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Hurt RC, Jin Z, Soufi M, Wong KK, Sawyer DP, Shen HK, Dutka P, Deshpande R, Zhang R, Mittelstein DR, Shapiro MG. Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening. bioRxiv 2024:2024.03.30.587094. [PMID: 38617214 PMCID: PMC11014471 DOI: 10.1101/2024.03.30.587094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation is ultrasound (US), with its penetration depth of several cm and spatial resolution on the order of 100 µm. 1 Within the past decade, reporter genes for US have been introduced 2,3 and engineered 4,5 to link cellular functions to US signals via heterologous expression in commensal bacteria and mammalian cells. These acoustic reporter genes (ARGs) represent a novel class of genetically encoded US contrast agent, and are based on air-filled protein nanostructures called gas vesicles (GVs). 6 Just as the discovery of fluorescent proteins was followed by the improvement and diversification of their optical properties through directed evolution, here we describe the evolution of GVs as acoustic reporters. To accomplish this task, we establish high-throughput, semi-automated acoustic screening of ARGs in bacterial cultures and use it to screen mutant libraries for variants with increased nonlinear US scattering. Starting with scanning site saturation libraries for two homologs of the primary GV structural protein, GvpA/B, two rounds of evolution resulted in GV variants with 5- and 14-fold stronger acoustic signals than the parent proteins. We anticipate that this and similar approaches will help high-throughput protein engineering play as large a role in the development of acoustic biomolecules as it has for their fluorescent counterparts.
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2
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Topaloğlu A, Esen Ö, Turanlı-Yıldız B, Arslan M, Çakar ZP. From Saccharomyces cerevisiae to Ethanol: Unlocking the Power of Evolutionary Engineering in Metabolic Engineering Applications. J Fungi (Basel) 2023; 9:984. [PMID: 37888240 PMCID: PMC10607480 DOI: 10.3390/jof9100984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. In parallel to the increased use of bioethanol in various fields such as transportation, heating and power generation, improvements in ethanol production processes turned out to be a global hot topic. Ethanol is by far the leading yeast output amongst a broad spectrum of bio-based industries. Thus, as a well-known platform microorganism and native ethanol producer, baker's yeast Saccharomyces cerevisiae has been the primary subject of interest for both academic and industrial perspectives in terms of enhanced ethanol production processes. Metabolic engineering strategies have been primarily adopted for direct manipulation of genes of interest responsible in mainstreams of ethanol metabolism. To overcome limitations of rational metabolic engineering, an alternative bottom-up strategy called inverse metabolic engineering has been widely used. In this context, evolutionary engineering, also known as adaptive laboratory evolution (ALE), which is based on random mutagenesis and systematic selection, is a powerful strategy to improve bioethanol production of S. cerevisiae. In this review, we focus on key examples of metabolic and evolutionary engineering for improved first- and second-generation S. cerevisiae bioethanol production processes. We delve into the current state of the field and show that metabolic and evolutionary engineering strategies are intertwined and many metabolically engineered strains for bioethanol production can be further improved by powerful evolutionary engineering strategies. We also discuss potential future directions that involve recent advancements in directed genome evolution, including CRISPR-Cas9 technology.
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Affiliation(s)
- Alican Topaloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Ömer Esen
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Burcu Turanlı-Yıldız
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Mevlüt Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Van Yüzüncü Yıl University, Van 65000, Türkiye;
| | - Zeynep Petek Çakar
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
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3
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Brkic A, Leibundgut M, Jablonska J, Zanki V, Car Z, Petrovic Perokovic V, Marsavelski A, Ban N, Gruic-Sovulj I. Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif. Nat Commun 2023; 14:5498. [PMID: 37679387 PMCID: PMC10485003 DOI: 10.1038/s41467-023-41244-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Antibiotics target key biological processes that include protein synthesis. Bacteria respond by developing resistance, which increases rapidly due to antibiotics overuse. Mupirocin, a clinically used natural antibiotic, inhibits isoleucyl-tRNA synthetase (IleRS), an enzyme that links isoleucine to its tRNAIle for protein synthesis. Two IleRSs, mupirocin-sensitive IleRS1 and resistant IleRS2, coexist in bacteria. The latter may also be found in resistant Staphylococcus aureus clinical isolates. Here, we describe the structural basis of mupirocin resistance and unravel a mechanism of hyper-resistance evolved by some IleRS2 proteins. We surprisingly find that an up to 103-fold increase in resistance originates from alteration of the HIGH motif, a signature motif of the class I aminoacyl-tRNA synthetases to which IleRSs belong. The structural analysis demonstrates how an altered HIGH motif could be adopted in IleRS2 but not IleRS1, providing insight into an elegant mechanism for coevolution of the key catalytic motif and associated antibiotic resistance.
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Affiliation(s)
- A Brkic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - M Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
| | - J Jablonska
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - V Zanki
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Z Car
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - V Petrovic Perokovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - A Marsavelski
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - N Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland.
| | - I Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia.
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4
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Ouyang B, Wang G, Zhang N, Zuo J, Huang Y, Zhao X. Recent Advances in β-Glucosidase Sequence and Structure Engineering: A Brief Review. Molecules 2023; 28:4990. [PMID: 37446652 DOI: 10.3390/molecules28134990] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
β-glucosidases (BGLs) play a crucial role in the degradation of lignocellulosic biomass as well as in industrial applications such as pharmaceuticals, foods, and flavors. However, the application of BGLs has been largely hindered by issues such as low enzyme activity, product inhibition, low stability, etc. Many approaches have been developed to engineer BGLs to improve these enzymatic characteristics to facilitate industrial production. In this article, we review the recent advances in BGL engineering in the field, including the efforts from our laboratory. We summarize and discuss the BGL engineering studies according to the targeted functions as well as the specific strategies used for BGL engineering.
