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Chaikaew S, Watanabe Y, Zheng D, Motojima F, Yamaguchi T, Asano Y. Structure-Based Site-Directed Mutagenesis of Hydroxynitrile Lyase from Cyanogenic Millipede, Oxidus gracilis for Hydrocyanation and Henry Reactions. Chembiochem 2024:e202400118. [PMID: 38526556 DOI: 10.1002/cbic.202400118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 03/26/2024]
Abstract
Hydroxynitrile lyase (HNL) from the cyanogenic millipede Oxidus gracillis (OgraHNL) is a crucial enzyme in the cyanogenesis pathway. Here, the crystal structures of OgraHNL complexed with sulfate, benzaldehyde (BA), (R)-mandelonitrile ((R)-Man), (R)-2-chloromandelonitrile ((R)-2-Cl-Man), and acetone cyanohydrin (ACN) were solved at 1.6, 1.7, 2.3, 2.1, and 2.0 Å resolutions, respectively. The structure of OgraHNL revealed that it belonged to the lipocalin superfamily. Based on this structure, positive variants were designed to further improve the catalytic activity and enantioselectivity of the enzyme for asymmetric hydrocyanation and Henry reactions.
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Affiliation(s)
- Siriporn Chaikaew
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST
| | - Yukio Watanabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Daijun Zheng
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST
| | - Fumihiro Motojima
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST
| | - Takuya Yamaguchi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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2
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Rinnofner C, Felber M, Pichler H. Strains and Molecular Tools for Recombinant Protein Production in Pichia pastoris. Methods Mol Biol 2022; 2513:79-112. [PMID: 35781201 DOI: 10.1007/978-1-0716-2399-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Within the last two decades, the methylotrophic yeast Pichia pastoris (Komagataella phaffii) has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.
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Affiliation(s)
- Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria.
- Bisy GmbH, Hofstaetten/Raab, Austria.
| | - Michael Felber
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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3
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Püllmann P, Weissenborn MJ. Improving the Heterologous Production of Fungal Peroxygenases through an Episomal Pichia pastoris Promoter and Signal Peptide Shuffling System. ACS Synth Biol 2021; 10:1360-1372. [PMID: 34075757 DOI: 10.1021/acssynbio.0c00641] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fungal peroxygenases (UPOs) have emerged as oxyfunctionalization catalysts of tremendous interest in recent years. However, their widespread use in the field of biocatalysis is still hampered by their challenging heterologous production, substantially limiting the panel of accessible enzymes for investigation and enzyme engineering. Building upon previous work on UPO production in yeast, we have developed a combined promoter and signal peptide shuffling system for episomal high throughput UPO production in the industrially relevant, methylotrophic yeast Pichia pastoris. Eleven endogenous and orthologous promoters were shuffled with a diverse set of 17 signal peptides. Three previously described UPOs were selected as first test set, leading to the identification of beneficial promoter/signal peptide combinations for protein production. We applied the system then successfully to produce two novel UPOs: MfeUPO from Myceliophthora fergusii and MhiUPO from Myceliophthora hinnulea. To demonstrate the feasibility of the developed system to other enzyme classes, it was applied for the industrially relevant lipase CalB and the laccase Mrl2. In total, approximately 3200 transformants of eight diverse enzymes were screened and the best promoter/signal peptide combinations studied at various cofeeding, derepression, and induction conditions. High volumetric production titers were achieved by subsequent creation of stable integration lines and harnessing orthologous promoters from Hansenula polymorpha. In most cases promising yields were also achieved without the addition of methanol under derepressed conditions. To foster the use of the episomal high throughput promoter/signal peptide Pichia pastoris system, we made all plasmids available through Addgene.
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Affiliation(s)
- Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 2, 06120 Halle (Saale), Germany
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4
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Zheng YC, Ding LY, Jia Q, Lin Z, Hong R, Yu HL, Xu JH. A High-Throughput Screening Method for the Directed Evolution of Hydroxynitrile Lyase towards Cyanohydrin Synthesis. Chembiochem 2021; 22:996-1000. [PMID: 33146944 DOI: 10.1002/cbic.202000658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/03/2020] [Indexed: 11/10/2022]
Abstract
Chiral cyanohydrins are useful intermediates in the pharmaceutical and agricultural industries. In nature, hydroxynitrile lyases (HNLs) are a kind of elegant tool for enantioselective hydrocyanation of carbonyl compounds. However, currently available methods for demonstrating hydrocyanation are still stalled at precise, but low-throughput, GC or HPLC analyses. Herein, we report a chromogenic high-throughput screening (HTS) method that is feasible for the cyanohydrin synthesis reaction. This method was highly anti-interference and sensitive, and could be used to directly profile the substrate scope of HNLs either in cell-free extract or fermentation clear broth. This HTS method was also validated by generating new variants of PcHNL5 that presented higher catalytic efficiency and stronger acidic tolerance in variant libraries.
