1
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Shankar UN, Shiraz M, Kumar P, Akif M. A comprehensive in silico analysis of putative outer membrane and secretory hydrolases from the pathogenic Leptospira: Possible implications in pathogenesis. Biotechnol Appl Biochem 2024. [PMID: 38733098 DOI: 10.1002/bab.2596] [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: 11/22/2023] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Outer surface/membrane and virulent secretory proteins are primarily crucial for pathogenesis. Secreted and outer membrane hydrolases of many pathogens play an important role in attenuating the host immune system. Leptospira expresses many such proteins, and few have been characterized to display various roles, including host immune evasion. However, identification, classification, characterization, and elucidation of the possible role of Leptospira's outer membrane and secretory hydrolases have yet to be explored. In the present study, we used bioinformatics tools to predict exported proteins from the pathogenic Leptospira proteome. Moreover, we focused on secretory and outer membrane putative hydrolases from the exported proteins to generate a deeper understanding. Our analysis yielded four putative outer/secretory hydrolases, LIC_10995, LIC_11183, LIC_11463, and LIC_12988, containing α/β hydrolase fold and displayed similarity with lipase motif. Moreover, their conservation analysis of the predicted hydrolases across the spectrum of different Leptospira species showed high clustering with the pathogenic species. Outer membrane and secretory proteins with lipolytic activity may have a role in pathogenesis. This is the first bioinformatics analysis of secretory and outer membrane α/β hydrolases from leptospiral species. However, experimental studies are indeed required to unravel this possibility.
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Affiliation(s)
- Umate Nachiket Shankar
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mohd Shiraz
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Pankaj Kumar
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mohd Akif
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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2
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Casadevall G, Casadevall J, Duran C, Osuna S. The shortest path method (SPM) webserver for computational enzyme design. Protein Eng Des Sel 2024; 37:gzae005. [PMID: 38431867 DOI: 10.1093/protein/gzae005] [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] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024] Open
Abstract
SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally-relevant positions of a given enzyme structure and dynamics. The server is built on top of the DynaComm.py code and enables the calculation and visualization of the SPM pathways. SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation. We provide in this publication information on how to generate the files for SPM construction even for non-expert users and discuss the most relevant parameters that can be modified. The tool is extremely fast (it takes less than one minute per job), thus allowing the rapid identification of distal positions connected to the active site pocket of the enzyme. SPM applications expand from computational enzyme design, especially if combined with other tools to identify the preferred substitution at the identified position, but also to rationalizing allosteric regulation, and even cryptic pocket identification for drug discovery. The simple user interface and setup make the SPM tool accessible to the whole scientific community. SPMweb is freely available for academia at http://spmosuna.com/.
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Affiliation(s)
- Guillem Casadevall
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
| | | | - Cristina Duran
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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3
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Xu SY, Zhou L, Xu Y, Hong HY, Dai C, Wang YJ, Zheng YG. Recent advances in structure-based enzyme engineering for functional reconstruction. Biotechnol Bioeng 2023; 120:3427-3445. [PMID: 37638646 DOI: 10.1002/bit.28540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
Structural information can help engineer enzymes. Usually, specific amino acids in particular regions are targeted for functional reconstruction to enhance the catalytic performance, including activity, stereoselectivity, and thermostability. Appropriate selection of target sites is the key to structure-based design, which requires elucidation of the structure-function relationships. Here, we summarize the mutations of residues in different specific regions, including active center, access tunnels, and flexible loops, on fine-tuning the catalytic performance of enzymes, and discuss the effects of altering the local structural environment on the functions. In addition, we keep up with the recent progress of structure-based approaches for enzyme engineering, aiming to provide some guidance on how to take advantage of the structural information.
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Affiliation(s)
- Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
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Duan S, Zhang N, Chao T, Wu Y, Wang M. The structural and molecular mechanisms of type II PETases: a mini review. Biotechnol Lett 2023; 45:1249-1263. [PMID: 37535135 DOI: 10.1007/s10529-023-03418-3] [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: 03/21/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023]
Abstract
The advent of plastics has led to significant advances for humans, although the accompanying pollution has also been a source of concern for countries globally. Consequently, a biological method to effectively degrade polyethylene terephthalate (PET) has been an area of significant scientific interest. Following the report of the highly efficient PET hydrolase from the bacterium Ideonella sakaiensis strain 201-F6 (i.e., IsPETase) in 2016, its structure has been extensively studied, showing that it belongs to the type II PETase group. Unlike type I PETases that include most known cutinases, structural investigations of type II PETases have only been conducted since 2017. Type II PETases are further divided into type IIa and IIb enzymes. Moreover, even less research has been conducted on type IIa plastic-degrading enzymes. Here, we present a review of recent studies of the structure and mechanism of type II PETases, using the known structure of the type IIa PETase PE-H from the marine bacterium Pseudomonas aestusnigri in addition to the type IIb enzyme IsPETase as representatives. These studies have provided new insights into the structural features of type II PETases that exhibit PET catalytic activity. In addition, recent studies investigating the rational design of IsPETases are reviewed and summarized alongside a discussion of controversies surrounding PETase investigations.
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Affiliation(s)
- Shuyan Duan
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China.
| | - Nan Zhang
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Tianzhu Chao
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Yaoyao Wu
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, 277160, Shandong, China
| | - Mengying Wang
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
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5
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Chatonnet A, Perochon M, Velluet E, Marchot P. The ESTHER database on alpha/beta hydrolase fold proteins - An overview of recent developments. Chem Biol Interact 2023; 383:110671. [PMID: 37582413 DOI: 10.1016/j.cbi.2023.110671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/01/2023] [Accepted: 08/12/2023] [Indexed: 08/17/2023]
Abstract
The ESTHER database, dedicated to ESTerases and alpha/beta-Hydrolase Enzymes and Relatives (https://bioweb.supagro.inra.fr/ESTHER/general?what=index), offers online access to a continuously updated, sequence-based classification of proteins harboring the alpha/beta hydrolase fold into families and subfamilies. In particular, the database proposes links to the sequences, structures, ligands and huge diversity of functions of these proteins, and to the related literature and other databases. Taking advantage of the promiscuity of enzymatic function, many engineered esterases, lipases, epoxide-hydrolases, haloalkane dehalogenases are used for biotechnological applications. Finding means for detoxifying those protein members that are targeted by insecticides, herbicides, antibiotics, or for reactivating human cholinesterases when inhibited by nerve gas, are still active areas of research. Using or improving the capacity of some enzymes to breakdown plastics with the aim to recycle valuable material and reduce waste is an emerging challenge. Most hydrolases in the superfamily are water-soluble and act on or are inhibited by small organic compounds, yet in a few subfamilies some members interact with other, unrelated proteins to modulate activity or trigger functional partnerships. Recent development in 3D structure prediction brought by AI-based programs now permits analysis of enzymatic mechanisms for a variety of hydrolases with no experimental 3D structure available. Finally, mutations in as many as 34 of the 120 human genes compiled in the database are now linked to genetic diseases, a feature fueling research on early detection, metabolic pathways, pharmacological treatment or enzyme replacement therapy. Here we review those developments in the database that took place over the latest decade and discuss potential new applications and recent and future expected research in the field.
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Affiliation(s)
- Arnaud Chatonnet
- DMEM, Université de Montpellier, INRAE, 34000 Montpellier, France.
| | - Michel Perochon
- DMEM, Université de Montpellier, INRAE, 34000 Montpellier, France
| | - Eric Velluet
- INRAE-AgroM / UIC, Place Viala, 34060, Montpellier, France
| | - Pascale Marchot
- CNRS / Aix-Marseille Univ, lab Architecture et Fonction des Macromolécules Biologiques, Marseille, France
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6
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Biochemical characterization, substrate and stereoselectivity of an outer surface putative α/β hydrolase from the pathogenic Leptospira. Int J Biol Macromol 2023; 229:803-813. [PMID: 36587638 DOI: 10.1016/j.ijbiomac.2022.12.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/13/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022]
Abstract
The genome of pathogenic leptospira encodes a plethora of outer surface and secretory proteins. The outer surface or secreted α/β hydrolases in a few pathogenic organisms are crucial virulent factors. They hydrolyze host immune factors and pathogen's immune-activating ligands, which help pathogens to evade the host's innate immunity. In this study, we report biochemical characterizations, substrate and stereoselectivity of one of the leptospiral outer surface putative α/β hydrolases, IQB77_09235 (LABH). Purified LABH displayed better kinetic parameters towards small water-soluble esters such as p-nitrophenyl acetate and p-nitrophenyl butyrate. The LABH exhibited moderate thermostability and displayed a pH optimum of 8.5. Remarkably, a phylogenetic study suggested that LABH does not cluster with other characterized bacterial esterases or lipases. Protein structural modeling revealed that some structural features are closely associated with Staphylococcus hycus lipase (SAH), a triacylglycerol hydrolase. The hydrolytic activity of the protein was found to be inhibited by a lipase inhibitor, orlistat. Biocatalytic application of the protein in the kinetic resolution of racemic 1-phenylethyl acetate reveals excellent enantioselectivity (E > 500) in the production of (R)-1-phenylethanol, a valuable chiral synthon in several industries. To our knowledge, this is the first detailed characterization of outer surface α/β hydrolases from leptospiral spp.