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Affiliation(s)
- Bei Ouyang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Guoping Wang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Nian Zhang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Jiali Zuo
- School of Computer and Information Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Yunhong Huang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
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5
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Helleckes LM, Müller C, Griesbach T, Waffenschmidt V, Moch M, Osthege M, Wiechert W, Oldiges M. Explore or exploit? A model-based screening strategy for PETase secretion by Corynebacterium glutamicum. Biotechnol Bioeng 2023; 120:139-153. [PMID: 36225165 DOI: 10.1002/bit.28261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/29/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
Abstract
Extracellular production of target proteins simplifies downstream processing due to obsolete cell disruption. However, optimal combinations of a heterologous protein, suitable signal peptide, and secretion host can currently not be predicted, resulting in large strain libraries that need to be tested. On the experimental side, this challenge can be tackled by miniaturization, parallelization, and automation, which provide high-throughput screening data. These data need to be condensed into a candidate ranking for decision-making to focus bioprocess development on the most promising candidates. We screened for Bacillus subtilis signal peptides mediating Sec secretion of two polyethylene terephthalate degrading enzymes (PETases), leaf-branch compost cutinase (LCC) and polyester hydrolase mutants, by Corynebacterium glutamicum. We developed a fully automated screening process and constructed an accompanying Bayesian statistical modeling framework, which we applied in screenings for highest activity in 4-nitrophenyl palmitate degradation. In contrast to classical evaluation methods, batch effects and biological errors are taken into account and their uncertainty is quantified. Within only two rounds of screening, the most suitable signal peptide was identified for each PETase. Results from LCC secretion in microliter-scale cultivation were shown to be scalable to laboratory-scale bioreactors. This work demonstrates an experiment-modeling loop that can accelerate early-stage screening in a way that experimental capacities are focused to the most promising strain candidates. Combined with high-throughput cloning, this paves the way for using large strain libraries of several hundreds of strains in a Design-Build-Test-Learn approach.
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Affiliation(s)
- Laura M Helleckes
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Carolin Müller
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Tim Griesbach
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Vera Waffenschmidt
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Matthias Moch
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Michael Osthege
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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6
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Vega-Rodríguez MAD, Rodríguez-González JA, Armendáriz-Ruiz MA, Asaff-Torres A, Sotelo-Mundo RR, Velasco-Lozano S, Mateos-Díaz JC. Feruloyl Esterases Protein Engineering to Enhance Their Performance as Biocatalysts: A Review. Chembiochem 2022; 23:e202200354. [PMID: 35781918 DOI: 10.1002/cbic.202200354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/01/2022] [Indexed: 02/03/2023]
Abstract
Feruloyl esterases (FAEs) are versatile enzymes able to release hydroxycinnamic acids or synthesize their ester derivatives, both molecules with interesting biological activities such as: antioxidants, antifungals, antivirals, antifibrotic, anti-inflammatory, among others. The importance of these molecules in medicine, food or cosmetic industries provides FAEs with several biotechnological applications as key industrial biocatalysts. However, FAEs have some operational limitations that must be overcome, which can be addressed through different protein engineering approaches to enhance their thermal stability, catalytic efficiencies, and selectivity. This review aims to present a brief historical tour through the mutagenesis strategies employed to improve enzymes performance and analyze the current protein engineering strategies applied to FAEs as interesting biocatalysts. Finally, an outlook of the future of FAEs protein engineering approaches to achieve successful industrial biocatalysts is given.
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Affiliation(s)
- Ms Ana Daniela Vega-Rodríguez
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Camino Arenero No. 1227 Colonia El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | - Jorge Alberto Rodríguez-González
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Camino Arenero No. 1227 Colonia El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | | | - Ali Asaff-Torres
- Unidad de Biotecnología Industrial, Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a la Victoria Km 0.6, 83304, Hermosillo, Sonora, Mexico
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a la Victoria Km 0.6, 83304, Hermosillo, Sonora (Mexico
| | - Susana Velasco-Lozano
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Miramon Pasealekua, 182, 20014, Donostia, Spain
| | - Juan Carlos Mateos-Díaz
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Camino Arenero No. 1227 Colonia El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
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7
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Camus A, Truong G, Mittl PRE, Markert G, Hilvert D. Reprogramming Nonribosomal Peptide Synthetases for Site-Specific Insertion of α-Hydroxy Acids. J Am Chem Soc 2022; 144:17567-17575. [PMID: 36070491 DOI: 10.1021/jacs.2c07013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-throughput engineering has the potential to revolutionize the customization of biosynthetic assembly lines for the sustainable production of pharmaceutically relevant natural product analogs. Here, we show that the substrate specificity of gatekeeper adenylation domains of nonribosomal peptide synthetases can be switched from an α-amino acid to an α-hydroxy acid in a single round of combinatorial mutagenesis and selection using yeast cell surface display. In addition to shedding light on how such proteins discriminate between amino and hydroxy groups, the remodeled domains function in a pathway context to produce α-hydroxy acid-containing linear peptides and cyclic depsipeptides with high efficiency. Site-specific replacement of backbone amines with oxygens by an engineered synthetase provides the means to probe and tune the activities of diverse peptide metabolites in a simple and predictable fashion.