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Affiliation(s)
- Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai, 200237, P. R. China
| | - Liang-Yi Ding
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai, 200237, P. R. China
| | - Qiao Jia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai, 200237, P. R. China
| | - Zuming Lin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry (CAS), Shanghai, 200032, P. R. China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry (CAS), Shanghai, 200032, P. R. China.,University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai, 200237, P. R. China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Shanghai, 200237, P. R. China
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5
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 540] [Impact Index Per Article: 180.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
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Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
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6
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biokatalyse: Enzymatische Synthese für industrielle Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006648] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shuke Wu
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Schweiz
| | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Kai Baldenius
- Baldenius Biotech Consulting Hafenstraße 31 68159 Mannheim Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
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7
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Nuylert A, Motojima F, Khanongnuch C, Hongpattarakere T, Asano Y. Stabilization of Hydroxynitrile Lyases from Two Variants of Passion Fruit, Passiflora edulis Sims and Passiflora edulis Forma flavicarpa, by C-Terminal Truncation. Chembiochem 2020; 21:181-189. [PMID: 31562666 DOI: 10.1002/cbic.201900468] [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: 07/29/2019] [Indexed: 11/07/2022]
Abstract
Because the synthesis of chiral compounds generally requires a broad range of substrate specificity and stable enzymes, screening for better enzymes and/or improvement of enzyme properties through molecular approaches is necessary for sustainable industrial development. Herein, the discovery of unique hydroxynitrile lyases (HNLs) from two species of passion fruits, Passiflora edulis forma flavicarpa (yellow passion fruit, PeHNL-Ny) and Passiflora edulis Sims (purple passion fruit, PeHNL-Np), isolated and purified from passion fruit leaves is reported. These are the smallest HNLs (comprising 121 amino acids). Amino acid sequences of both enzymes are 99 % identical; there is a difference of one amino acid in a consensus sequence. PeHNL-Np has an Ala residue at position 107 and is nonglycosylated at Asn105. Because it was confirmed that natural and glycosylated PeHNL-Ny showed superior thermostability, pH stability, and organic tolerance to that of PeHNL-Np, it has been speculated that protein engineering around the only glycosylation site, Asn105, located at the C-terminal region of PeHNL-Ny, might contribute to the stabilization of PeHNL. Therefore, the focus is on improved stability of the nonglycosylated PeHNL by truncating its C-terminal region. The C-terminal-truncated PeHNLΔ107 was obtained by truncating 15 amino acids from the C terminus followed by expression in Escherichia coli. PeHNLΔ107 expressed in E. coli was not glycosylated, and showed improved thermostability, solvent stability, and reusability similar to that of the wild-type glycosylated form of PeHNL expressed in Pichia pastoris. These data reveal that the lack of the high-flexibility region at the C terminus of PeHNL might be a possible reason for improving the stability of PeHNL.
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Affiliation(s)
- Aem Nuylert
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Fumihiro Motojima
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Chartchai Khanongnuch
- Division of Biotechnology, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Tipparat Hongpattarakere
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Yasuhisa Asano
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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8
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Ma C, Tan ZL, Lin Y, Han S, Xing X, Zhang C. Gel microdroplet–based high-throughput screening for directed evolution of xylanase-producing Pichia pastoris. J Biosci Bioeng 2019; 128:662-668. [DOI: 10.1016/j.jbiosc.2019.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 01/24/2023]
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9
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Effect of Plasmid Design and Type of Integration Event on Recombinant Protein Expression in Pichia pastoris. Appl Environ Microbiol 2018; 84:AEM.02712-17. [PMID: 29330186 DOI: 10.1128/aem.02712-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/04/2018] [Indexed: 12/31/2022] Open
Abstract
Pichia pastoris (syn. Komagataella phaffii) is one of the most common eukaryotic expression systems for heterologous protein production. Expression cassettes are typically integrated in the genome to obtain stable expression strains. In contrast to Saccharomyces cerevisiae, where short overhangs are sufficient to target highly specific integration, long overhangs are more efficient in P. pastoris and ectopic integration of foreign DNA can occur. Here, we aimed to elucidate the influence of ectopic integration by high-throughput screening of >700 transformants and whole-genome sequencing of 27 transformants. Different vector designs and linearization approaches were used to mimic the most common integration events targeted in P. pastoris Fluorescence of an enhanced green fluorescent protein (eGFP) reporter protein was highly uniform among transformants when the expression cassettes were correctly integrated in the targeted locus. Surprisingly, most nonspecifically integrated transformants showed highly uniform expression that was comparable to specific integration, suggesting that nonspecific integration does not necessarily influence expression. However, a few clones (<10%) harboring ectopically integrated cassettes showed a greater variation spanning a 25-fold range, surpassing specifically integrated reference strains up to 6-fold. High-expression strains showed a correlation between increased gene copy numbers and high reporter protein fluorescence levels. Our results suggest that for comparing expression levels between strains, the integration locus can be neglected as long as a sufficient numbers of transformed strains are compared. For expression optimization of highly expressible proteins, increasing copy number appears to be the dominant positive influence rather than the integration locus, genomic rearrangements, deletions, or single-nucleotide polymorphisms (SNPs).IMPORTANCE Yeasts are commonly used as biotechnological production hosts for proteins and metabolites. In the yeast Saccharomyces cerevisiae, expression cassettes carrying foreign genes integrate highly specifically at the targeted sites in the genome. In contrast, cassettes often integrate at random genomic positions in nonconventional yeasts, such as Pichia pastoris (syn. Komagataella phaffii). Hence, cells from the same transformation event often behave differently, with significant clonal variation necessitating the screening of large numbers of strains. The importance of this study is that we systematically investigated the influence of integration events in more than 700 strains. Our findings provide novel insight into clonal variation in P. pastoris and, thus, how to avoid pitfalls and obtain reliable results. The underlying mechanisms may also play a role in other yeasts and hence could be generally relevant for recombinant yeast protein production strains.