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7
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Do H, Yoo W, Wang Y, Nam Y, Shin SC, Kim HW, Kim KK, Lee JH. Crystal structure and biochemical analysis of acetylesterase (LgEstI) from Lactococcus garvieae. PLoS One 2023; 18:e0280988. [PMID: 36745644 PMCID: PMC9901739 DOI: 10.1371/journal.pone.0280988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/12/2023] [Indexed: 02/07/2023] Open
Abstract
Esterase, a member of the serine hydrolase family, catalyzes the cleavage and formation of ester bonds with high regio- and stereospecificity, making them attractive biocatalysts for the synthesis of optically pure molecules. In this study, we performed an in-depth biochemical and structural characterization of a novel microbial acetylesterase, LgEstI, from the bacterial fish pathogen Lactococcus garvieae. The dimeric LgEstI displayed substrate preference for the short acyl chain of p-nitrophenyl esters and exhibited increased activity with F207A mutation. Comparative analysis with other esterases indicated that LgEstI has a narrow and shallow active site that may exhibit substrate specificity to short acyl chains. Unlike other esterases, LgEstI contains bulky residues such as Trp89, Phe194, and Trp217, which block the acyl chain channel. Furthermore, immobilized LgEstI retained approximately 90% of its initial activity, indicating its potential in industrial applications. This study expands our understanding of LgEstI and proposes novel ideas for improving its catalytic efficiency and substrate specificity for various applications.
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Affiliation(s)
- Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
| | - Wanki Yoo
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Ying Wang
- Department of Chemistry, Graduate School of General Studies, Sookmyung Women’s University, Seoul, Korea
| | - Yewon Nam
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Han-Woo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Korea
- * E-mail:
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8
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Brown RWB, Sharma AI, Villanueva MR, Li X, Onguka O, Zilbermintz L, Nguyen H, Falk BA, Olson CL, Taylor JM, Epting CL, Kathayat RS, Amara N, Dickinson BC, Bogyo M, Engman DM. Trypanosoma brucei Acyl-Protein Thioesterase-like (TbAPT-L) Is a Lipase with Esterase Activity for Short and Medium-Chain Fatty Acids but Has No Depalmitoylation Activity. Pathogens 2022; 11:1245. [PMID: 36364996 PMCID: PMC9693859 DOI: 10.3390/pathogens11111245] [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] [Received: 09/30/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 02/12/2024] Open
Abstract
Dynamic post-translational modifications allow the rapid, specific, and tunable regulation of protein functions in eukaryotic cells. S-acylation is the only reversible lipid modification of proteins, in which a fatty acid, usually palmitate, is covalently attached to a cysteine residue of a protein by a zDHHC palmitoyl acyltransferase enzyme. Depalmitoylation is required for acylation homeostasis and is catalyzed by an enzyme from the alpha/beta hydrolase family of proteins usually acyl-protein thioesterase (APT1). The enzyme responsible for depalmitoylation in Trypanosoma brucei parasites is currently unknown. We demonstrate depalmitoylation activity in live bloodstream and procyclic form trypanosomes sensitive to dose-dependent inhibition with the depalmitoylation inhibitor, palmostatin B. We identified a homologue of human APT1 in Trypanosoma brucei which we named TbAPT-like (TbAPT-L). Epitope-tagging of TbAPT-L at N- and C- termini indicated a cytoplasmic localization. Knockdown or over-expression of TbAPT-L in bloodstream forms led to robust changes in TbAPT-L mRNA and protein expression but had no effect on parasite growth in vitro, or cellular depalmitoylation activity. Esterase activity in cell lysates was also unchanged when TbAPT-L was modulated. Unexpectedly, recombinant TbAPT-L possesses esterase activity with specificity for short- and medium-chain fatty acid substrates, leading to the conclusion, TbAPT-L is a lipase, not a depalmitoylase.
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Affiliation(s)
- Robert W. B. Brown
- Departments of Pathology, Microbiology-Immunology and Pediatrics, Northwestern University, Chicago, IL 60611, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aabha I. Sharma
- Departments of Pathology, Microbiology-Immunology and Pediatrics, Northwestern University, Chicago, IL 60611, USA
| | - Miguel Rey Villanueva
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xiaomo Li
- Departments of Pathology, Microbiology-Immunology and Pediatrics, Northwestern University, Chicago, IL 60611, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ouma Onguka
- Departments of Pathology and Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leeor Zilbermintz
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Helen Nguyen
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ben A. Falk
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Cheryl L. Olson
- Departments of Pathology, Microbiology-Immunology and Pediatrics, Northwestern University, Chicago, IL 60611, USA
| | - Joann M. Taylor
- Departments of Pathology, Microbiology-Immunology and Pediatrics, Northwestern University, Chicago, IL 60611, USA
| | - Conrad L. Epting
- Departments of Pathology, Microbiology-Immunology and Pediatrics, Northwestern University, Chicago, IL 60611, USA
| | - Rahul S. Kathayat
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Neri Amara
- Departments of Pathology and Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Matthew Bogyo
- Departments of Pathology and Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David M. Engman
- Departments of Pathology, Microbiology-Immunology and Pediatrics, Northwestern University, Chicago, IL 60611, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Cadet XF, Gelly JC, van Noord A, Cadet F, Acevedo-Rocha CG. Learning Strategies in Protein Directed Evolution. Methods Mol Biol 2022; 2461:225-275. [PMID: 35727454 DOI: 10.1007/978-1-0716-2152-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic biology is a fast-evolving research field that combines biology and engineering principles to develop new biological systems for medical, pharmacological, and industrial applications. Synthetic biologists use iterative "design, build, test, and learn" cycles to efficiently engineer genetic systems that are reliable, reproducible, and predictable. Protein engineering by directed evolution can benefit from such a systematic engineering approach for various reasons. Learning can be carried out before starting, throughout or after finalizing a directed evolution project. Computational tools, bioinformatics, and scanning mutagenesis methods can be excellent starting points, while molecular dynamics simulations and other strategies can guide engineering efforts. Similarly, studying protein intermediates along evolutionary pathways offers fascinating insights into the molecular mechanisms shaped by evolution. The learning step of the cycle is not only crucial for proteins or enzymes that are not suitable for high-throughput screening or selection systems, but it is also valuable for any platform that can generate a large amount of data that can be aided by machine learning algorithms. The main challenge in protein engineering is to predict the effect of a single mutation on one functional parameter-to say nothing of several mutations on multiple parameters. This is largely due to nonadditive mutational interactions, known as epistatic effects-beneficial mutations present in a genetic background may not be beneficial in another genetic background. In this work, we provide an overview of experimental and computational strategies that can guide the user to learn protein function at different stages in a directed evolution project. We also discuss how epistatic effects can influence the success of directed evolution projects. Since machine learning is gaining momentum in protein engineering and the field is becoming more interdisciplinary thanks to collaboration between mathematicians, computational scientists, engineers, molecular biologists, and chemists, we provide a general workflow that familiarizes nonexperts with the basic concepts, dataset requirements, learning approaches, model capabilities and performance metrics of this intriguing area. Finally, we also provide some practical recommendations on how machine learning can harness epistatic effects for engineering proteins in an "outside-the-box" way.
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Affiliation(s)
- Xavier F Cadet
- PEACCEL, Artificial Intelligence Department, Paris, France
| | - Jean Christophe Gelly
- Laboratoire d'Excellence GR-Ex, Paris, France
- BIGR, DSIMB, UMR_S1134, INSERM, University of Paris & University of Reunion, Paris, France
| | | | - Frédéric Cadet
- Laboratoire d'Excellence GR-Ex, Paris, France
- BIGR, DSIMB, UMR_S1134, INSERM, University of Paris & University of Reunion, Paris, France
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10
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The Cytotoxic Necrotizing Factors (CNFs)-A Family of Rho GTPase-Activating Bacterial Exotoxins. Toxins (Basel) 2021; 13:toxins13120901. [PMID: 34941738 PMCID: PMC8709095 DOI: 10.3390/toxins13120901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 11/17/2022] Open
Abstract
The cytotoxic necrotizing factors (CNFs) are a family of Rho GTPase-activating single-chain exotoxins that are produced by several Gram-negative pathogenic bacteria. Due to the pleiotropic activities of the targeted Rho GTPases, the CNFs trigger multiple signaling pathways and host cell processes with diverse functional consequences. They influence cytokinesis, tissue integrity, cell barriers, and cell death, as well as the induction of inflammatory and immune cell responses. This has an enormous influence on host-pathogen interactions and the severity of the infection. The present review provides a comprehensive insight into our current knowledge of the modular structure, cell entry mechanisms, and the mode of action of this class of toxins, and describes their influence on the cell, tissue/organ, and systems levels. In addition to their toxic functions, possibilities for their use as drug delivery tool and for therapeutic applications against important illnesses, including nervous system diseases and cancer, have also been identified and are discussed.