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Affiliation(s)
- Anna Camus
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zurich, Switzerland
| | - Gisèle Truong
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zurich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Greta Markert
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zurich, Switzerland
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8
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Linars A, Silamikelis I, Gudra D, Roga A, Fridmanis D. OverFlap PCR: A reliable approach for generating plasmid DNA libraries containing random sequences without a template bias. PLoS One 2022; 17:e0262968. [PMID: 35939421 PMCID: PMC9359533 DOI: 10.1371/journal.pone.0262968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022] Open
Abstract
Over the decades, practical biotechnology researchers have aimed to improve naturally occurring proteins and create novel ones. It is widely recognized that coupling protein sequence randomization with various effect screening methodologies is one of the most powerful techniques for quickly, efficiently, and purposefully acquiring these desired improvements. Over the years, considerable advancements have been made in this field. However, developing PCR-based or template-guided methodologies has been hampered by resultant template sequence biases. Here, we present a novel whole plasmid amplification-based approach, which we named OverFlap PCR, for randomizing virtually any region of plasmid DNA without introducing a template sequence bias.
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9
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Müller C, Bakkes PJ, Lenz P, Waffenschmidt V, Helleckes LM, Jaeger KE, Wiechert W, Knapp A, Freudl R, Oldiges M. Accelerated strain construction and characterization of C. glutamicum protein secretion by laboratory automation. Appl Microbiol Biotechnol 2022; 106:4481-4497. [PMID: 35759036 PMCID: PMC9259529 DOI: 10.1007/s00253-022-12017-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
Secretion of bacterial proteins into the culture medium simplifies downstream processing by avoiding cell disruption for target protein purification. However, a suitable signal peptide for efficient secretion needs to be identified, and currently, there are no tools available to predict optimal combinations of signal peptides and target proteins. The selection of such a combination is influenced by several factors, including protein biosynthesis efficiency and cultivation conditions, which both can have a significant impact on secretion performance. As a result, a large number of combinations must be tested. Therefore, we have developed automated workflows allowing for targeted strain construction and secretion screening using two platforms. Key advantages of this experimental setup include lowered hands-on time and increased throughput. In this study, the automated workflows were established for the heterologous production of Fusarium solani f. sp. pisi cutinase in Corynebacterium glutamicum. The target protein was monitored in culture supernatants via enzymatic activity and split GFP assay. Varying spacer lengths between the Shine-Dalgarno sequence and the start codon of Bacillus subtilis signal peptides were tested. Consistent with previous work on the secretory cutinase production in B. subtilis, a ribosome binding site with extended spacer length to up to 12 nt, which likely slows down translation initiation, does not necessarily lead to poorer cutinase secretion by C. glutamicum. The best performing signal peptides for cutinase secretion with a standard spacer length were identified in a signal peptide screening. Additional insights into the secretion process were gained by monitoring secretion stress using the C. glutamicum K9 biosensor strain. KEY POINTS: • Automated workflows for strain construction and screening of protein secretion • Comparison of spacer, signal peptide, and host combinations for cutinase secretion • Signal peptide screening for secretion by C. glutamicum using the split GFP assay.
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Affiliation(s)
- Carolin Müller
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Patrick J Bakkes
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Patrick Lenz
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Vera Waffenschmidt
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Laura M Helleckes
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52062, Aachen, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany.,Castrol Germany GmbH, 41179, Mönchengladbach, Germany
| | - Roland Freudl
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany.
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10
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Chen W, She W, Li A, Zhai C, Ma L. Site-Directed Mutagenesis Method Mediated by Cas9. Methods Mol Biol 2022; 2461:165-174. [PMID: 35727450 DOI: 10.1007/978-1-0716-2152-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
This study presents an in vitro CRISPR/Cas9-mediated mutagenic (ICM) system that allows rapid construction of designed mutants or site-saturation mutagenesis libraries in a PCR-independent manner. The plasmid DNA is double digested with Cas9 bearing specific single guide RNAs to remove the target nucleotides. Next, T5 exonuclease excises both 5'-ends of the linearized plasmid to generate homologous regions of approximately 15 nt. Subsequently, a short dsDNA of approximately 30-50 bp containing the desired mutation cyclizes the plasmid through base pairing and introduces the mutation into the plasmid. The gaps are repaired in Escherichia coli host cells after transformation. This method is highly efficient and accurate. Both single and multiple site-directed mutagenesis can be successfully performed, especially to large sized plasmids. This method demonstrates the great potential for creating high-quality mutant libraries in directed evolution as an alternative to PCR-based saturation mutagenesis, thus facilitating research on synthetic biology.
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Affiliation(s)
- Wanping Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Wenwen She
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China.
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, People's Republic of China.
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11
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Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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12
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Madhavan A, Arun KB, Binod P, Sirohi R, Tarafdar A, Reshmy R, Kumar Awasthi M, Sindhu R. Design of novel enzyme biocatalysts for industrial bioprocess: Harnessing the power of protein engineering, high throughput screening and synthetic biology. Bioresour Technol 2021; 325:124617. [PMID: 33450638 DOI: 10.1016/j.biortech.2020.124617] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 05/13/2023]
Abstract
Biocatalysts have wider applications in various industries. Biocatalysts are generating bigger attention among researchers due to their unique catalytic properties like activity, specificity and stability. However the industrial use of many enzymes is hindered by low catalytic efficiency and stability during industrial processes. Properties of enzymes can be altered by protein engineering. Protein engineers are increasingly study the structure-function characteristics, engineering attributes, design of computational tools for enzyme engineering, and functional screening processes to improve the design and applications of enzymes. The potent and innovative techniques of enzyme engineering deliver outstanding opportunities for tailoring industrially important enzymes for the versatile production of biochemicals. An overview of the current trends in enzyme engineering is explored with important representative examples.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India
| | - Ranjna Sirohi
- The Center for Energy and Environmental Sustainability, Lucknow 226 010, Uttar Pradesh, India
| | - Ayon Tarafdar
- Division of Livestock Production and Management, ICAR - Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West A & F University, Yangling, Shaanxi 712 100, China
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India.