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Bracco P, Busch H, von Langermann J, Hanefeld U. Enantioselective synthesis of cyanohydrins catalysed by hydroxynitrile lyases - a review. Org Biomol Chem 2018; 14:6375-89. [PMID: 27282284 DOI: 10.1039/c6ob00934d] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The first enantioselective synthesis was the selective addition of cyanide to benzaldehyde catalysed by a hydroxynitrile lyase (HNL). Since then these enzymes have been developed into a reliable tool in organic synthesis. HNLs to prepare either the (R)- or the (S)-enantiomer of the desired cyanohydrin are available and a wide variety of reaction conditions can be applied. As a result of this, numerous applications of these enzymes in organic synthesis have been described. Here the examples of the last decade are summarised, the enzyme catalysed step is discussed and the follow-up chemistry is shown. This proves HNLs to be part of main stream organic synthesis. Additionally the newest approaches via immobilisation and reaction engineering are introduced.
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Affiliation(s)
- Paula Bracco
- Gebouw voor Scheikunde, Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628BL Delft, The Netherlands.
| | - Hanna Busch
- Gebouw voor Scheikunde, Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628BL Delft, The Netherlands.
| | - Jan von Langermann
- Institute of Chemistry, University of Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
| | - Ulf Hanefeld
- Gebouw voor Scheikunde, Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628BL Delft, The Netherlands.
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Zheng YC, Xu JH, Wang H, Lin GQ, Hong R, Yu HL. Hydroxynitrile Lyase Isozymes fromPrunus communis: Identification, Characterization and Synthetic Applications. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201601332] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 People's Republic of China
| | - Hui Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 People's Republic of China
| | - Guo-Qiang Lin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; Shanghai 200032 People's Republic of China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; Shanghai 200032 People's Republic of China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 People's Republic of China
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12
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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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13
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Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs. J Biotechnol 2016; 235:24-31. [DOI: 10.1016/j.jbiotec.2016.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 11/21/2022]
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14
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Tachioka M, Sugimoto N, Nakamura A, Sunagawa N, Ishida T, Uchiyama T, Igarashi K, Samejima M. Development of simple random mutagenesis protocol for the protein expression system in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:199. [PMID: 27660653 PMCID: PMC5028916 DOI: 10.1186/s13068-016-0613-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Random mutagenesis is a powerful technique to obtain mutant proteins with different properties from the wild-type molecule. Error-prone PCR is often employed for random mutagenesis in bacterial protein expression systems, but has rarely been used in the methylotrophic yeast Pichia pastoris system, despite its significant advantages, mainly because large (μg-level) amounts of plasmids are required for transformation. RESULTS We developed a quick and easy technique for random mutagenesis in P. pastoris by sequential Phi29 DNA polymerase-based amplification methods, error-prone rolling circle amplification (RCA) and multiple displacement amplification (MDA). The methodology was validated by applying it for random mutation of the gene encoding cellulase from the basidiomycete Phanerochaete chrysosporium (PcCel6A), a key enzyme in degradation of cellulosic biomass. In the error-prone RCA step, the concentrations of manganese ion (Mn(2+)) and cellulase gene-containing plasmid were varied, and the products obtained under each condition were subjected to the second MDA step in the absence of Mn(2+). The maximum error rate was 2.6 mutations/kb, as evaluated from the results of large-scale sequencing. Several μg of MDA products was transformed by electroporation into Pichia cells, and the activities of extracellularly expressed PcCel6A mutants towards crystalline and amorphous celluloses were compared with those of wild-type enzyme to identify key amino acid residues affecting degradation of crystalline cellulose. CONCLUSIONS We present a rapid and convenient random mutagenesis method that does not require laborious steps such as ligation, cloning, and synthesis of specific primers. This method was successfully applied to the protein expression system in P. pastoris.