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11
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Maldonado MR, Alnoch RC, de Almeida JM, Santos LAD, Andretta AT, Ropaín RDPC, de Souza EM, Mitchell DA, Krieger N. Key mutation sites for improvement of the enantioselectivity of lipases through protein engineering. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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12
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Schuiten ED, Badenhorst CPS, Palm GJ, Berndt L, Lammers M, Mican J, Bednar D, Damborsky J, Bornscheuer UT. Promiscuous Dehalogenase Activity of the Epoxide Hydrolase CorEH from Corynebacterium sp. C12. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Eva D. Schuiten
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany
| | - Gottfried J. Palm
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany
| | - Jan Mican
- Loschmidt Laboratories, Department of Experimental Biology RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s Hospital, 656 91 Brno, Czech Republic
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487 Greifswald, Germany
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13
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Badenhorst CP, Bornscheuer UT. Droplet microfluidics: From simple activity screening to sophisticated kinetics. Chem 2021. [DOI: 10.1016/j.chempr.2021.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Doble MV, Obrecht L, Joosten HJ, Lee M, Rozeboom HJ, Branigan E, Naismith JH, Janssen DB, Jarvis AG, Kamer PCJ. Engineering Thermostability in Artificial Metalloenzymes to Increase Catalytic Activity. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Megan V. Doble
- School of Chemistry, University of St Andrews, KY16 9ST St Andrews, U.K
| | - Lorenz Obrecht
- School of Chemistry, University of St Andrews, KY16 9ST St Andrews, U.K
| | - Henk-Jan Joosten
- Bio-Prodict, Nieuwe Marktstraat 54E, 6511 AA Nijmegen, The Netherlands
| | - Misun Lee
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Henriette J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Emma Branigan
- School of Chemistry, University of St Andrews, KY16 9ST St Andrews, U.K
| | - James. H. Naismith
- School of Chemistry, University of St Andrews, KY16 9ST St Andrews, U.K
- Rosalind Franklin Institute, Harwell Campus, OX11 0FA Didcot, U.K
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Amanda G. Jarvis
- School of Chemistry, University of St Andrews, KY16 9ST St Andrews, U.K
- School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Kings Buildings, EH9 3FJ Edinburgh, U.K
| | - Paul C. J. Kamer
- School of Chemistry, University of St Andrews, KY16 9ST St Andrews, U.K
- Bioinspired Homo- & Heterogeneous Catalysis, Leibniz Institute for Catalysis, Albert-Einstein-Straße 29 a, Rostock 18059, Germany
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15
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Information System for Selection of Conditions and Equipment for Mammalian Cell Cultivation. DATA 2021. [DOI: 10.3390/data6030023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Over the past few decades, animal cell culture technology has advanced significantly. It is now considered a reliable, functional, and relatively well-developed technology. At present, biotherapeutic drugs are synthesized using cell culture techniques by large manufacturing enterprises that produce products for commercial use and clinical research. The reliable implementation of mammalian cell culture technology requires the optimization of a number of variables, including the culture environment and bioreactor conditions, suitable cell lines, operating costs, efficient process management and, most importantly, quality. Successful implementation also requires an appropriate process development strategy, industrial scale, and characteristics, as well as the certification of sustainable procedures that meet the requirements of current regulations. All of this has led to a trend of increasing research in the field of biotechnology and, as a result, to a great accumulation of scientific information which, however, remains fragmentary and non-systematic. The development of information and network technologies allow us to solve this problem. Information system creation allows for implementation of the modern concept of integrating various structured and unstructured data, as well as the collection of information from internal and external sources. We propose and develop an information system which contains the conditions and various parameters of cultivation processes. The associated ranking system is the result of the set of recommendations—both from technological and hardware solutions—which allow for choosing the optimal conditions for the cultivation of mammalian cells at the stage of scientific research, thereby significantly reducing the time and cost of work. The proposed information system allows for the accumulation of experience regarding existing technologies for the cultivation of mammalian cells, along with application to the development of new technologies. The main goal of the present work is to discuss information systems, the organizational support of scientific research in the field of mammalian cell cultivation, and to provide a detailed description of the developed system and its main modules, including the conceptual and logical scheme of the database.
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16
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Miguel-Ruano V, Rivera I, Rajkovic J, Knapik K, Torrado A, Otero JM, Beneventi E, Becerra M, Sánchez-Costa M, Hidalgo A, Berenguer J, González-Siso MI, Cruces J, Rúa ML, Hermoso JA. Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. Comput Struct Biotechnol J 2021; 19:1214-1232. [PMID: 33680362 PMCID: PMC7905190 DOI: 10.1016/j.csbj.2021.01.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/31/2022] Open
Abstract
A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60°C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the α/β-hydrolase superfamily. The canonical α/β-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo. Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.
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Key Words
- CHCA, cyclohexane carboxylic acid
- CMC, critical micellar concentration
- CV, column volume
- Crystal structure
- DMSO, dimethyl sulfoxide
- DSF, Differential scanning fluorimetry
- Enzyme-substrate complex
- FLU, fluorescein
- HSL, hormone-sensitive lipase
- LDAO, N,N-dimethyldodecylamine N-oxide
- MNP, methyl-naproxen
- Metagenomic
- NP, naproxen
- PPL, Porcine Pancreatic Lipase
- Thermophilic esterase
- pNP, 4-nitrophenol
- α/β hydrolase fold
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Affiliation(s)
- Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
| | - Ivanna Rivera
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
| | - Jelena Rajkovic
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | - Kamila Knapik
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | - Ana Torrado
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | | | | | - Manuel Becerra
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | - Mercedes Sánchez-Costa
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - José Berenguer
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - María-Isabel González-Siso
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | | | - María L. Rúa
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
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17
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Da Costa M, Gevaert O, Van Overtveldt S, Lange J, Joosten HJ, Desmet T, Beerens K. Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering. Biotechnol Adv 2021; 48:107705. [PMID: 33571638 DOI: 10.1016/j.biotechadv.2021.107705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/18/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
Short-chain Dehydrogenase/Reductase enzymes that are active on nucleotide sugars (abbreviated as NS-SDR) are of paramount importance in the biosynthesis of rare sugars and glycosides. Some family members have already been extensively characterized due to their direct implication in metabolic disorders or in the biosynthesis of virulence factors. In this review, we combine the knowledge gathered from studies that typically focused only on one NS-SDR activity with an in-depth analysis and overview of all of the different NS-SDR families (169,076 enzyme sequences). Through this structure-based multiple sequence alignment of NS-SDRs retrieved from public databases, we could identify clear patterns in conservation and correlation of crucial residues. Supported by this analysis, we suggest updating and extending the UDP-galactose 4-epimerase "hexagonal box model" to an "heptagonal box model" for all NS-SDR enzymes. This specificity model consists of seven conserved regions surrounding the NDP-sugar substrate that serve as fingerprint for each specificity. The specificity fingerprints highlighted in this review will be beneficial for functional annotation of the large group of NS-SDR enzymes and form a guide for future enzyme engineering efforts focused on the biosynthesis of rare and specialty carbohydrates.
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Affiliation(s)
- Matthieu Da Costa
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Ophelia Gevaert
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Stevie Van Overtveldt
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Joanna Lange
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Tom Desmet
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - Koen Beerens
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
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18
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Osuna S. The challenge of predicting distal active site mutations in computational enzyme design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1502] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Girona Spain
- ICREA Barcelona Spain
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19
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Abstract
Microbial lipases represent one of the most important groups of biotechnological biocatalysts. However, the high-level production of lipases requires an understanding of the molecular mechanisms of gene expression, folding, and secretion processes. Stable, selective, and productive lipase is essential for modern chemical industries, as most lipases cannot work in different process conditions. However, the screening and isolation of a new lipase with desired and specific properties would be time consuming, and costly, so researchers typically modify an available lipase with a certain potential for minimizing cost. Improving enzyme properties is associated with altering the enzymatic structure by changing one or several amino acids in the protein sequence. This review detailed the main sources, classification, structural properties, and mutagenic approaches, such as rational design (site direct mutagenesis, iterative saturation mutagenesis) and direct evolution (error prone PCR, DNA shuffling), for achieving modification goals. Here, both techniques were reviewed, with different results for lipase engineering, with a particular focus on improving or changing lipase specificity. Changing the amino acid sequences of the binding pocket or lid region of the lipase led to remarkable enzyme substrate specificity and enantioselectivity improvement. Site-directed mutagenesis is one of the appropriate methods to alter the enzyme sequence, as compared to random mutagenesis, such as error-prone PCR. This contribution has summarized and evaluated several experimental studies on modifying the substrate specificity of lipases.
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20
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Bun JS, Slack MD, Schemenauer DE, Johnson RJ. Comparative analysis of the human serine hydrolase OVCA2 to the model serine hydrolase homolog FSH1 from S. cerevisiae. PLoS One 2020; 15:e0230166. [PMID: 32182256 PMCID: PMC7077851 DOI: 10.1371/journal.pone.0230166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 11/22/2022] Open
Abstract
Over 100 metabolic serine hydrolases are present in humans with confirmed functions in metabolism, immune response, and neurotransmission. Among potentially clinically-relevant but uncharacterized human serine hydrolases is OVCA2, a serine hydrolase that has been linked with a variety of cancer-related processes. Herein, we developed a heterologous expression system for OVCA2 and determined the comprehensive substrate specificity of OVCA2 against two ester substrate libraries. Based on this analysis, OVCA2 was confirmed as a serine hydrolase with a strong preference for long-chain alkyl ester substrates (>10-carbons) and high selectivity against a variety of short, branched, and substituted esters. Substitutional analysis was used to identify the catalytic residues of OVCA2 with a Ser117-His206-Asp179 classic catalytic triad. Comparison of the substrate specificity of OVCA2 to the model homologue FSH1 from Saccharomyces cerevisiae illustrated the tighter substrate selectivity of OVCA2, but their overlapping substrate preference for extended straight-chain alkyl esters. Conformation of the overlapping biochemical properties of OVCA2 and FSH1 was used to model structural information about OVCA2. Together our analysis provides detailed substrate specificity information about a previously, uncharacterized human serine hydrolase and begins to define the biological properties of OVCA2.