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13
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Mahlich Y, Miller M, Zeng Z, Bromberg Y. Low Diversity of Human Variation Despite Mostly Mild Functional Impact of De Novo Variants. Front Mol Biosci 2021; 8:635382. [PMID: 33816556 PMCID: PMC8012514 DOI: 10.3389/fmolb.2021.635382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 01/07/2023] Open
Abstract
Non-synonymous Single Nucleotide Variants (nsSNVs), resulting in single amino acid variants (SAVs), are important drivers of evolutionary adaptation across the tree of life. Humans carry on average over 10,000 SAVs per individual genome, many of which likely have little to no impact on the function of the protein they affect. Experimental evidence for protein function changes as a result of SAVs remain sparse – a situation that can be somewhat alleviated by predicting their impact using computational methods. Here, we used SNAP to examine both observed and in silico generated human variation in a set of 1,265 proteins that are consistently found across a number of diverse species. The number of SAVs that are predicted to have any functional effect on these proteins is smaller than expected, suggesting sequence/function optimization over evolutionary timescales. Additionally, we find that only a few of the yet-unobserved SAVs could drastically change the function of these proteins, while nearly a quarter would have only a mild functional effect. We observed that variants common in the human population localized to less conserved protein positions and carried mild to moderate functional effects more frequently than rare variants. As expected, rare variants carried severe effects more frequently than common variants. In line with current assumptions, we demonstrated that the change of the human reference sequence amino acid to the reference of another species (a cross-species variant) is unlikely to significantly impact protein function. However, we also observed that many cross-species variants may be weakly non-neutral for the purposes of quick adaptation to environmental changes, but may not be identified as such by current state-of-the-art methodology.
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Affiliation(s)
- Yannick Mahlich
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Maximillian Miller
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Zishuo Zeng
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States.,Department of Genetics, Rutgers University, Piscataway, NJ, United States
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14
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Hou Q, Li N, Chao Y, Li S, Zhang L. Design and regulation of the surface and interfacial behavior of protein molecules. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Banerjee S, Mitra D. Structural Basis of Design and Engineering for Advanced Plant Optogenetics. Trends Plant Sci 2020; 25:35-65. [PMID: 31699521 DOI: 10.1016/j.tplants.2019.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.
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Affiliation(s)
- Sudakshina Banerjee
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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16
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Abstract
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
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Affiliation(s)
| | - Tomaž Bratkovič
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, SI-1000 Ljubljana, Slovenia;
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17
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Affiliation(s)
- Ratul Chowdhury
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania
| | - Costas D. Maranas
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania
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18
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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19
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She W, Ni J, Shui K, Wang F, He R, Xue J, Reetz MT, Li A, Ma L. Rapid and Error-Free Site-Directed Mutagenesis by a PCR-Free In Vitro CRISPR/Cas9-Mediated Mutagenic System. ACS Synth Biol 2018; 7:2236-2244. [PMID: 30075075 DOI: 10.1021/acssynbio.8b00245] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The quality and efficiency of any PCR-based mutagenesis technique may not be optimal due to, among other things, amino acid bias, which means that the development of efficient PCR-free methods is desirable. Here, we present a highly efficient in vitro CRISPR/Cas9-mediated mutagenic (ICM) system that allows rapid construction of designed mutants in a PCR-free manner. First, it involves plasmid digestion by utilizing a complex of Cas9 with specific single guide RNA (sgRNA) followed by degradation with T5 exonuclease to generate a 15 nt homologous region. Second, primers containing the desired mutations are annealed to form the double-stranded DNA fragments, which are then ligated into the linearized plasmid. In theory, neither the size of the target plasmid nor the unavailable restriction enzyme site poses any problems that may arise in traditional techniques. In this study, single and multiple site-directed mutagenesis were successfully performed even for a large size plasmid (up to 9.0 kb). Moreover, a PCR-free site-saturation mutagenesis library on single site and two adjacent sites of a green fluorescent protein was also generated with promising results. This demonstrates the great potential of the ICM system for creating high-quality mutant libraries in directed evolution as an alternative to PCR-based saturation mutagenesis, thus facilitating research on synthetic biology.
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Affiliation(s)
- Wenwen She
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Jing Ni
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fei Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Ruyi He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Jinhui Xue
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
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20
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21
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Abstract
Directed evolution is a powerful technique for generating tailor-made enzymes for a wide range of biocatalytic applications. Following the principles of natural evolution, iterative cycles of mutagenesis and screening or selection are applied to modify protein properties, enhance catalytic activities, or develop completely new protein catalysts for non-natural chemical transformations. This review briefly surveys the experimental methods used to generate genetic diversity and screen or select for improved enzyme variants. Emphasis is placed on a key challenge, namely how to generate novel catalytic activities that expand the scope of natural reactions. Two particularly effective strategies, exploiting catalytic promiscuity and rational design, are illustrated by representative examples of successfully evolved enzymes. Opportunities for extending these approaches to more complex biocatalytic systems are also considered.
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Affiliation(s)
- Cathleen Zeymer
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland;,
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland;,
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22
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Sadler JC, Green L, Swainston N, Kell DB, Currin A. Fast and Flexible Synthesis of Combinatorial Libraries for Directed Evolution. Methods Enzymol 2018; 608:59-79. [PMID: 30173773 DOI: 10.1016/bs.mie.2018.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Directed evolution (DE) is a powerful tool for optimizing an enzyme's properties toward a particular objective, such as broader substrate scope, greater thermostability, or increased kcat. A successful DE project requires the generation of genetic diversity and subsequent screening or selection to identify variants with improved fitness. In contrast to random methods (error-prone PCR or DNA shuffling), site-directed mutagenesis enables the rational design of variant libraries and provides control over the nature and frequency of the encoded mutations. Knowledge of protein structure, dynamics, enzyme mechanisms, and natural evolution demonstrates that multiple (combinatorial) mutations are required to discover the most improved variants. To this end, we describe an experimentally straightforward and low-cost method for the preparation of combinatorial variant libraries. Our approach employs a two-step PCR protocol, first producing mutagenic megaprimers, which can then be combined in a "mix-and-match" fashion to generate diverse sets of combinatorial variant libraries both quickly and accurately.
