than that achieved by wild‑type WcaH. The accumulated L‑fucose concentration in a 5 L bioreactor reached 6.4 g/L. CONCLUSIONS In this study, we established a novel microbial engineering platform for the fermentation production of L‑fucose. Additionally, we found an efficient GDP‑mannose mannosyl hydrolase mutant for L‑fucose biosynthesis that directly hydrolyzes GDP‑L‑fucose. The engineered strain system established in this study is expected to provide new solutions for L‑fucose or its high value‑added derivatives production.
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Affiliation(s)
- Cong Fu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuexia Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Yukang Xie
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufei Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ai Chen
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jenny M Blamey
- Fundación Biociencia, José Domingo Cañas, 2280, Ñuñoa, Santiago, Chile
- Facultad de Química Y Biología, Universidad de Santiago de Chile, 3363, Alameda, Estación Central, Santiago, Chile
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
| | - Junsong Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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MOZART, a QSAR Multi-Target Web-Based Tool to Predict Multiple Drug-Enzyme Interactions. Molecules 2023; 28:molecules28031182. [PMID: 36770857 PMCID: PMC9921108 DOI: 10.3390/molecules28031182] [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: 11/21/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Developing models able to predict interactions between drugs and enzymes is a primary goal in computational biology since these models may be used for predicting both new active drugs and the interactions between known drugs on untested targets. With the compilation of a large dataset of drug-enzyme pairs (62,524), we recognized a unique opportunity to attempt to build a novel multi-target machine learning (MTML) quantitative structure-activity relationship (QSAR) model for probing interactions among different drugs and enzyme targets. To this end, this paper presents an MTML-QSAR model based on using the features of topological drugs together with the artificial neural network (ANN) multi-layer perceptron (MLP). Validation of the final best model found was carried out by internal cross-validation statistics and other relevant diagnostic statistical parameters. The overall accuracy of the derived model was found to be higher than 96%. Finally, to maximize the diffusion of this model, a public and accessible tool has been developed to allow users to perform their own predictions. The developed web-based tool is public accessible and can be downloaded as free open-source software.
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Srouji JR, Xu A, Park A, Kirsch JF, Brenner SE. The evolution of function within the Nudix homology clan. Proteins 2017; 85:775-811. [PMID: 27936487 PMCID: PMC5389931 DOI: 10.1002/prot.25223] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/15/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
Abstract
The Nudix homology clan encompasses over 80,000 protein domains from all three domains of life, defined by homology to each other. Proteins with a domain from this clan fall into four general functional classes: pyrophosphohydrolases, isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), and nonenzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed a structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 "select" Nudix homology domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix homology clan revealed general monophyly with regard to function and a few instances of probable homoplasy. Proteins 2017; 85:775-811. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- John R. Srouji
- Plant and Microbial Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Present address: Molecular and Cellular Biology DepartmentHarvard UniversityCambridgeMassachusetts02138
| | - Anting Xu
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
| | - Annsea Park
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
| | - Jack F. Kirsch
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
| | - Steven E. Brenner
- Plant and Microbial Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Molecular and Cell Biology DepartmentUniversity of CaliforniaBerkeleyCalifornia94720
- Graduate Study in Comparative Biochemistry, University of CaliforniaBerkeleyCalifornia94720
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Giust S, La Sorella G, Sperni L, Strukul G, Scarso A. Substrate selective amide coupling driven by encapsulation of a coupling agent within a self-assembled hexameric capsule. Chem Commun (Camb) 2015; 51:1658-61. [DOI: 10.1039/c4cc08833f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Encapsulation of a cationic carbodiimide condensing agent within a self-assembled hexameric capsule made of resorcin[4]arene units provides a nano-environment that efficiently steers the substrate selectivity in the amide synthesis reaction between carboxylic acids and primary amines.
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Affiliation(s)
- Sonia Giust
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
| | - Giorgio La Sorella
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
| | - Laura Sperni
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
| | - Giorgio Strukul
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
| | - Alessandro Scarso
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
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