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Affiliation(s)
- Jessica S. Bun
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - Michael D. Slack
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - Daniel E. Schemenauer
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - R. Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
- * E-mail:
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21
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Wu Z, Liu H, Xu L, Chen HF, Feng Y. Algorithm-based coevolution network identification reveals key functional residues of the α/β hydrolase subfamilies. FASEB J 2020; 34:1983-1995. [PMID: 31907985 DOI: 10.1096/fj.201900948rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 11/11/2022]
Abstract
Covariant residues identified by computational algorithms have provided new insights into enzyme evolutionary routes. However, the reliability and accuracy of routine statistical coupling analysis (SCA) are unable to satisfy the needs of protein engineering because SCA depends only on sequence information. Here, we set up a new SCA algorithm, SCA.SIM, by integrating structure information and MD simulation data. The more reliable covariant residues with high-quality scores are obtained from sequence alignment weighted by residual movement for eight related subfamilies, belonging to α/β hydrolase family, with Candida antarctica lipase B (CALB). The 38 predicted covariant residues are tested for function by high-throughput quantitative evaluation in combination with activity and thermostability assays of a mutant library and deep sequencing. Based on the landscapes of both activity and thermostability, most mutants play key roles in catalysis, and some mutants gain 2.4- to 6-fold increase in half-life at 50°C and 9- to 12-fold improvement in catalytic efficiency. The activity of double mutants for A225F/T103A is higher than those of A225F and T103A which means that SCA.SIM method might be useful for identifying the allosteric coupling. The SCA.SIM algorithm can be used for protein coevolution and enzyme engineering research.
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Affiliation(s)
- Zhiyun Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lishi Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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22
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Ortiz-Soto ME, Reising S, Schlosser A, Seibel J. Structural and functional role of disulphide bonds and substrate binding residues of the human beta-galactoside alpha-2,3-sialyltransferase 1 (hST3Gal1). Sci Rep 2019; 9:17993. [PMID: 31784620 PMCID: PMC6884586 DOI: 10.1038/s41598-019-54384-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/11/2019] [Indexed: 12/27/2022] Open
Abstract
Overexpression of hST3Gal1 leads to hypersialylation of cell-surface glycoconjugates, a cancer-associated condition that promotes cell growth, migration and invasion. Upregulation of this enzyme in ovarian cancer is linked to cancer progression and metastasis, contributing also to chemotherapy resistance. Strategies for preventing metastasis include the inhibition of hST3Gal1, which demands structure-based studies on its strict regioselectivity and substrate/donor preference. Herein we describe the contribution of various residues constituting donor CMP-Neu5Ac and acceptor Galβ1-3GalNAc-R binding sites to catalysis. Removal of hydrogen bonds and/or stacking interactions among substrates and residues Y191, Y230, N147, S148 and N170 affected the enzyme’s activity to a different extent, revealing the fine control needed for an optimal catalytic performance. To gain further understanding of the correlation among structure, activity and stability, the in vitro role of hST3Gal1 disulphide bonds was analysed. As expected, disruption of the Glycosyltransferase family 29 (GT29) invariant bond C142-C281, as well as the ST3Gal1 subfamily conserved disulphide C61-C139 inactivates the enzyme. While disulphide C59-C64 is not essential for function, its absence reduces the activity (kcat) for donor and acceptor substrates to about 67 and 72%, respectively, and diminishes the enzyme’s melting temperature (Tm) by 7 °C.
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Affiliation(s)
- Maria Elena Ortiz-Soto
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Sabine Reising
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Zentrum für Experimentelle Biomedizin, Universität Würzburg, Josef-Schneider Str. 2, Haus D15, 97080, Würzburg, Germany
| | - Jürgen Seibel
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.
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23
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Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application. CRYSTALS 2019. [DOI: 10.3390/cryst9110597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.
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24
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Bauer TL, Buchholz PCF, Pleiss J. The modular structure of α/β-hydrolases. FEBS J 2019; 287:1035-1053. [PMID: 31545554 DOI: 10.1111/febs.15071] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/15/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022]
Abstract
The α/β-hydrolase fold family is highly diverse in sequence, structure and biochemical function. To investigate the sequence-structure-function relationships, the Lipase Engineering Database (https://led.biocatnet.de) was updated. Overall, 280 638 protein sequences and 1557 protein structures were analysed. All α/β-hydrolases consist of the catalytically active core domain, but they might also contain additional structural modules, resulting in 12 different architectures: core domain only, additional lids at three different positions, three different caps, additional N- or C-terminal domains and combinations of N- and C-terminal domains with caps and lids respectively. In addition, the α/β-hydrolases were distinguished by their oxyanion hole signature (GX-, GGGX- and Y-types). The N-terminal domains show two different folds, the Rossmann fold or the β-propeller fold. The C-terminal domains show a β-sandwich fold. The N-terminal β-propeller domain and the C-terminal β-sandwich domain are structurally similar to carbohydrate-binding proteins such as lectins. The classification was applied to the newly discovered polyethylene terephthalate (PET)-degrading PETases and MHETases, which are core domain α/β-hydrolases of the GX- and the GGGX-type respectively. To investigate evolutionary relationships, sequence networks were analysed. The degree distribution followed a power law with a scaling exponent γ = 1.4, indicating a highly inhomogeneous network which consists of a few hubs and a large number of less connected sequences. The hub sequences have many functional neighbours and therefore are expected to be robust toward possible deleterious effects of mutations. The cluster size distribution followed a power law with an extrapolated scaling exponent τ = 2.6, which strongly supports the connectedness of the sequence space of α/β-hydrolases. DATABASE: Supporting data about domains from other proteins with structural similarity to the N- or C-terminal domains of α/β-hydrolases are available in Data Repository of the University of Stuttgart (DaRUS) under doi: https://doi.org/10.18419/darus-458.
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Affiliation(s)
- Tabea L Bauer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
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25
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Suplatov DA, Kopylov KE, Popova NN, Voevodin VV, Švedas VK. Mustguseal: a server for multiple structure-guided sequence alignment of protein families. Bioinformatics 2019; 34:1583-1585. [PMID: 29309510 DOI: 10.1093/bioinformatics/btx831] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/21/2017] [Indexed: 01/23/2023] Open
Abstract
Motivation Comparative analysis of homologous proteins in a functionally diverse superfamily is a valuable tool at studying structure-function relationship, but represents a methodological challenge. Results The Mustguseal web-server can automatically build large structure-guided sequence alignments of functionally diverse protein families that include thousands of proteins basing on all available information about their structures and sequences in public databases. Superimposition of protein structures is implemented to compare evolutionarily distant relatives, whereas alignment of sequences is used to compare close homologues. The final alignment can be downloaded for a local use or operated on-line with the built-in interactive tools and further submitted to the integrated sister web-servers of Mustguseal to analyze conserved, subfamily-specific and co-evolving residues at studying a protein function and regulation, designing improved enzyme variants for practical applications and selective ligands to modulate functional properties of proteins. Availability and implementation Freely available on the web at https://biokinet.belozersky.msu.ru/mustguseal. Contact vytas@belozersky.msu.ru. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Nina N Popova
- Faculty of Computational Mathematics and Cybernetics
| | - Vladimir V Voevodin
- Faculty of Computational Mathematics and Cybernetics.,Research Computing Center of the Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vytas K Švedas
- Belozersky Institute of Physicochemical Biology.,Faculty of Bioengineering and Bioinformatics
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26
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Soni S, Sathe SS, Sheth RR, Tiwari P, Vadgama RKN, Odaneth AA, Lali AM, Chandrayan SK. N-terminal domain replacement changes an archaeal monoacylglycerol lipase into a triacylglycerol lipase. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:110. [PMID: 31080517 PMCID: PMC6501381 DOI: 10.1186/s13068-019-1452-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/25/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Lipolytic enzymes of hyperthermophilic archaea generally prefer small carbon chain fatty acid esters (C2-C12) and are categorized as esterases. However, a few have shown activity with long-chain fatty acid esters, but none of them have been classified as a true lipase except a lipolytic enzyme AFL from Archaeglobus fulgidus. Thus, our main objective is to engineer an archaeal esterase into a true thermostable lipase for industrial applications. Lipases which hydrolyze long-chain fatty acid esters display an interfacial activation mediated by the lid domain which lies over active site and switches to open conformation at the oil-water interface. Lid domains modulate enzyme activities, substrate specificities, and stabilities which have been shown by protein engineering and mutational analyses. Here, we report engineering of an uncharacterized monoacylglycerol lipase (TON-LPL) from an archaeon Thermococcus onnurineus (strain NA1) into a triacylglycerol lipase (rc-TGL) by replacing its 61 N-terminus amino acid residues with 118 residues carrying lid domain of a thermophilic fungal lipase-Thermomyces lanuginosus (TLIP). RESULTS TON-LPL and rc-TGL were cloned and overexpressed in E. coli, and the proteins were purified by Ni-NTA affinity chromatography for biochemical studies. Both enzymes were capable of hydrolyzing various monoglycerides and shared the same optimum pH of 7.0. However, rc-TGL showed a significant decrease of 10 °C in its optimum temperature (Topt). The far UV-CD spectrums were consistent with a well-folded α/β-hydrolase fold for both proteins, but gel filtration chromatography revealed a change in quaternary structure from trimer (TON-LPL) to monomer (rc-TGL). Seemingly, the difference in the oligomeric state of rc-TGL may be linked to a decrease in temperature optimum. Nonetheless, rc-TGL hydrolyzed triglycerides and castor oil, while TON-LPL was not active with these substrates. CONCLUSIONS Here, we have confirmed the predicted esterase activity of TON-LPL and also performed the lid engineering on TON-LPL which effectively expanded its substrate specificity from monoglycerides to triglycerides. This approach provides a way to engineer other hyperthermophilic esterases into industrially suitable lipases by employing N-terminal domain replacement. The immobilized preparation of rc-TGL has shown significant activity with castor oil and has a potential application in castor oil biorefinery to obtain value-added chemicals.