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23
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Li A, Acevedo-Rocha CG, Reetz MT. Boosting the efficiency of site-saturation mutagenesis for a difficult-to-randomize gene by a two-step PCR strategy. Appl Microbiol Biotechnol 2018; 102:6095-6103. [PMID: 29785500 PMCID: PMC6013526 DOI: 10.1007/s00253-018-9041-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/13/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022]
Abstract
Site-saturation mutagenesis (SSM) has been used in directed evolution of proteins for a long time. As a special form of saturation mutagenesis, it involves individual randomization at a given residue with formation of all 19 amino acids. To date, the most efficient embodiment of SSM is a one-step PCR-based approach using NNK codon degeneracy. However, in the case of difficult-to-randomize genes, SSM may not deliver all of the expected 19 mutants, which compels the user to invest further efforts by applying site-directed mutagenesis for the construction of the missing mutants. To solve this problem, we developed a two-step PCR-based technique in which a mutagenic primer and a non-mutagenic (silent) primer are used to generate a short DNA fragment, which is recovered and then employed as a megaprimer to amplify the whole plasmid. The present two-step and older one-step (partially overlapped primer approach) procedures were compared by utilizing cytochrome P450-BM3, which is a "difficult-to-randomize" gene. The results document the distinct superiority of the new method by checking the library quality on DNA level based on massive sequence data, but also at amino acid level. Various future applications in biotechnology can be expected, including the utilization when constructing mutability landscapes, which provide semi-rational information for identifying hot spots for protein engineering and directed evolution.
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Affiliation(s)
- Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Muelheim, Germany.,Department of Chemistry, Philipps-Universität, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | | | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Muelheim, Germany. .,Department of Chemistry, Philipps-Universität, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany.
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24
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Abstract
Saturation mutagenesis is conveniently located between the two extremes of protein engineering, namely random mutagenesis, and rational design. It involves mutating a confined number of target residues to other amino acids, and hence requires knowledge regarding the sites for mutagenesis, but not their final identity. There are many different strategies for performing and designing such experiments, ranging from simple single degenerate codons to codon collections that code for distinct sets of amino acids. Here, we provide detailed information on the Dynamic Management for Codon Compression (DYNAMCC) approaches that allow us to precisely define the desired amino acid composition to be introduced to a specific target site. DYNAMCC allows us to set usage thresholds and to eliminate undesirable stop and wild-type codons, thus allowing us to control library size and subsequently downstream screening efforts. The DYNAMCC algorithms are free of charge and are implemented in a website for easy access and usage: www.dynamcc.com .
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Affiliation(s)
- Gur Pines
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA. .,Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA.,Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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25
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Bratulic S, Badran AH. Modern methods for laboratory diversification of biomolecules. Curr Opin Chem Biol 2017; 41:50-60. [PMID: 29096324 PMCID: PMC6062405 DOI: 10.1016/j.cbpa.2017.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/03/2017] [Accepted: 10/08/2017] [Indexed: 11/29/2022]
Abstract
Genetic variation fuels Darwinian evolution, yet spontaneous mutation rates are maintained at low levels to ensure cellular viability. Low mutation rates preclude the exhaustive exploration of sequence space for protein evolution and genome engineering applications, prompting scientists to develop methods for efficient and targeted diversification of nucleic acid sequences. Directed evolution of biomolecules relies upon the generation of unbiased genetic diversity to discover variants with desirable properties, whereas genome-engineering applications require selective modifications on a genomic scale with minimal off-targets. Here, we review the current toolkit of mutagenesis strategies employed in directed evolution and genome engineering. These state-of-the-art methods enable facile modifications and improvements of single genes, multicomponent pathways, and whole genomes for basic and applied research, while simultaneously paving the way for genome editing therapeutic interventions.
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Affiliation(s)
- Sinisa Bratulic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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26
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Abstract
Beyond the natural proteome, high-throughput mutagenesis offers the protein engineer an opportunity to "tweak" the wild-type activity of a protein to create a recombinant protein with required attributes. Of the various approaches available, saturation mutagenesis is one of the core techniques employed by protein engineers, and in recent times, nondegenerate saturation mutagenesis is emerging as the approach of choice. This review compares the current methodologies available for conducting nondegenerate saturation mutagenesis with traditional, degenerate saturation and briefly outlines the options available for screening the resulting libraries, to discover a novel protein with the required activity and/or specificity.
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Affiliation(s)
- M M Ferreira Amaral
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom
| | - L Frigotto
- Isogenica Ltd., The Mansion, Chesterford Research Park, Essex, United Kingdom
| | - A V Hine
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom.
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27
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28
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Abstract
Directed evolution has proved to be an effective strategy for improving or altering the activity of biomolecules for industrial, research and therapeutic applications. The evolution of proteins in the laboratory requires methods for generating genetic diversity and for identifying protein variants with desired properties. This Review describes some of the tools used to diversify genes, as well as informative examples of screening and selection methods that identify or isolate evolved proteins. We highlight recent cases in which directed evolution generated enzymatic activities and substrate specificities not known to exist in nature.
