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Choe K, Sweedler JV. Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies. Bio Protoc 2023; 13:e4862. [PMID: 37969752 PMCID: PMC10632168 DOI: 10.21769/bioprotoc.4862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 11/17/2023] Open
Abstract
High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries. Key features • Mass spectrometry analyzes a range of compounds from E. coli colonies as a proxy for liquid culture testing enzyme mutant libraries. • Colonies are transferred to a MALDI target plate by a simple imprinting method. • The screen compares the ratio among several products or searches for the qualitative presence of specific compounds. • The protocol requires a MALDI mass spectrometer.
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Affiliation(s)
- Kisurb Choe
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Li SF, Cheng F, Wang YJ, Zheng YG. Strategies for tailoring pH performances of glycoside hydrolases. Crit Rev Biotechnol 2023; 43:121-141. [PMID: 34865578 DOI: 10.1080/07388551.2021.2004084] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Glycoside hydrolases (GHs) exhibit high activity and stability under harsh conditions, such as high temperatures and extreme pHs, given their wide use in industrial biotechnology. However, strategies for improving the acidophilic and alkalophilic adaptations of GHs are poorly summarized due to the complexity of the mechanisms of these adaptations. This review not only highlights the adaptation mechanisms of acidophilic and alkalophilic GHs under extreme pH conditions, but also summarizes the recent advances in engineering the pH performances of GHs with a focus on four strategies of protein engineering, enzyme immobilization, chemical modification, and medium engineering (additives). The examples described here summarize the methods used in modulating the pH performances of GHs and indicate that methods integrated in different protein engineering techniques or methods are efficient to generate industrial biocatalysts with the desired pH performance and other adapted enzyme properties.
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Affiliation(s)
- Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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Gargiulo S, Soumillion P. Directed evolution for enzyme development in biocatalysis. Curr Opin Chem Biol 2020; 61:107-113. [PMID: 33385931 DOI: 10.1016/j.cbpa.2020.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
As an important sector of the chemical industry, biocatalysis requires the continuous development of enzymes with tailor-made activity, selectivity, stability, or tolerance to unnatural environments. This is now routinely achieved by directed evolution based on iterative cycles of genetic diversification and activity screening. Here, we highlight its recent developments. First, the design of "smarter" libraries by focused mutagenesis may be a crucial start-up for a fast and successful outcome. Then library assembly and expression are also key steps that benefits from modern molecular biology progresses. Finally, various strategies may be considered for library screening depending on the final objective: while low-throughput direct assays have been very successful in generating enzymes for important biocatalytic processes, even in bringing completely new chemistries to the enzyme world, ultrahigh-throughput screening methods are emerging as powerful approaches for engineering the next generation of industrial enzymes.
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Affiliation(s)
- Serena Gargiulo
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium.
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Dadwal A, Sharma S, Satyanarayana T. Progress in Ameliorating Beneficial Characteristics of Microbial Cellulases by Genetic Engineering Approaches for Cellulose Saccharification. Front Microbiol 2020; 11:1387. [PMID: 32670240 PMCID: PMC7327088 DOI: 10.3389/fmicb.2020.01387] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/29/2020] [Indexed: 12/15/2022] Open
Abstract
Lignocellulosic biomass is a renewable and sustainable energy source. Cellulases are the enzymes that cleave β-1, 4-glycosidic linkages in cellulose to liberate sugars that can be fermented to ethanol, butanol, and other products. Low enzyme activity and yield, and thermostability are, however, some of the limitations posing hurdles in saccharification of lignocellulosic residues. Recent advancements in synthetic and systems biology have generated immense interest in metabolic and genetic engineering that has led to the development of sustainable technology for saccharification of lignocellulosics in the last couple of decades. There have been several attempts in applying genetic engineering in the production of a repertoire of cellulases at a low cost with a high biomass saccharification. A diverse range of cellulases are produced by different microbes, some of which are being engineered to evolve robust cellulases. This review summarizes various successful genetic engineering strategies employed for improving cellulase kinetics and cellulolytic efficiency.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
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Dedisch S, Wiens A, Davari MD, Söder D, Rodriguez‐Emmenegger C, Jakob F, Schwaneberg U. Matter‐
tag
: A universal immobilization platform for enzymes on polymers, metals, and silicon‐based materials. Biotechnol Bioeng 2019; 117:49-61. [DOI: 10.1002/bit.27181] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Sarah Dedisch
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
| | - Annika Wiens
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
| | - Dominik Söder
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
| | - Cesar Rodriguez‐Emmenegger
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityAachen Germany
| | - Felix Jakob
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
| | - Ulrich Schwaneberg
- DWI – Leibniz‐Institute for Interactive MaterialsAachen Germany
- Lehrstuhl für BiotechnologieRWTH Aachen UniversityAachen Germany
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Herrmann KR, Ruff AJ, Infanzón B, Schwaneberg U. Engineered phytases for emerging biotechnological applications beyond animal feeding. Appl Microbiol Biotechnol 2019; 103:6435-6448. [DOI: 10.1007/s00253-019-09962-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 12/26/2022]
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