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Affiliation(s)
- Mikako Tachioka
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naohisa Sugimoto
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Biomaterial in Tokyo Co., Ltd., Fukuoka Lab, Ōnojō, Fukuoka 816-0905 Japan
| | - Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Institute for Molecular Science, National Institute of Natural Sciences, Okazaki, 444-8787 Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Takuya Ishida
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Taku Uchiyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
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15
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Wang S, Liu Z. Oxygenation cascade analysis in conversion ofn-octane catalyzed by cytochrome P450 CYP102A3 mutants at the P331 site. Biotechnol Appl Biochem 2016; 64:14-19. [DOI: 10.1002/bab.1472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/17/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Songhe Wang
- Institute of Chemical and Engineering Sciences; Jurong Island 627833 Singapore
| | - Zhibin Liu
- Institute of Chemical and Engineering Sciences; Jurong Island 627833 Singapore
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16
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Haon M, Grisel S, Navarro D, Gruet A, Berrin JG, Bignon C. Recombinant protein production facility for fungal biomass-degrading enzymes using the yeast Pichia pastoris. Front Microbiol 2015; 6:1002. [PMID: 26441929 PMCID: PMC4585289 DOI: 10.3389/fmicb.2015.01002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/07/2015] [Indexed: 01/15/2023] Open
Abstract
Filamentous fungi are the predominant source of lignocellulolytic enzymes used in industry for the transformation of plant biomass into high-value molecules and biofuels. The rapidity with which new fungal genomic and post-genomic data are being produced is vastly outpacing functional studies. This underscores the critical need for developing platforms dedicated to the recombinant expression of enzymes lacking confident functional annotation, a prerequisite to their functional and structural study. In the last decade, the yeast Pichia pastoris has become increasingly popular as a host for the production of fungal biomass-degrading enzymes, and particularly carbohydrate-active enzymes (CAZymes). This study aimed at setting-up a platform to easily and quickly screen the extracellular expression of biomass-degrading enzymes in P. pastoris. We first used three fungal glycoside hydrolases (GHs) that we previously expressed using the protocol devised by Invitrogen to try different modifications of the original protocol. Considering the gain in time and convenience provided by the new protocol, we used it as basis to set-up the facility and produce a suite of fungal CAZymes (GHs, carbohydrate esterases and auxiliary activity enzyme families) out of which more than 70% were successfully expressed. The platform tasks range from gene cloning to automated protein purifications and activity tests, and is open to the CAZyme users' community.
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Affiliation(s)
- Mireille Haon
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France
| | - Sacha Grisel
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France
| | - David Navarro
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France
| | - Antoine Gruet
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York NY, USA
| | - Jean-Guy Berrin
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France
| | - Christophe Bignon
- Architecture et Fonction des Macromolècules Biologiques, CNRS-Aix-Marseille University UMR 7257 Marseille, France ; INRA, USC 1408 AFMB Marseille, France
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Vogl T, Ahmad M, Krainer FW, Schwab H, Glieder A. Restriction site free cloning (RSFC) plasmid family for seamless, sequence independent cloning in Pichia pastoris. Microb Cell Fact 2015; 14:103. [PMID: 26169367 PMCID: PMC4501187 DOI: 10.1186/s12934-015-0293-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Tagging proteins is a standard method facilitating protein detection, purification or targeting. When tagging a certain protein of interest, it is challenging to predict which tag will give optimal results and will not interfere with protein folding, activity or yields. Ideally, multiple tags and positions are tested which however complicates molecular cloning and expression vector generation. In conventional cloning, tags are either added on PCR primers (requiring a distinct primer and PCR product per tag) or provided on the vector (typically leaving a restriction site scar). RESULTS Here we report a vector family of 40 plasmids allowing simple, seamless fusions of a single PCR product with various N- and C-terminal tags, signal sequences and promoters. The restriction site free cloning (RSFC) strategy presented in this paper relies on seamless cloning using type IIS restriction endonucleases. After cutting out a stuffer (placeholder) fragment from the vectors, a single PCR product can be directly inserted in frame into all 40 plasmids using blunt end or TA ligations, requiring only verification of the orientation. We have established a RSFC vector family for the commonly used protein expression host Pichia pastoris and demonstrated the system with the secretory expression of horseradish peroxidase (HRP). HRP fusions to four tags (Myc, FLAG, His, Strep) and two fusion proteins (GFP and MBP) showed a 31-fold difference in volumetric activities. C-terminal tagging caused in some cases almost a complete loss of function, whereas N-terminal tags showed moderate differences. CONCLUSIONS The RSFC vectors provide an unprecedented toolbox for expression optimization in P. pastoris. The results obtained with HRP underline the importance of comparing different tags to maximize activities of fusion proteins. In a similar fashion the RSFC strategy can be applied in other expression hosts to screen for optimal promoters, signal sequences or to facilitate the evaluation of (iso-) enzyme families.
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Affiliation(s)
- Thomas Vogl
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria. .,Queensland University of Technology, 2 George St., Brisbane, QLD, 4000, Australia.
| | - Mudassar Ahmad
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Florian W Krainer
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Helmut Schwab
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
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Wiedner R, Kothbauer B, Pavkov-Keller T, Gruber-Khadjawi M, Gruber K, Schwab H, Steiner K. Improving the Properties of BacterialR-Selective Hydroxynitrile Lyases for Industrial Applications. ChemCatChem 2014. [DOI: 10.1002/cctc.201402742] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Mitrovic A, Flicker K, Steinkellner G, Gruber K, Reisinger C, Schirrmacher G, Camattari A, Glieder A. Thermostability improvement of endoglucanase Cel7B from Hypocrea pseudokoningii. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Vogl T, Thallinger GG, Zellnig G, Drew D, Cregg JM, Glieder A, Freigassner M. Towards improved membrane protein production in Pichia pastoris: general and specific transcriptional response to membrane protein overexpression. N Biotechnol 2014; 31:538-52. [PMID: 24594271 DOI: 10.1016/j.nbt.2014.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/20/2014] [Accepted: 02/23/2014] [Indexed: 01/13/2023]
Abstract
Membrane proteins are the largest group of human drug targets and are also used as biocatalysts. However, due to their complexity, efficient expression remains a bottleneck for high level production. In recent years, the methylotrophic yeast Pichia pastoris has emerged as one of the most commonly used expression systems for membrane protein production. Here, we have analysed the transcriptomes of P. pastoris strains producing different classes of membrane proteins (mitochondrial, ER/Golgi and plasma membrane localized) to understand the cellular response and to identify targets to engineer P. pastoris towards an improved chassis for membrane protein production. Microarray experiments revealed varying transcriptional responses depending on the enzymatic activity, subcellular localization and physiological role of the membrane proteins. While an alternative oxidase evoked primarily a response within the mitochondria, the overexpression of transporters entering the secretory pathway had a wide effect on lipid metabolism and induced the upregulation of the UPR (unfolded protein response) transcription factor Hac1p. Coexpression of P. pastoris endogenous HAC1 increased the levels of ER-resident membrane proteins 1.5- to 2.1-fold. Subsequent transcriptome analysis of HAC1 coexpression revealed an upregulation of the folding machinery correlating with an expansion of the ER membrane capacity, thus boosting membrane protein production. Hence, our study has helped to elucidate the cellular response of P. pastoris to the expression of different classes of membrane proteins and led specifically to new insights into the effect of PpHac1p on membrane proteins entering the secretory pathway.