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Affiliation(s)
- Surabhi Soni
- DBT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga East, Mumbai, Maharashtra 400019 India
| | - Sneha S. Sathe
- DBT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga East, Mumbai, Maharashtra 400019 India
| | - Rutuja R. Sheth
- DBT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga East, Mumbai, Maharashtra 400019 India
| | - Prince Tiwari
- IISER Mohali, Knowledge City, Sector 81, Manauli PO, Sahibzada Ajit Singh Nagar, Punjab 140306 India
| | - Rajesh-Kumar N. Vadgama
- DBT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga East, Mumbai, Maharashtra 400019 India
| | - Annamma Anil Odaneth
- DBT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga East, Mumbai, Maharashtra 400019 India
| | - Arvind M. Lali
- DBT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga East, Mumbai, Maharashtra 400019 India
- Department of Chemical Engineering, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga East, Mumbai, Maharashtra 400019 India
| | - Sanjeev K. Chandrayan
- DBT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga East, Mumbai, Maharashtra 400019 India
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Bornscheuer UT, Hauer B, Jaeger KE, Schwaneberg U. Gerichtete Evolution ermöglicht das Design von maßgeschneiderten Proteinen zur nachhaltigen Produktion von Chemikalien und Pharmazeutika. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Uwe T. Bornscheuer
- Biotechnologie & Enzymkatalyse; Institut für Biochemie; Universität Greifswald; Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Bernhard Hauer
- Institut für Technische Biochemie; Universität Stuttgart; Allmandring 31 70569 Stuttgart Deutschland
| | - Karl Erich Jaeger
- Institut für Molekulare Enzymtechnologie; Heinrich-Heine-, Universität Düsseldorf & Forschungszentrum Jülich; Wilhelm-Johnen-Straße 52426 Jülich Deutschland
| | - Ulrich Schwaneberg
- ABBt-Institut für Biotechnologie; RWTH Aachen und DWI Leibniz-Institut für Interaktive Materialien; Worringer Weg 3 52074 Aachen Deutschland
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28
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Bornscheuer UT, Hauer B, Jaeger KE, Schwaneberg U. Directed Evolution Empowered Redesign of Natural Proteins for the Sustainable Production of Chemicals and Pharmaceuticals. Angew Chem Int Ed Engl 2018; 58:36-40. [DOI: 10.1002/anie.201812717] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Uwe T. Bornscheuer
- Biotechnology & Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix Hausdorff Strasse 4 17487 Greifswald Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Karl Erich Jaeger
- Institute of Molecular Enzyme Technology; Heinrich Heine University Düsseldorf and Research Center Jülich; Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Ulrich Schwaneberg
- ABBt-Institute of Biotechnology; RWTH Aachen University and DWI Leibniz Institute for, Interactive Materials; Worringer Weg 3 52074 Aachen Germany
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29
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Kuatsjah E, Chan ACK, Hurst TE, Snieckus V, Murphy MEP, Eltis LD. Metal- and Serine-Dependent Meta-Cleavage Product Hydrolases Utilize Similar Nucleophile-Activation Strategies. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Timothy E. Hurst
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Victor Snieckus
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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Larsen EM, Johnson RJ. Microbial esterases and ester prodrugs: An unlikely marriage for combating antibiotic resistance. Drug Dev Res 2018; 80:33-47. [PMID: 30302779 DOI: 10.1002/ddr.21468] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022]
Abstract
The rise of antibiotic resistance necessitates the search for new platforms for drug development. Prodrugs are common tools for overcoming drawbacks typically associated with drug formulation and delivery, with ester prodrugs providing a classic strategy for masking polar alcohol and carboxylic acid functionalities and improving cell permeability. Ester prodrugs are normally designed to have simple ester groups, as they are expected to be cleaved and reactivated by a wide spectrum of cellular esterases. However, a number of pathogenic and commensal microbial esterases have been found to possess significant substrate specificity and can play an unexpected role in drug metabolism. Ester protection can also introduce antimicrobial properties into previously nontoxic drugs through alterations in cell permeability or solubility. Finally, mutation to microbial esterases is a novel mechanism for the development of antibiotic resistance. In this review, we highlight the important pathogenic and xenobiotic functions of microbial esterases and discuss the development and application of ester prodrugs for targeting microbial infections and combating antibiotic resistance. Esterases are often overlooked as therapeutic targets. Yet, with the growing need to develop new antibiotics, a thorough understanding of the specificity and function of microbial esterases and their combined action with ester prodrug antibiotics will support the design of future therapeutics.
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Affiliation(s)
- Erik M Larsen
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana.,Department of Chemistry and Biochemistry, Bloomsburg University, Bloomsburg, Pennsylvania
| | - R Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana
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31
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Noby N, Saeed H, Embaby AM, Pavlidis IV, Hussein A. Cloning, expression and characterization of cold active esterase (EstN7) from Bacillus cohnii strain N1: A novel member of family IV. Int J Biol Macromol 2018; 120:1247-1255. [PMID: 30063933 DOI: 10.1016/j.ijbiomac.2018.07.169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 01/11/2023]
Abstract
Esterases and lipases from extremophiles have attracted great attention due to their unique characteristics and wide applications. In the present study, an open reading frame (ORF) encoding a novel cold active esterase (EstN7) from Bacillus cohnii strain N1 was cloned and expressed in Escherichia coli. The full-length esterase gene encoding a protein of 320 amino acids with estimated molecular weight of 37.0 kDa. Amino acid sequence analysis revealed that the EstN7 belongs to family IV lipases with a characteristic penta-peptide motif (GXSXG), the catalytic triad Ser, Asp, His and the conserved HGGG motif of the family IV. The recombinant enzyme was purified to apparent homogeneity using nickel-affinity chromatography with a purification fold of 5 and recovery 94.5%. The specific activity of the purified enzyme was 336.89 U/mg. The recombinant EstN7 showed optimal activity at 5 °C moreover, EstN7 displayed full robust stability in the presence of wide range of organic solvents. The purified enzyme had Km and Vmax of 45 ± 0.019 μM and 1113 μmol min-1 mg-1, respectively on p-NP-acetate. These promising characteristics of the recombinant EstN7 would underpin its possible usage with high potential in the synthesis of fragile compounds in pharmaceutical industries.
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Affiliation(s)
- Nehad Noby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt.
| | - Hesham Saeed
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt.
| | - Amira M Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | | | - Ahmed Hussein
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
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32
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White A, Koelper A, Russell A, Larsen EM, Kim C, Lavis LD, Hoops GC, Johnson RJ. Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases. J Biol Chem 2018; 293:13851-13862. [PMID: 30006352 DOI: 10.1074/jbc.ra118.003972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/11/2018] [Indexed: 01/08/2023] Open
Abstract
Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure-activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. Vibrio cholerae esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from Mycobacterium tuberculosis displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr-119 in ybfF and His-187 in Rv0045c; reciprocal substitution of these residues shifted each esterase's substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multifaceted future applications, including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.
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Affiliation(s)
- Alex White
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Andrew Koelper
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Arielle Russell
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Erik M Larsen
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - Charles Kim
- the Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147-2439
| | - Luke D Lavis
- the Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147-2439
| | - Geoffrey C Hoops
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
| | - R Jeremy Johnson
- From the Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208-3443 and
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33
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Smith MA, Phillips WK, Rabin PL, Johnson RJ. A dynamic loop provides dual control over the catalytic and membrane binding activity of a bacterial serine hydrolase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:925-932. [PMID: 29857162 DOI: 10.1016/j.bbapap.2018.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/11/2018] [Accepted: 05/24/2018] [Indexed: 10/16/2022]
Abstract
The bacterial acyl protein thioesterase (APT) homologue FTT258 from the gram-negative pathogen Francisella tularensis exists in equilibrium between a closed and open state. Interconversion between these two states is dependent on structural rearrangement of a dynamic loop overlapping its active site. The dynamics and structural properties of this loop provide a simple model for how the catalytic activity of FTT258 could be spatiotemporally regulated within the cell. Herein, we characterized the dual roles of this dynamic loop in controlling its catalytic and membrane binding activity. Using a comprehensive library of loop variants, we determined the relative importance of each residue in the loop to these two biological functions. For the catalytic activity, a centrally located tryptophan residue (Trp66) was essential, with the resulting alanine variant showing complete ablation of enzyme activity. Detailed analysis of Trp66 showed that its hydrophobicity in combination with spatial arrangement defined its essential role in catalysis. Substitution of other loop residues congregated along the N-terminal side of the loop also significantly impacted catalytic activity, indicating a critical role for this loop in controlling catalytic activity. For membrane binding, the centrally located hydrophobic residues played a surprising minor role in membrane binding. Instead general electrostatic interactions regulated membrane binding with positively charged residues bracketing the dynamic loop controlling membrane binding. Overall for FTT258, this dynamic loop dually controlled its biological activities through distinct residues within the loop and this regulation provides a new model for the spatiotemporal control over FTT258 and potentially homologous APT function.