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Affiliation(s)
- Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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29
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Saeed S, Jowitt TA, Warwicker J, Hayes F. Breaking and restoring the hydrophobic core of a centromere-binding protein. J Biol Chem 2015; 290:9273-83. [PMID: 25713077 DOI: 10.1074/jbc.m115.638148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Indexed: 11/06/2022] Open
Abstract
The ribbon-helix-helix (RHH) superfamily of DNA-binding proteins is dispersed widely in procaryotes. The dimeric RHH fold is generated by interlocking of two monomers into a 2-fold symmetrical structure that comprises four α-helices enwrapping a pair of antiparallel β-strands (ribbon). Residues in the ribbon region are the principal determinants of DNA binding, whereas the RHH hydrophobic core is assembled from amino acids in both the α-helices and ribbon element. The ParG protein encoded by multiresistance plasmid TP228 is a RHH protein that functions dually as a centromere binding factor during segrosome assembly and as a transcriptional repressor. Here we identify residues in the α-helices of ParG that are critical for DNA segregation and in organization of the protein hydrophobic core. A key hydrophobic aromatic amino acid at one position was functionally substitutable by other aromatic residues, but not by non-aromatic hydrophobic amino acids. Nevertheless, intramolecular suppression of the latter by complementary change of a residue that approaches nearby from the partner monomer fully restored activity in vivo and in vitro. The interactions involved in assembling the ParG core may be highly malleable and suggest that RHH proteins are tractable platforms for the rational design of diverse DNA binding factors useful for synthetic biology and other purposes.
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Affiliation(s)
- Sadia Saeed
- From the Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Thomas A Jowitt
- From the Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Jim Warwicker
- From the Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Finbarr Hayes
- From the Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
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30
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31
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Ramesh S, Cherkupally P, Govender T, Kruger HG, Albericio F, de la Torre BG. Chemical Platforms for Peptide Vaccine Constructs. Peptide and Protein Vaccines. Elsevier; 2015. pp. 99-130. [DOI: 10.1016/bs.apcsb.2015.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register]
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32
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Gajula KS, Huwe PJ, Mo CY, Crawford DJ, Stivers JT, Radhakrishnan R, Kohli RM. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase. Nucleic Acids Res 2014; 42:9964-75. [PMID: 25064858 PMCID: PMC4150791 DOI: 10.1093/nar/gku689] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Antibody maturation is a critical immune process governed by the enzyme activation-induced deaminase (AID), a member of the AID/APOBEC DNA deaminase family. AID/APOBEC deaminases preferentially target cytosine within distinct preferred sequence motifs in DNA, with specificity largely conferred by a small 9–11 residue protein loop that differs among family members. Here, we aimed to determine the key functional characteristics of this protein loop in AID and to thereby inform our understanding of the mode of DNA engagement. To this end, we developed a methodology (Sat-Sel-Seq) that couples saturation mutagenesis at each position across the targeting loop, with iterative functional selection and next-generation sequencing. This high-throughput mutational analysis revealed dominant characteristics for residues within the loop and additionally yielded enzymatic variants that enhance deaminase activity. To rationalize these functional requirements, we performed molecular dynamics simulations that suggest that AID and its hyperactive variants can engage DNA in multiple specific modes. These findings align with AID's competing requirements for specificity and flexibility to efficiently drive antibody maturation. Beyond insights into the AID-DNA interface, our Sat-Sel-Seq approach also serves to further expand the repertoire of techniques for deep positional scanning and may find general utility for high-throughput analysis of protein function.
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Affiliation(s)
- Kiran S Gajula
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter J Huwe
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlie Y Mo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Crawford
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Meng F, Chen C, Li Y, Wan H, Zhou Q. [A highly efficient in vitro site-directed mutagenesis protocol for introducing multiple-site mutations into target genes]. Zhongguo Fei Ai Za Zhi 2014; 17:469-73. [PMID: 24949687 PMCID: PMC6000103 DOI: 10.3779/j.issn.1009-3419.2014.06.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
背景与目的 在基因序列中引入点突变是研究基因结构和功能及其相关性的重要手段。目前已有多种对基因序列进行突变的方法,然而,这些方法大多对单一位置的基因突变有效,而对在基因序列中引入多位点突变,还有待方法的进一步改进。为适应这一需要,本研究提供了一种高效的可在基因序列的多个位点引入突变的方法。 方法 该方法依赖于一种Type Ⅱs类的限制性内切酶,例如Esp 3I等。本研究所提供的方法中,针对每一个突变位点,合成一对含有突变点和所选择的Type Ⅱs类的限制性内切酶位点的引物,当需要引入多位点突变时,则利用邻近的两个突变位点的引物做PCR反应,多个位点的突变,就可以得到多个扩增片段,将这些片段用和引物上的限制性内切酶位点对应的酶进行反应,然后用连接反应将片段连接形成突变基因。 结果 本研究所提供的方法非常简便,主要实验步骤可以在一天之内完成。我们已经利用这种方法,在绿色荧光蛋白(enhanced green fluorecence protein, EGFP)和nm23基因中,引入3个或4个突变,突变效率几乎为100%。 结论 本研究所提供的方法可以成为研究基因功能的有用工具。
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Affiliation(s)
- Fanrong Meng
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chen Chen
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yongwen Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Haisu Wan
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qinghua Zhou
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
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Singh SK, Heng C, Braker JD, Chan VJ, Lee CC, Jordan DB, Yuan L, Wagschal K. Directed evolution of GH43 β-xylosidase XylBH43 thermal stability and L186 saturation mutagenesis. J Ind Microbiol Biotechnol 2013; 41:489-98. [PMID: 24292973 DOI: 10.1007/s10295-013-1377-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 10/24/2013] [Indexed: 11/28/2022]
Abstract
Directed evolution of β-xylosidase XylBH43 using a single round of gene shuffling identified three mutations, R45K, M69P, and L186Y, that affect thermal stability parameter K(t)⁰·⁵ by -1.8 ± 0.1, 1.7 ± 0.3, and 3.2 ± 0.4 °C, respectively. In addition, a cluster of four mutations near hairpin loop-D83 improved K(t)⁰·⁵ by ~3 °C; none of the individual amino acid changes measurably affect K(t)⁰·⁵. Saturation mutagenesis of L186 identified the variant L186K as having the most improved K(t)⁰·⁵ value, by 8.1 ± 0.3 °C. The L186Y mutation was found to be additive, resulting in K(t)⁰·⁵ increasing by up to 8.8 ± 0.3 °C when several beneficial mutations were combined. While k cat of xylobiose and 4-nitrophenyl-β-D-xylopyranoside were found to be depressed from 8 to 83 % in the thermally improved mutants, K(m), K(ss) (substrate inhibition), and K(i) (product inhibition) values generally increased, resulting in lessened substrate and xylose inhibition.