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Affiliation(s)
- Thomas Vogl
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/5, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8036 Graz, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/5, 8010 Graz, Austria
| | - Guenther Zellnig
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, 8010 Graz, Austria
| | - David Drew
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James M Cregg
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA
| | - Anton Glieder
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/5, 8010 Graz, Austria
| | - Maria Freigassner
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria.
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Camattari A, Weinhandl K, Gudiminchi RK. Methods for efficient high-throughput screening of protein expression in recombinant Pichia pastoris strains. Methods Mol Biol 2014; 1152:113-123. [PMID: 24744029 DOI: 10.1007/978-1-4939-0563-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The methylotrophic yeast Pichia pastoris is becoming one of the favorite industrial workhorses for protein expression. Due to the widespread use of integration vectors, which generates significant clonal variability, screening methods allowing assaying hundreds of individual clones are of particular importance. Here we describe methods to detect and analyze protein expression, developed in a 96-well format for high-throughput screening of recombinant P. pastoris strains. The chapter covers essentially three common scenarios: (1) an enzymatic assay for proteins expressed in the cell cytoplasm, requiring cell lysis; (2) a whole-cell assay for a fungal cytochrome P450; and (3) a nonenzymatic assay for detection and quantification of tagged protein secreted into the supernatant.
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Affiliation(s)
- Andrea Camattari
- Graz University of Technology, Petersgasse 14, 8010, Graz, Austria,
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Abstract
Within the last two decades, the methylotrophic yeast Pichia pastoris has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.
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23
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Zhang SB, Zhai HC, Wang L, Yu GH. Expression, purification and characterization of a feruloyl esterase A from Aspergillus flavus. Protein Expr Purif 2013; 92:36-40. [DOI: 10.1016/j.pep.2013.08.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/16/2013] [Accepted: 08/16/2013] [Indexed: 11/24/2022]
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Geier M, Braun A, Fladischer P, Stepniak P, Rudroff F, Hametner C, Mihovilovic MD, Glieder A. Double site saturation mutagenesis of the human cytochrome P450 2D6 results in regioselective steroid hydroxylation. FEBS J 2013; 280:3094-108. [PMID: 23552177 DOI: 10.1111/febs.12270] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 11/29/2022]
Abstract
The human cytochrome P450 2D6 (CYP2D6) is one of the major human drug metabolizing enzymes and acts preferably on substrates containing a basic nitrogen atom. Testosterone - just as other steroids - is an atypical substrate and only poorly metabolized by CYP2D6. The present study intended to investigate the influence of the two active site residues 216 and 483 on the capability of CYP2D6 to hydroxylate steroids such as for example testosterone. All 400 possible combinatorial mutations at these two positions have been generated and expressed individually in Pichia pastoris. Employing whole-cell biotransformations coupled with HPLC-MS analysis the testosterone hydroxylase activity and regioselectivity of every single CYP2D6 variant was determined. Covering the whole sequence space, CYP2D6 variants with improved activity and so far unknown regio-preference in testosterone hydroxylation were identified. Most intriguingly and in contrast to previous literature reports about mutein F483I, the mutation F483G led to preferred hydroxylation at the 2β-position, while the slow formation of 6β-hydroxytestosterone, the main product of wild-type CYP2D6, was further reduced. Two point mutations have already been sufficient to convert CYP2D6 into a steroid hydroxylase with the highest ever reported testosterone hydroxylation rate for this enzyme, which is of the same order of magnitude as for the conversion of the standard substrate bufuralol by wild-type CYP2D6. Furthermore, this study is also an example for efficient human CYP engineering in P. pastoris for biocatalytic applications and to study so far unknown pharmacokinetic effects of individual and combined mutations in these key enzymes of the human drug metabolism.