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Affiliation(s)
- Mackenzie A Smith
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208, USA
| | - Whitney K Phillips
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208, USA
| | - Perry L Rabin
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208, USA
| | - R Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208, USA.
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34
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Clonal variation in productivity and proteolytic clipping of an Fc-fusion protein in CHO cells: Proteomic analysis suggests a role for defective protein folding and the UPR. J Biotechnol 2018; 281:21-30. [PMID: 29860056 DOI: 10.1016/j.jbiotec.2018.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 05/27/2018] [Accepted: 05/30/2018] [Indexed: 11/21/2022]
Abstract
Product degradation, such as clipping, is a common quality issue in the production of Fc-fusion proteins from Chinese hamster ovary (CHO) cells. Degradation of proteins is mainly due to the action of either intracellular or extracellular host cell proteases. This study was carried out to understand more fundamentally the intracellular events that may play a role in determining why cell lines from the same cell line development project can vary with regards to the extent of Fc-fusion protein clipping. The cell lines that displayed the highest levels of clipping also produced less product than the cell lines with a lower level of clipping. In this study we applied differential quantitative label-free LC-MS/MS proteomic analysis to group clonally-derived cell lines (CDCLs) based on the level of clipping of the Fc-fusion protein. The analysis was carried out over two times points in culture and clones were designated as either having 'high' or 'low' clipping phenotypes. We have identified 200 differentially expressed proteins using quantitative label-free LC-MS/MS analysis between the two experimental groups. Functional assessment of the resultant proteomic data using Gene Ontology analysis showed a significant enrichment of biological processes and molecular functions related to protein folding, response to unfolded protein and protein translation. The levels of several proteases were also increased. This study identified protein targets that could be modified using cell line engineering approaches to improve the quality of recombinant Fc-fusion protein production in the biopharmaceutical industry.
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35
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Fesko K, Suplatov D, Švedas V. Bioinformatic analysis of the fold type I PLP-dependent enzymes reveals determinants of reaction specificity in l-threonine aldolase from Aeromonas jandaei. FEBS Open Bio 2018; 8:1013-1028. [PMID: 29928580 PMCID: PMC5986058 DOI: 10.1002/2211-5463.12441] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/27/2018] [Indexed: 01/19/2023] Open
Abstract
Understanding the role of specific amino acid residues in the molecular mechanism of a protein's function is one of the most challenging problems in modern biology. A systematic bioinformatic analysis of protein families and superfamilies can help in the study of structure–function relationships and in the design of improved variants of enzymes/proteins, but represents a methodological challenge. The pyridoxal‐5′‐phosphate (PLP)‐dependent enzymes are catalytically diverse and include the aspartate aminotransferase superfamily which implements a common structural framework known as type fold I. In this work, the recently developed bioinformatic online methods Mustguseal and Zebra were used to collect and study a large representative set of the aspartate aminotransferase superfamily with high structural, but low sequence similarity to l‐threonine aldolase from Aeromonas jandaei (LTAaj), in order to identify conserved positions that provide general properties in the superfamily, and to reveal family‐specific positions (FSPs) responsible for functional diversity. The roles of the identified residues in the catalytic mechanism and reaction specificity of LTAaj were then studied by experimental site‐directed mutagenesis and molecular modelling. It was shown that FSPs determine reaction specificity by coordinating the PLP cofactor in the enzyme's active centre, thus influencing its activation and the tautomeric equilibrium of the intermediates, which can be used as hotspots to modulate the protein's functional properties. Mutagenesis at the selected FSPs in LTAaj led to a reduction in a native catalytic activity and increased the rate of promiscuous reactions. The results provide insight into the structural basis of catalytic promiscuity of the PLP‐dependent enzymes and demonstrate the potential of bioinformatic analysis in studying structure–function relationship in protein superfamilies.
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Affiliation(s)
- Kateryna Fesko
- Institute of Organic Chemistry Graz University of Technology Austria
| | - Dmitry Suplatov
- Belozersky Institute of Physicochemical Biology Lomonosov Moscow State University Russia
| | - Vytas Švedas
- Belozersky Institute of Physicochemical Biology Lomonosov Moscow State University Russia
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36
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Joo S, Cho IJ, Seo H, Son HF, Sagong HY, Shin TJ, Choi SY, Lee SY, Kim KJ. Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation. Nat Commun 2018; 9:382. [PMID: 29374183 PMCID: PMC5785972 DOI: 10.1038/s41467-018-02881-1] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/02/2018] [Indexed: 01/07/2023] Open
Abstract
Plastics, including poly(ethylene terephthalate) (PET), possess many desirable characteristics and thus are widely used in daily life. However, non-biodegradability, once thought to be an advantage offered by plastics, is causing major environmental problem. Recently, a PET-degrading bacterium, Ideonella sakaiensis, was identified and suggested for possible use in degradation and/or recycling of PET. However, the molecular mechanism of PET degradation is not known. Here we report the crystal structure of I. sakaiensis PETase (IsPETase) at 1.5 Å resolution. IsPETase has a Ser-His-Asp catalytic triad at its active site and contains an optimal substrate binding site to accommodate four monohydroxyethyl terephthalate (MHET) moieties of PET. Based on structural and site-directed mutagenesis experiments, the detailed process of PET degradation into MHET, terephthalic acid, and ethylene glycol is suggested. Moreover, other PETase candidates potentially having high PET-degrading activities are suggested based on phylogenetic tree analysis of 69 PETase-like proteins.
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Affiliation(s)
- Seongjoon Joo
- 0000 0001 0661 1556grid.258803.4School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - In Jin Cho
- 0000 0001 2292 0500grid.37172.30Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and KAIST Institute (KI) for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Hogyun Seo
- 0000 0001 0661 1556grid.258803.4School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Hyeoncheol Francis Son
- 0000 0001 0661 1556grid.258803.4School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Hye-Young Sagong
- 0000 0001 0661 1556grid.258803.4School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Tae Joo Shin
- 0000 0004 0381 814Xgrid.42687.3fUNIST Central Research Facilities & School of Natural Science, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919 Republic of Korea
| | - So Young Choi
- 0000 0001 2292 0500grid.37172.30Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and KAIST Institute (KI) for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Sang Yup Lee
- 0000 0001 2292 0500grid.37172.30Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and KAIST Institute (KI) for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Kyung-Jin Kim
- 0000 0001 0661 1556grid.258803.4School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
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37
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Bornscheuer UT. The fourth wave of biocatalysis is approaching. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2018; 376:rsta.2017.0063. [PMID: 29175831 DOI: 10.1098/rsta.2017.0063] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/06/2017] [Indexed: 05/24/2023]
Abstract
Biocatalysis has undergone a tremendous development in the past few years. A plethora of methods enable the rather rapid tailored-design of an enzyme for a targeted reaction such as asymmetric synthesis of a chiral building block by the combination of information from sequence and structure databases with modern molecular biology methods and high-throughput screening tools. Moreover, novel non-natural reactions could be implemented into protein scaffolds and new enzyme classes are emerging, both broadening the repertoire of reactions now available for organic synthesis. Furthermore, impressive examples of metabolic engineering-the combination of several newly introduced reaction steps in a microbial host-have been developed, paving the way for large-scale processes for both pharmaceuticals and bulk chemicals. This contribution highlights recent developments in this area and points out future challenges.This article is part of a discussion meeting issue 'Providing sustainable catalytic solutions for a rapidly changing world'.
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Affiliation(s)
- Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
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De Vitis V, Nakhnoukh C, Pinto A, Contente ML, Barbiroli A, Milani M, Bolognesi M, Molinari F, Gourlay LJ, Romano D. A stereospecific carboxyl esterase from Bacillus coagulans hosting nonlipase activity within a lipase-like fold. FEBS J 2018; 285:903-914. [PMID: 29278448 DOI: 10.1111/febs.14368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/30/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022]
Abstract
Microbial carboxylesterases are important biocatalysts that selectively hydrolyze an extensive range of esters. Here, we report the biochemical and structural characterization of an atypical carboxylesterase from Bacillus coagulans (BCE), endowed with high enantioselectivity toward different 1,2-O-isopropylideneglycerol (IPG or solketal) esters. BCE efficiently catalyzes the production of enantiopure (S)-IPG, a chiral building block for the synthesis of β-blockers, glycerophospholipids, and prostaglandins; efficient hydrolysis was observed up to 65 °C. To gain insight into the mechanistic bases of such enantioselectivity, we solved the crystal structures of BCE in apo- and glycerol-bound forms at resolutions of 1.9 and 1.8 Å, respectively. In silico docking studies on the BCE structure confirmed that IPG esters with small acyl chains (≤ C6) were easily accommodated in the active site pocket, indicating that small conformational changes are necessary to accept longer substrates. Furthermore, docking studies suggested that enantioselectivity may be due to an improved stabilization of the tetrahedral reaction intermediate for the S-enantiomer. Contrary to the above functional data implying nonlipolytic functions, BCE displays a lipase-like 3D structure that hosts a "lid" domain capping the main entrance to the active site. In lipases the lid mediates catalysis through interfacial activation, a process that we did not observe for BCE. Overall, we present the functional-structural properties of an atypical carboxyl esterase that has nonlipase-like functions, yet possesses a lipase-like 3D fold. Our data provide original enzymatic information in view of BCE applications as an inexpensive, efficient biocatalyst for the production of enantiopure (S)-IPG. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank (www.rcsb.org) under accession numbers 5O7G (apo-BCE) and 5OLU (glycerol-bound BCE).