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Affiliation(s)
- Sanjay K Singh
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
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Kille S, Acevedo-Rocha CG, Parra LP, Zhang ZG, Opperman DJ, Reetz MT, Acevedo JP. Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis. ACS Synth Biol 2013; 2:83-92. [PMID: 23656371 DOI: 10.1021/sb300037w] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Saturation mutagenesis probes define sections of the vast protein sequence space. However, even if randomization is limited this way, the combinatorial numbers problem is severe. Because diversity is created at the codon level, codon redundancy is a crucial factor determining the necessary effort for library screening. Additionally, due to the probabilistic nature of the sampling process, oversampling is required to ensure library completeness as well as a high probability to encounter all unique variants. Our trick employs a special mixture of three primers, creating a degeneracy of 22 unique codons coding for the 20 canonical amino acids. Therefore, codon redundancy and subsequent screening effort is significantly reduced, and a balanced distribution of codon per amino acid is achieved, as demonstrated exemplarily for a library of cyclohexanone monooxygenase. We show that this strategy is suitable for any saturation mutagenesis methodology to generate less-redundant libraries.
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Affiliation(s)
- Sabrina Kille
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Loreto P. Parra
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Zhi-Gang Zhang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Diederik J. Opperman
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1,
45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße,
35043 Marburg, Germany
| | - Juan Pablo Acevedo
- Facultad
de Medicina y Facultad
de Ingeniería de la Universidad de los Andes, Santiago, Chile
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Reetz MT. The Importance of Additive and Non-Additive Mutational Effects in Protein Engineering. Angew Chem Int Ed Engl 2013; 52:2658-66. [DOI: 10.1002/anie.201207842] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/19/2012] [Indexed: 01/01/2023]
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Bordes F, Tarquis L, Nicaud JM, Marty A. Isolation of a thermostable variant of Lip2 lipase from Yarrowia lipolytica by directed evolution and deeper insight into the denaturation mechanisms involved. J Biotechnol 2011; 156:117-24. [DOI: 10.1016/j.jbiotec.2011.06.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 06/22/2011] [Accepted: 06/29/2011] [Indexed: 10/18/2022]
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Wan H, Li Y, Fan Y, Meng F, Chen C, Zhou Q. A site-directed mutagenesis method particularly useful for creating otherwise difficult-to-make mutants and alanine scanning. Anal Biochem 2011; 420:163-70. [PMID: 22001375 DOI: 10.1016/j.ab.2011.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/16/2011] [Accepted: 09/17/2011] [Indexed: 11/26/2022]
Abstract
Site-directed mutagenesis has become routine in molecular biology. However, many mutants can still be very difficult to create. Complicated chimerical mutations, tandem repeats, inverted sequences, GC-rich regions, and/or heavy secondary structures can cause inefficient or incorrect binding of the mutagenic primer to the target sequence and affect the subsequent amplification. In theory, these problems can be avoided by introducing the mutations into the target sequence using mutagenic fragments and so removing the need for primer-template annealing. The cassette mutagenesis uses the mutagenic fragment in its protocol; however, in most cases it needs to perform two rounds of mutagenic primer-based mutagenesis to introduce suitable restriction enzyme sites into templates and is not suitable for routine mutagenesis. Here we describe a highly efficient method in which the template except the region to be mutated is amplified by polymerase chain reaction (PCR) and the type IIs restriction enzyme-digested PCR product is directly ligated with the mutagenic fragment. Our method requires no assistance of mutagenic primers. We have used this method to create various types of difficult-to-make mutants with mutagenic frequencies of nearly 100%. Our protocol has many advantages over the prevalent QuikChange method and is a valuable tool for studies on gene structure and function.
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Affiliation(s)
- Haisu Wan
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, People's Republic of China
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Gumulya Y, Reetz MT. Enhancing the Thermal Robustness of an Enzyme by Directed Evolution: Least Favorable Starting Points and Inferior Mutants Can Map Superior Evolutionary Pathways. Chembiochem 2011; 12:2502-10. [DOI: 10.1002/cbic.201100412] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Indexed: 12/22/2022]
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Estell DA, Graycar TP, Miller JV, Powers DB, Wells JA, Burnier JP, Ng PG. Probing steric and hydrophobic effects on enzyme-substrate interactions by protein engineering. Science 2010; 233:659-63. [PMID: 17835820 DOI: 10.1126/science.233.4764.659] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Steric and hydrophobic effects on substrate specificity were probed by protein engineering of subtilisin. Subtilisin has broad peptidase specificity and contains a large hydrophobic substrate binding cleft. A conserved glycine (Gly(166)), located at the bottom of the substrate binding left, was replaced by 12 nonionic amino acids by the cassette mutagenesis method. Mutant enzymes showed large changes in specificity toward substrates of increasing size and hydrophobicity. In general, the catalytic efficiency (k(cat)/K(m)) toward small hydrophobic substrates was increased (up to 16 times) by hydrophobic substitutions at position 166 in the binding cleft. Exceeding the optimal binding volume of the cleft ( approximately 160 A(3)), by enlarging either the substrate side chain or the side chain at position 166, evoked precipitous drops in catalytic efficiency (k(cat)/K(m)) (up to 5000 times) as a result of steric hindrance.