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Affiliation(s)
- Martina Geier
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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25
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26
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Pourmir A, Johannes TW. Directed evolution: selection of the host organism. Comput Struct Biotechnol J 2012; 2:e201209012. [PMID: 24688653 PMCID: PMC3962113 DOI: 10.5936/csbj.201209012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/06/2012] [Accepted: 10/12/2012] [Indexed: 11/29/2022] Open
Abstract
Directed evolution has become a well-established tool for improving proteins and biological systems. A critical aspect of directed evolution is the selection of a suitable host organism for achieving functional expression of the target gene. To date, most directed evolution studies have used either Escherichia coli or Saccharomyces cerevisiae as a host; however, other bacterial and yeast species, as well as mammalian and insect cell lines, have also been successfully used. Recent advances in synthetic biology and genomics have opened the possibility of expanding the use of directed evolution to new host organisms such as microalgae. This review focuses on the different host organisms used in directed evolution and highlights some of the recent directed evolution strategies used in these organisms.
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Affiliation(s)
- Azadeh Pourmir
- Department of Chemical Engineering, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, United States
| | - Tyler W Johannes
- Department of Chemical Engineering, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, United States
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Enhanced thermostability of a Rhizopus chinensis lipase by in vivo recombination in Pichia pastoris. Microb Cell Fact 2012; 11:102. [PMID: 22866667 PMCID: PMC3503730 DOI: 10.1186/1475-2859-11-102] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 07/28/2012] [Indexed: 11/25/2022] Open
Abstract
Background Lipase from Rhizopus chinensis is a versatile biocatalyst for various bioconversions and has been expressed at high-level in Pichia pastoris. However, the use of R. chinensis lipase in industrial applications is restricted by its low thermostability. Directed evolution has been proven to be a powerful and efficient protein engineering tool for improvement of biocatalysts. The present work describes improvement of the thermostability of R. chinensis lipase by directed evolution using P. pastoris as the host. Results An efficient, fast and highly simplified method was developed to create a mutant gene library in P. pastoris based on in vivo recombination, whose recombination efficiency could reach 2.3 × 105 /μg DNA. The thermostability of r27RCL was improved significantly by two rounds of error-prone PCR and two rounds of DNA shuffling in P. pastoris. The S4-3 variant was found to be the most thermostable lipase, under the conditions tested. Compared with the parent, the optimum temperature of S4-3 was two degrees higher, Tm was 22 degrees higher and half-lives at 60°C and 65°C were 46- and 23- times longer. Moreover, the catalytic efficiency kcat/Km of S4-3 was comparable to the parent. Stabilizing mutations probably increased thermostability by increasing the hydrophilicity and polarity of the protein surface and creating hydrophobic contacts inside the protein. Conclusions P. pastoris was shown to be a valuable cell factory to improve thermostability of enzymes by directed evolution and it also could be used for improving other properties of enzymes. In this study, by using P. pastoris as a host to build mutant pool, we succeeded in obtaining a thermostable variant S4-3 without compromising enzyme activity and making it a highly promising candidate for future applications at high temperatures.
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Zhang SB, Pei XQ, Wu ZL. Multiple amino acid substitutions significantly improve the thermostability of feruloyl esterase A from Aspergillus niger. BIORESOURCE TECHNOLOGY 2012; 117:140-7. [PMID: 22613889 DOI: 10.1016/j.biortech.2012.04.042] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/23/2012] [Accepted: 04/10/2012] [Indexed: 05/11/2023]
Abstract
Feruloyl esterase A from Aspergillus niger (AnFaeA) is one of the most important feruloyl esterases of industrial relevance. Previous work aided by the PoPMuSiC algorithm has identified two beneficial mutants (D93G and S187F) with thermostabilization effect. In this work, twelve additional amino acid substitutions were identified to be beneficial to the thermostability of AnFaeA after screening a random mutagenesis library constructed in Pichia pastoris. Combination of these mutations resulted in a mutant with 80% residual activity after heat treatment at 90 °C for 15 min and a half-life increasing from 15 min to >4000 min at 55 °C. The thermostabilized mutant displayed significantly enhanced performance compared to the parental AnFaeA when applied to the treatment of steam-exploded corn stalk at 60 °C together with an xylanase, demonstrating its great potential for industrial application.
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Affiliation(s)
- Shuai-Bing Zhang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, PR China
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Reetz MT. Artificial Metalloenzymes as Catalysts in Stereoselective Diels-Alder Reactions. CHEM REC 2012; 12:391-406. [DOI: 10.1002/tcr.201100043] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Indexed: 11/05/2022]
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Gonzalez-Perez D, Garcia-Ruiz E, Alcalde M. Saccharomyces cerevisiae in directed evolution: An efficient tool to improve enzymes. Bioeng Bugs 2012; 3:172-7. [PMID: 22572788 DOI: 10.4161/bbug.19544] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Over the past 20 years, directed evolution has been seen to be the most reliable approach to protein engineering. Emulating the natural selection algorithm, ad hoc enzymes with novel features can be tailor-made for practical purposes through iterative rounds of random mutagenesis, DNA recombination and screening. Of the heterologous hosts used in laboratory evolution experiments, the budding yeast Saccharomyces cerevisiae has become the best choice to express eukaryotic proteins with improved properties. S. cerevisiae not only allows mutant enzymes to be secreted but also, it permits a wide range of genetic manipulations to be employed, ranging from in vivo cloning to the creation of greater molecular diversity, thanks to its efficient DNA recombination apparatus. Here, we summarize some successful examples of the use of the S. cerevisiae machinery to accelerate artificial evolution, complementing the traditional in vitro methods to generate tailor-made enzymes.