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Affiliation(s)
- Valerio De Vitis
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | | | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Martina L Contente
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy.,School of Chemistry, University of Nottingham, UK
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Mario Milani
- Biophysics Institute, National Research Council c/o, Department of Biosciences, Università degli Studi di Milano, Italy
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Italy.,Biophysics Institute, National Research Council c/o, Department of Biosciences, Università degli Studi di Milano, Italy.,Pediatric Research Center "Romeo e Enrica Invernizzi", Cryo Electron Microscopy Laboratory, University of Milano, Italy
| | - Francesco Molinari
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Louise J Gourlay
- Department of Biosciences, Università degli Studi di Milano, Italy
| | - Diego Romano
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
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Abstract
The last decade has seen a dramatic increase in the utilization of enzymes as green and sustainable (bio)catalysts in pharmaceutical and industrial applications. This trend has to a significant degree been fueled by advances in scientists' and engineers' ability to customize native enzymes by protein engineering. A review of the literature quickly reveals the tremendous success of this approach; protein engineering has generated enzyme variants with improved catalytic activity, broadened or altered substrate specificity, as well as raised or reversed stereoselectivity. Enzymes have been tailored to retain activity at elevated temperatures and to function in the presence of organic solvents, salts and pH values far from physiological conditions. However, readers unfamiliar with the field will soon encounter the confusingly large number of experimental techniques that have been employed to accomplish these engineering feats. Herein, we use history to guide a brief overview of the major strategies for protein engineering-past, present, and future.
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Affiliation(s)
- Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA.
| | - Samantha M Iamurri
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA
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40
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Sherlin D, Anishetty S. A pipeline for proteome-scale identification and studies on hormone sensitive lipases in Mycobacterium tuberculosis. Comput Biol Chem 2017; 71:201-206. [PMID: 29145154 DOI: 10.1016/j.compbiolchem.2017.11.003] [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: 08/03/2016] [Revised: 05/25/2017] [Accepted: 11/06/2017] [Indexed: 12/01/2022]
Abstract
Hormone sensitive lipases (HSLs) play an important role in the survival of M. tuberculosis during dormancy. They help in the utilization of fatty acids from stored lipids. The objective of the current study was to identify all HSLs from the proteome of M. tuberculosis H37Rv. We have developed a novel HSL identification pipeline, based on amino acid sequence homology, presence of conserved motifs and other sequence features deciphered from known HSL dataset. Through this pipeline, we identified 10 proteins as putative HSLs in M. tuberculosis. We have annotated a lipase LipT, as putative p-nitrobenzyl esterase and also identified a new motif "PGG" which is a possible characteristic motif of a subfamily of HSLs.
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Affiliation(s)
- Durairaj Sherlin
- Centre for Biotechnology, Anna University, Chennai, 600 025, India
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41
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Jones BJ, Lim HY, Huang J, Kazlauskas RJ. Comparison of Five Protein Engineering Strategies for Stabilizing an α/β-Hydrolase. Biochemistry 2017; 56:6521-6532. [PMID: 29087185 DOI: 10.1021/acs.biochem.7b00571] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A review of the previous stabilization of α/β-hydrolase fold enzymes revealed many different strategies, but no comparison of strategies on the same enzyme. For this reason, we compared five strategies to identify stabilizing mutations in a model α/β-hydrolase fold enzyme, salicylic acid binding protein 2, to reversible denaturation by urea and to irreversible denaturation by heat. The five strategies included one location agnostic approach (random mutagenesis using error-prone polymerase chain reaction), two structure-based approaches [computational design (Rosetta, FoldX) and mutation of flexible regions], and two sequence-based approaches (addition of proline at locations where a more stable homologue has proline and mutation to consensus). All strategies identified stabilizing mutations, but the best balance of success rate, degree of stabilization, and ease of implementation was mutation to consensus. A web-based automated program that predicts substitutions needed to mutate to consensus is available at http://kazlab.umn.edu .
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Affiliation(s)
- Bryan J Jones
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Huey Yee Lim
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Jun Huang
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States.,School of Biological and Chemical Engineering, Zhejiang University of Science and Technology , Hangzhou 310023, People's Republic of China
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota , 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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42
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Infanzón B, Sotelo PH, Martínez J, Diaz P. Rational evolution of the unusual Y-type oxyanion hole of Rhodococcus sp. CR53 lipase LipR. Enzyme Microb Technol 2017; 108:26-33. [PMID: 29108624 DOI: 10.1016/j.enzmictec.2017.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/26/2017] [Accepted: 09/02/2017] [Indexed: 01/10/2023]
Abstract
Rhodococcus sp CR-53 lipase LipR was the first characterized member of bacterial lipase family X. Interestingly, LipR displays some similarity with α/β-hydrolases of the C. antartica lipase A (CAL-A)-like superfamily (abH38), bearing a Y-type oxyanion hole, never found before among bacterial lipases. In order to explore this unusual Y-type oxyanion hole, and to improve LipR performance, two modification strategies based on site directed or saturation mutagenesis were addressed. Initially, a small library of mutants was designed to convert LipR Y-type oxyanion hole (YDS) into one closer to those most frequently found in bacteria (GGG(X)). However, activity was completely lost in all mutants obtained, indicating that the Y-type oxyanion hole of LipR is required for activity. A second approach was addressed to modify the two main oxyanion hole residues Tyr110 and Asp111, previously described for CAL-A as the most relevant amino acids involved in stabilization of the enzyme-substrate complex. A saturation mutagenesis library was prepared for each residue (Tyr110 and Asp111), and activity of the resulting variants was assayed on different chain length substrates. No functional LipR variants could be obtained when Tyr110 was replaced by any other amino acids, indicating that this is a crucial residue for catalysis. However, among the Asp111 variants obtained, LipR D111G produced a functional enzyme. Interestingly, this LipR-YGS variant showed less activity than wild type LipR on short- or mid- chain substrates but displayed a 5.6-fold increased activity on long chain length substrates. Analysis of the 3D model and in silico docking studies of this enzyme variant suggest that substitution of Asp by Gly produces a wider entrance tunnel that would allow for a better and tight accommodation of larger substrates, thus justifying the experimental results obtained.
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Affiliation(s)
- Belén Infanzón
- Department of Genetics, Microbiology & Statistics, University of Barcelona, Av. Diagonal 643, 08028-Barcelona, Spain
| | - Pablo H Sotelo
- Department of Biotechnology, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Campus Universitario, P.0. Box 1055, San Lorenzo, Paraguay
| | - Josefina Martínez
- Department of Genetics, Microbiology & Statistics, University of Barcelona, Av. Diagonal 643, 08028-Barcelona, Spain; Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Spain
| | - Pilar Diaz
- Department of Genetics, Microbiology & Statistics, University of Barcelona, Av. Diagonal 643, 08028-Barcelona, Spain; Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Spain.
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43
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Kuatsjah E, Chan ACK, Kobylarz MJ, Murphy MEP, Eltis LD. The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the α/β-hydrolase superfamily. J Biol Chem 2017; 292:18290-18302. [PMID: 28935670 DOI: 10.1074/jbc.m117.797696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/15/2017] [Indexed: 01/27/2023] Open
Abstract
Strain SYK-6 of the bacterium Sphingobium sp. catabolizes lignin-derived biphenyl via a meta-cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the meta-cleavage product (MCP) 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate. Here, we validated this reaction by identifying 5-carboxyvanillate and 4-carboxy-2-hydroxypenta-2,4-dienoate as the products and determined the kcat and kcat/Km values as 9.3 ± 0.6 s-1 and 2.5 ± 0.2 × 107 m-1 s-1, respectively. Sequence analyses and a 1.9 Å resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the α/β-hydrolase superfamily. The active-site architecture of LigY resembled that of α-amino-β-carboxymuconic-ϵ-semialdehyde decarboxylase, a class III amidohydrolase, with a single zinc ion coordinated by His-6, His-8, His-179, and Glu-282. Interestingly, we found that LigY lacks the acidic residue proposed to activate water for hydrolysis in other class III amidohydrolases. Moreover, substitution of His-223, a conserved residue proposed to activate water in other amidohydrolases, reduced the kcat to a much lesser extent than what has been reported for other amidohydrolases, suggesting that His-223 has a different role in LigY. Substitution of Arg-72, Tyr-190, Arg-234, or Glu-282 reduced LigY activity over 100-fold. On the basis of these results, we propose a catalytic mechanism involving substrate tautomerization, substrate-assisted activation of water for hydrolysis, and formation of a gem-diol intermediate. This last step diverges from what occurs in serine-dependent MCP hydrolases. This study provides insight into C-C-hydrolyzing enzymes and expands the known range of reactions catalyzed by the amidohydrolase superfamily.