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Jarjour J, West-Foyle H, Certo MT, Hubert CG, Doyle L, Getz MM, Stoddard BL, Scharenberg AM. High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display. Nucleic Acids Res 2009; 37:6871-80. [PMID: 19740766 PMCID: PMC2777416 DOI: 10.1093/nar/gkp726] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Experimental analysis and manipulation of protein–DNA interactions pose unique biophysical challenges arising from the structural and chemical homogeneity of DNA polymers. We report the use of yeast surface display for analytical and selection-based applications for the interaction between a LAGLIDADG homing endonuclease and its DNA target. Quantitative flow cytometry using oligonucleotide substrates facilitated a complete profiling of specificity, both for DNA-binding and catalysis, with single base pair resolution. These analyses revealed a comprehensive segregation of binding specificity and affinity to one half of the pseudo-dimeric interaction, while the entire interface contributed specificity at the level of catalysis. A single round of targeted mutagenesis with tandem affinity and catalytic selection steps provided mechanistic insights to the origins of binding and catalytic specificity. These methods represent a dynamic new approach for interrogating specificity in protein–DNA interactions.
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Affiliation(s)
- Jordan Jarjour
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
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Abstract
Current approaches to protein site-directed mutagenesis require an independent user operation for each mutation. This can impede large-scale scanning mutagenesis projects such as the mapping of protein interaction surfaces, active sites, or epitopes. It also prevents the creation of protein libraries of defined complexity for directed evolution purposes. Here we present a simple, fast, and effective way to perform scanning codon mutagenesis throughout a protein sequence. The process allows the researcher to define the new codon change, and therefore any amino acid mutation can be achieved. We demonstrate this approach by creating a library of proteins that contain single unnatural amino acid mutations encoded by the amber stop codon, TAG. The mutant proteins generated by this method can be expressed and assayed individually or used together as a mixed population of "rationally diversified" protein sequences.
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Affiliation(s)
- Kelly A. Daggett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Mark Layer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - T. Ashton Cropp
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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Abstract
Iterative saturation mutagenesis (ISM) is a new and efficient method for the directed evolution of functional enzymes. It reduces the necessary molecular biological work and the screening effort drastically. It is based on a Cartesian view of the protein structure, performing iterative cycles of saturation mutagenesis at rationally chosen sites in an enzyme, a given site being composed of one, two or three amino acid positions. The basis for choosing these sites depends on the nature of the catalytic property to be improved, e.g., enantioselectivity, substrate acceptance or thermostability. In the case of thermostability, sites showing highest B-factors (available from X-ray data) are chosen. The pronounced increase in thermostability of the lipase from Bacillus subtilis (Lip A) as a result of applying ISM is illustrated here.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany.
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Reetz MT, Carballeira JD, Peyralans J, Höbenreich H, Maichele A, Vogel A. Expanding the substrate scope of enzymes: combining mutations obtained by CASTing. Chemistry 2007; 12:6031-8. [PMID: 16789057 DOI: 10.1002/chem.200600459] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In a previous paper, the combinatorial active-site saturation test (CAST) was introduced as an effective strategy for the directed evolution of enzymes toward broader substrate acceptance. CASTing comprises the systematic design and screening of focused libraries around the complete binding pocket, but it is only the first step of an evolutionary process because only the initial libraries of mutants are considered. In the present study, a simple method is presented for further optimization of initial hits by combining the mutational changes obtained from two different libraries. Combined lipase mutants were screened for hydrolytic activity against six notoriously difficult substrates (bulky carboxylic acid esters) and improved mutants showing significantly higher activity were identified. The enantioselectivity of the mutants in the hydrolytic kinetic resolution of two substrates was also studied, with the best mutant-substrate combination resulting in a selectivity factor of E=49. Finally, the catalytic profile of the evolved mutants in the hydrolysis of simple nonbranched carboxylic acid esters, ranging from acetate to palmitate, was studied for theoretical reasons.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany.
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Aravindhan V, Narayanan S, Gautham N, Prasad V, Kannan P, Jacobs WR, Narayanan P. T-h-2 immunity and CD3+CD45RBlow-activated T cells in mice immunized with recombinant bacillus CalmetteâGuérin expressing HIV-1 principal neutralizing determinant epitope. ACTA ACUST UNITED AC 2006; 47:45-55. [PMID: 16706787 DOI: 10.1111/j.1574-695x.2006.00061.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The genetic engineering of Mycobacterium bovis-bacillus Calmette-Guérin to express foreign epitopes is an attractive strategy in the field of epitope vaccines. We constructed an 'epitope-trap vector' with Mycobacterium tuberculosis chaperonin-10 as a carrier antigen and used it to express the HIV-1 principal neutralizing determinant epitope. We also identified a new chaperonin-10 promoter that was hyperexpressive compared with the heat shock protein-65 promoter. Splenocytes from recombinant bacillus Calmette-Guérin-immunized mice showed enhanced lymphocyte proliferation and interleukin-4 (but not interferon-gamma) secretion. The recombinant bacillus Calmette-Guérin-immunized group also exhibited mild delayed-type hypersensitivity reaction and a high frequency of CD3+CD45RBlow-activated T cells, together with high titer of antiprincipal neutralizing determinant immunoglobulin G antibodies. Thus, this epitope delivery system induced strong epitope-specific T-h-2 polarization.
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Reetz MT, Wang LW, Bocola M. Directed Evolution of Enantioselective Enzymes: Iterative Cycles of CASTing for Probing Protein-Sequence Space. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502746] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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