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Maté D, García-Ruiz E, Camarero S, Alcalde M. Directed evolution of fungal laccases. Curr Genomics 2011; 12:113-22. [PMID: 21966249 PMCID: PMC3129045 DOI: 10.2174/138920211795564322] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 11/29/2022] Open
Abstract
Fungal laccases are generalists biocatalysts with potential applications that range from bioremediation to novel green processes. Fuelled by molecular oxygen, these enzymes can act on dozens of molecules of different chemical nature, and with the help of redox mediators, their spectrum of oxidizable substrates is further pushed towards xenobiotic compounds (pesticides, industrial dyes, PAHs), biopolymers (lignin, starch, cellulose) and other complex molecules. In recent years, extraordinary efforts have been made to engineer fungal laccases by directed evolution and semi-rational approaches to improve their functional expression or stability. All these studies have taken advantage of Saccharomyces cerevisiae as a heterologous host, not only to secrete the enzyme but also, to emulate the introduction of genetic diversity through in vivo DNA recombination. Here, we discuss all these endeavours to convert fungal laccases into valuable biomolecular platforms on which new functions can be tailored by directed evolution.
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Affiliation(s)
- Diana Maté
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
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Zhao GJ, Yang ZQ, Guo YH. Cloning and expression of hydroxynitrile lyase gene from Eriobotrya japonica in Pichia pastoris. J Biosci Bioeng 2011; 112:321-5. [DOI: 10.1016/j.jbiosc.2011.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 06/27/2011] [Accepted: 06/27/2011] [Indexed: 11/25/2022]
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Dadashipour M, Asano Y. Hydroxynitrile Lyases: Insights into Biochemistry, Discovery, and Engineering. ACS Catal 2011. [DOI: 10.1021/cs200325q] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mohammad Dadashipour
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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Strohmeier GA, Pichler H, May O, Gruber-Khadjawi M. Application of Designed Enzymes in Organic Synthesis. Chem Rev 2011; 111:4141-64. [DOI: 10.1021/cr100386u] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gernot A. Strohmeier
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Oliver May
- DSM—Innovative Synthesis BV, Geleen, P.O. Box 18, 6160 MD Geleen, The Netherlands
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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Abad S, Kitz K, Hörmann A, Schreiner U, Hartner FS, Glieder A. Real-time PCR-based determination of gene copy numbers inPichia pastoris. Biotechnol J 2010; 5:413-20. [DOI: 10.1002/biot.200900233] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ueatrongchit T, Tamura K, Ohmiya T, H-Kittikun A, Asano Y. Hydroxynitrile lyase from Passiflora edulis: Purification, characteristics and application in asymmetric synthesis of (R)-mandelonitrile. Enzyme Microb Technol 2010; 46:456-65. [PMID: 25919621 DOI: 10.1016/j.enzmictec.2010.02.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/17/2009] [Accepted: 02/16/2010] [Indexed: 10/19/2022]
Abstract
A hydroxynitrile lyase from leaves of Passiflora edulis (PeHNL) was purified and characterized for the first time. The enzyme is a monomer of 15kDa and 18kDa by SDS-PAGE, and gel filtration, respectively. Asymmetric synthesis of (R)-mandelonitrile from benzaldehyde and acetone cyanohydrin in a biphasic system employing the PeHNL from rinds of P. edulis was carried out. Several parameters influenced the enantiomeric purity of the product and initial velocity of the reaction. Both pH and temperature were important parameters controlling the enantiomeric purity of the product. The optimum pH and temperature were pH 4 and 10°C, respectively. At the optimum pH and temperature, the spontaneous non-enzymatic reaction yielding the racemic mandelonitrile was almost completely suppressed. The PeHNL was stable (more than 80% residual activity after incubation for 12h) in the system of methyl-t-butyl ether (MTBE), dibutyl ether (DBE), hexane (HEX), and diisopropyl ether (DIPE) while diethyl ether (DEE) and ethyl acetate (EA) were not suitable solvents. The initial velocity was markedly affected by the type of organic solvent in the biphasic system, while high enantiomeric purity was obtained when organic solvents having logP lower than 3.5 were used. The highest initial velocity of reaction and enantiomeric purity of (R)-mandelonitrile were obtained in the biphasic system of DBE with the aqueous phase content of 30% (v/v). The optimum substrate concentrations were 250mM for benzaldehyde and 900mM for acetone cyanohydrin, and the optimum enzyme concentration was 26.7units/ml. The highest enantiomeric purity of (R)-mandelonitrile was successfully obtained with conversion and enantiomeric excess of 31.6% and 98.6%, respectively. The enzyme showed considerable reusability in batch reaction with high enantiomeric purity of product. Herein, we reported the characteristics of a unique (R)-PeHNL from leaves of P. edulis. The PeHNL from rinds had been isolated for the first time and the enzyme showed great ability in transcyanation of (R)-mandelonitrile with high e.e. in DBE as the co-organic solvent in a biphasic system.
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Affiliation(s)
- Techawaree Ueatrongchit
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Ken'ichirou Tamura
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tohru Ohmiya
- Toyama Prefectural Agricultural, Forestry and Fisheries Center, Forestry Research Institute Yoshimine, Tateyama-machi, Toyama 930-1362, Japan
| | - Aran H-Kittikun
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand.