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Affiliation(s)
| | - Anson C K Chan
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Marek J Kobylarz
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E P Murphy
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- From the Genome Science and Technology Program and .,the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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44
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van den Bergh T, Tamo G, Nobili A, Tao Y, Tan T, Bornscheuer UT, Kuipers RKP, Vroling B, de Jong RM, Subramanian K, Schaap PJ, Desmet T, Nidetzky B, Vriend G, Joosten HJ. CorNet: Assigning function to networks of co-evolving residues by automated literature mining. PLoS One 2017; 12:e0176427. [PMID: 28545124 PMCID: PMC5436653 DOI: 10.1371/journal.pone.0176427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 12/12/2016] [Indexed: 12/30/2022] Open
Abstract
CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. CorNet projects external information such as mutation data extracted from literature on interactively displayed groups of co-evolving residue positions to shed light on the functions associated with these groups and the residues in them. We used CorNet to analyse six enzyme super-families and found that groups of strongly co-evolving residues tend to consist of residues involved in a same function such as activity, specificity, co-factor binding, or enantioselectivity. This finding allows to assign a function to residues for which no data is available yet in the literature. A mutant library was designed to mutate residues observed in a group of co-evolving residues predicted to be involved in enantioselectivity, but for which no literature data is available yet. The resulting set of mutations indeed showed many instances of increased enantioselectivity.
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Affiliation(s)
- Tom van den Bergh
- Bio-Prodict, Nijmegen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | | | - Alberto Nobili
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Greifswald, Germany
| | - Yifeng Tao
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Greifswald, Germany
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Chaoyang, Beijing, China
| | - Tianwei Tan
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Chaoyang, Beijing, China
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Greifswald, Germany
| | | | | | | | | | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Tom Desmet
- Centre for Industrial Biotechnology and Biocatalysis, Ghent University, Ghent, Belgium
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Graz, Austria
| | | | - Henk-Jan Joosten
- Bio-Prodict, Nijmegen, The Netherlands
- CMBI, Radboudumc, Nijmegen, The Netherlands
- * E-mail:
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45
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Khan FI, Lan D, Durrani R, Huan W, Zhao Z, Wang Y. The Lid Domain in Lipases: Structural and Functional Determinant of Enzymatic Properties. Front Bioeng Biotechnol 2017; 5:16. [PMID: 28337436 PMCID: PMC5343024 DOI: 10.3389/fbioe.2017.00016] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Lipases are important industrial enzymes. Most of the lipases operate at lipid–water interfaces enabled by a mobile lid domain located over the active site. Lid protects the active site and hence responsible for catalytic activity. In pure aqueous media, the lid is predominantly closed, whereas in the presence of a hydrophobic layer, it is partially opened. Hence, the lid controls the enzyme activity. In the present review, we have classified lipases into different groups based on the structure of lid domains. It has been observed that thermostable lipases contain larger lid domains with two or more helices, whereas mesophilic lipases tend to have smaller lids in the form of a loop or a helix. Recent developments in lipase engineering addressing the lid regions are critically reviewed here. After on, the dramatic changes in substrate selectivity, activity, and thermostability have been reported. Furthermore, improved computational models can now rationalize these observations by relating it to the mobility of the lid domain. In this contribution, we summarized and critically evaluated the most recent developments in experimental and computational research on lipase lids.
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Affiliation(s)
- Faez Iqbal Khan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China; School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
| | - Rabia Durrani
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Weiqian Huan
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Zexin Zhao
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
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46
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Romero-Rivera A, Garcia-Borràs M, Osuna S. Computational tools for the evaluation of laboratory-engineered biocatalysts. Chem Commun (Camb) 2016; 53:284-297. [PMID: 27812570 PMCID: PMC5310519 DOI: 10.1039/c6cc06055b] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive, Los Angeles, California 90095, USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
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47
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Padhi SK. Modern Approaches to Discovering New Hydroxynitrile Lyases for Biocatalysis. Chembiochem 2016; 18:152-160. [DOI: 10.1002/cbic.201600495] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Santosh Kumar Padhi
- Biocatalysis and Enzyme Engineering Laboratory; Department of Biochemistry; School of Life Sciences; University of Hyderabad; Hyderabad 500 046 India
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48
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Ma F, Xie Y, Luo M, Wang S, Hu Y, Liu Y, Feng Y, Yang GY. Sequence homolog-based molecular engineering for shifting the enzymatic pH optimum. Synth Syst Biotechnol 2016; 1:195-206. [PMID: 29062943 PMCID: PMC5640797 DOI: 10.1016/j.synbio.2016.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 10/29/2022] Open
Abstract
Cell-free synthetic biology system organizes multiple enzymes (parts) from different sources to implement unnatural catalytic functions. Highly adaption between the catalytic parts is crucial for building up efficient artificial biosynthetic systems. Protein engineering is a powerful technology to tailor various enzymatic properties including catalytic efficiency, substrate specificity, temperature adaptation and even achieve new catalytic functions. However, altering enzymatic pH optimum still remains a challenging task. In this study, we proposed a novel sequence homolog-based protein engineering strategy for shifting the enzymatic pH optimum based on statistical analyses of sequence-function relationship data of enzyme family. By two statistical procedures, artificial neural networks (ANNs) and least absolute shrinkage and selection operator (Lasso), five amino acids in GH11 xylanase family were identified to be related to the evolution of enzymatic pH optimum. Site-directed mutagenesis of a thermophilic xylanase from Caldicellulosiruptor bescii revealed that four out of five mutations could alter the enzymatic pH optima toward acidic condition without compromising the catalytic activity and thermostability. Combination of the positive mutants resulted in the best mutant M31 that decreased its pH optimum for 1.5 units and showed increased catalytic activity at pH < 5.0 compared to the wild-type enzyme. Structure analysis revealed that all the mutations are distant from the active center, which may be difficult to be identified by conventional rational design strategy. Interestingly, the four mutation sites are clustered at a certain region of the enzyme, suggesting a potential "hot zone" for regulating the pH optima of xylanases. This study provides an efficient method of modulating enzymatic pH optima based on statistical sequence analyses, which can facilitate the design and optimization of suitable catalytic parts for the construction of complicated cell-free synthetic biology systems.
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Affiliation(s)
- Fuqiang Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yuan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Manjie Luo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Shuhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - You Hu
- School of Statistics, East China Normal University, Shanghai 200241, China
| | - Yukun Liu
- School of Statistics, East China Normal University, Shanghai 200241, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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49
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Oh J, Hwang I, Rhee S. Structural Insights into an Oxalate-producing Serine Hydrolase with an Unusual Oxyanion Hole and Additional Lyase Activity. J Biol Chem 2016; 291:15185-95. [PMID: 27226606 DOI: 10.1074/jbc.m116.727180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Indexed: 11/06/2022] Open
Abstract
In Burkholderia species, the production of oxalate, an acidic molecule, is a key event for bacterial growth in the stationary phase. Oxalate plays a central role in maintaining environmental pH, which counteracts inevitable population-collapsing alkaline toxicity in amino acid-based culture medium. In the phytopathogen Burkholderia glumae, two enzymes are responsible for oxalate production. First, the enzyme oxalate biosynthetic component A (ObcA) catalyzes the formation of a tetrahedral C6-CoA adduct from the substrates acetyl-CoA and oxaloacetate. Then the ObcB enzyme liberates three products from the C6-CoA adduct: oxalate, acetoacetate, and CoA. Interestingly, these two stepwise reactions are catalyzed by a single bifunctional enzyme, Obc1, from Burkholderia thailandensis and Burkholderia pseudomallei Obc1 has an ObcA-like N-terminal domain and shows ObcB activity in its C-terminal domain despite no sequence homology with ObcB. We report the crystal structure of Obc1 in its apo and glycerol-bound form at 2.5 Å and 2.8 Å resolution, respectively. The Obc1 N-terminal domain is essentially identical both in structure and function to that of ObcA. Its C-terminal domain has an α/β hydrolase fold that has a catalytic triad for oxalate production and a novel oxyanion hole distinct from the canonical HGGG motif in other α/β hydrolases. Functional analyses through mutagenesis studies suggested that His-934 is an additional catalytic acid/base for its lyase activity and liberates two additional products, acetoacetate and CoA. These results provide structural and functional insights into bacterial oxalogenesis and an example of divergent evolution of the α/β hydrolase fold, which has both hydrolase and lyase activity.
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Affiliation(s)
- Juntaek Oh
- From the Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Ingyu Hwang
- From the Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Sangkee Rhee
- From the Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
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50
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Zorn K, Oroz-Guinea I, Brundiek H, Bornscheuer UT. Engineering and application of enzymes for lipid modification, an update. Prog Lipid Res 2016; 63:153-64. [DOI: 10.1016/j.plipres.2016.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/30/2016] [Accepted: 06/10/2016] [Indexed: 12/21/2022]
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