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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Fernández L, Jiao N, Soni P, Gumulya Y, de Oliveira LG, Reetz MT. An efficient method for mutant library creation inPichia pastorisuseful in directed evolution. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.3109/10242420903505834] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Freigassner M, Pichler H, Glieder A. Tuning microbial hosts for membrane protein production. Microb Cell Fact 2009; 8:69. [PMID: 20040113 PMCID: PMC2807855 DOI: 10.1186/1475-2859-8-69] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 12/29/2009] [Indexed: 12/22/2022] Open
Abstract
The last four years have brought exciting progress in membrane protein research. Finally those many efforts that have been put into expression of eukaryotic membrane proteins are coming to fruition and enable to solve an ever-growing number of high resolution structures. In the past, many skilful optimization steps were required to achieve sufficient expression of functional membrane proteins. Optimization was performed individually for every membrane protein, but provided insight about commonly encountered bottlenecks and, more importantly, general guidelines how to alleviate cellular limitations during microbial membrane protein expression. Lately, system-wide analyses are emerging as powerful means to decipher cellular bottlenecks during heterologous protein production and their use in microbial membrane protein expression has grown in popularity during the past months. This review covers the most prominent solutions and pitfalls in expression of eukaryotic membrane proteins using microbial hosts (prokaryotes, yeasts), highlights skilful applications of our basic understanding to improve membrane protein production. Omics technologies provide new concepts to engineer microbial hosts for membrane protein production.
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Affiliation(s)
- Maria Freigassner
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
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How to overcome limitations in biotechnological processes - examples from hydroxynitrile lyase applications. Trends Biotechnol 2009; 27:599-607. [DOI: 10.1016/j.tibtech.2009.07.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/01/2009] [Accepted: 07/13/2009] [Indexed: 11/17/2022]
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Bazan SB, de Alencar Muniz Chaves A, Aires KA, Cianciarullo AM, Garcea RL, Ho PL. Expression and characterization of HPV-16 L1 capsid protein in Pichia pastoris. Arch Virol 2009; 154:1609-17. [PMID: 19756360 DOI: 10.1007/s00705-009-0484-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 07/24/2009] [Indexed: 11/25/2022]
Abstract
Human papillomaviruses (HPVs) are responsible for the most common human sexually transmitted viral infections. Infection with high-risk HPVs, particularly HPV16, is associated with the development of cervical cancer. The papillomavirus L1 major capsid protein, the basis of the currently marketed vaccines, self-assembles into virus-like particles (VLPs). Here, we describe the expression, purification and characterization of recombinant HPV16 L1 produced by a methylotrophic yeast. A codon-optimized HPV16 L1 gene was cloned into a non-integrative expression vector under the regulation of a methanol-inducible promoter and used to transform competent Pichia pastoris cells. Purification of L1 protein from yeast extracts was performed using heparin-sepharose chromatography, followed by a disassembly/reassembly step. VLPs could be assembled from the purified L1 protein, as demonstrated by electron microscopy. The display of conformational epitopes on the VLPs surface was confirmed by hemagglutination and hemagglutination inhibition assays and by immuno-electron microscopy. This study has implications for the development of an alternative platform for the production of a papillomavirus vaccine that could be provided by public health programs, especially in resource-poor areas, where there is a great demand for low-cost vaccines.
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Affiliation(s)
- Silvia Boschi Bazan
- Centro de Biotecnologia, Instituto Butantan, Av. Vital Brasil, Sao Paulo, SP, Brazil
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Sandström AG, Engström K, Nyhlén J, Kasrayan A, Bäckvall JE. Directed evolution of Candida antarctica lipase A using an episomaly replicating yeast plasmid†. Protein Eng Des Sel 2009; 22:413-20. [DOI: 10.1093/protein/gzp019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Pscheidt B, Liu Z, Gaisberger R, Avi M, Skranc W, Gruber K, Griengl H, Glieder A. Efficient Biocatalytic Synthesis of (R)-Pantolactone. Adv Synth Catal 2008. [DOI: 10.1002/adsc.200800354] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hartner FS, Ruth C, Langenegger D, Johnson SN, Hyka P, Lin-Cereghino GP, Lin-Cereghino J, Kovar K, Cregg JM, Glieder A. Promoter library designed for fine-tuned gene expression in Pichia pastoris. Nucleic Acids Res 2008; 36:e76. [PMID: 18539608 PMCID: PMC2475614 DOI: 10.1093/nar/gkn369] [Citation(s) in RCA: 219] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (PAOX1) sequence. This first library initially spanned an activity range between ∼6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing a green fluorescent protein (GFP) variant, the new regulatory toolbox was successfully utilized in a ‘real case’, i.e. the expression of industrial enzymes. Characterization of the library under repressing, derepressing and inducing conditions displayed at least 12 cis-acting elements involved in PAOX1-driven high-level expression. Based on this deletion analysis, novel short artificial promoter variants were constructed by combining cis-acting elements with basal promoter. In addition to improving yields and quality of heterologous protein production, the new PAOX1 synthetic promoter library constitutes a basic toolbox to fine-tune gene expression in metabolic engineering and sequential induction of protein expression in synthetic biology.
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Affiliation(s)
- Franz S Hartner
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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