1
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Yao Z, Jeon HS, Yoo JY, Kang YJ, Kim MJ, Kim TJ, Kim JH. DNA Shuffling of aprE Genes to Increase Fibrinolytic Activity and Thermostability. J Microbiol Biotechnol 2022; 32:800-807. [PMID: 35484964 PMCID: PMC9628911 DOI: 10.4014/jmb.2202.02017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022]
Abstract
Four aprE genes encoding alkaline serine proteases from B. subtilis strains were used as template genes for family gene shuffling. Shuffled genes obtained by DNase I digestion followed by consecutive primerless and regular PCR reactions were ligated with pHY300PLK, an E. coli-Bacillus shuttle vector. The ligation mixture was introduced into B. subtilis WB600 and one transformant (FSM4) showed higher fibrinolytic activity. DNA sequencing confirmed that the shuffled gene (aprEFSM4) consisted of DNA mostly originated from either aprEJS2 or aprE176 in addition to some DNA from either aprE3-5 or aprESJ4. Mature AprEFSM4 (275 amino acids) was different from mature AprEJS2 in 4 amino acids and mature AprE176 in 2 amino acids. aprEFSM4 was overexpressed in E. coli BL21 (DE3) by using pET26b(+) and recombinant AprEFSM4 was purified. The optimal temperature and pH of AprEFSM4 were similar to those of parental enzymes. However, AprEFM4 showed better thermostability and fibrinogen hydrolytic activity than the parental enzymes. The results indicated that DNA shuffling could be used to improve fibrinolytic enzymes from Bacillus sp. for industrial applications.
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Affiliation(s)
- Zhuang Yao
- Division of Applied Life Science (BK21 4), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hye Sung Jeon
- Division of Applied Life Science (BK21 4), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ji Yeon Yoo
- Division of Applied Life Science (BK21 4), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yun Ji Kang
- Division of Applied Life Science (BK21 4), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Min Jae Kim
- Division of Applied Life Science (BK21 4), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Tae Jin Kim
- Division of Applied Life Science (BK21 4), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jeong Hwan Kim
- Division of Applied Life Science (BK21 4), Graduate School, Gyeongsang National University, Jinju 52828, Republic of Korea,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea,Corresponding author Phone: +82-55-772-1904 Fax: +82-55-772-1909 E-mail:
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2
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Sankara Narayanan P, Runthala A. Accurate computational evolution of proteins and its dependence on deep learning and machine learning strategies. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2030317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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3
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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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4
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Heckmann CM, Paradisi F. Looking Back: A Short History of the Discovery of Enzymes and How They Became Powerful Chemical Tools. ChemCatChem 2020; 12:6082-6102. [PMID: 33381242 PMCID: PMC7756376 DOI: 10.1002/cctc.202001107] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/02/2020] [Indexed: 12/20/2022]
Abstract
Enzymatic approaches to challenges in chemical synthesis are increasingly popular and very attractive to industry given their green nature and high efficiency compared to traditional methods. In this historical review we highlight the developments across several fields that were necessary to create the modern field of biocatalysis, with enzyme engineering and directed evolution at its core. We exemplify the modular, incremental, and highly unpredictable nature of scientific discovery, driven by curiosity, and showcase the resulting examples of cutting-edge enzymatic applications in industry.
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Affiliation(s)
- Christian M Heckmann
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Francesca Paradisi
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
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5
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Mangiagalli M, Lapi M, Maione S, Orlando M, Brocca S, Pesce A, Barbiroli A, Camilloni C, Pucciarelli S, Lotti M, Nardini M. The co-existence of cold activity and thermal stability in an Antarctic GH42 β-galactosidase relies on its hexameric quaternary arrangement. FEBS J 2020; 288:546-565. [PMID: 32363751 DOI: 10.1111/febs.15354] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 11/28/2022]
Abstract
To survive in cold environments, psychrophilic organisms produce enzymes endowed with high specific activity at low temperature. The structure of these enzymes is usually flexible and mostly thermolabile. In this work, we investigate the structural basis of cold adaptation of a GH42 β-galactosidase from the psychrophilic Marinomonas ef1. This enzyme couples cold activity with astonishing robustness for a psychrophilic protein, for it retains 23% of its highest activity at 5 °C and it is stable for several days at 37 °C and even 50 °C. Phylogenetic analyses indicate a close relationship with thermophilic β-galactosidases, suggesting that the present-day enzyme evolved from a thermostable scaffold modeled by environmental selective pressure. The crystallographic structure reveals the overall similarity with GH42 enzymes, along with a hexameric arrangement (dimer of trimers) not found in psychrophilic, mesophilic, and thermophilic homologues. In the quaternary structure, protomers form a large central cavity, whose accessibility to the substrate is promoted by the dynamic behavior of surface loops, even at low temperature. A peculiar cooperative behavior of the enzyme is likely related to the increase of the internal cavity permeability triggered by heating. Overall, our results highlight a novel strategy of enzyme cold adaptation, based on the oligomerization state of the enzyme, which effectively challenges the paradigm of cold activity coupled with intrinsic thermolability. DATABASE: Structural data are available in the Protein Data Bank database under the accession number 6Y2K.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Michela Lapi
- Department of Biosciences, University of Milano, Italy
| | - Serena Maione
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | | | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Italy
| | | | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
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6
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Pekrun K, De Alencastro G, Luo QJ, Liu J, Kim Y, Nygaard S, Galivo F, Zhang F, Song R, Tiffany MR, Xu J, Hebrok M, Grompe M, Kay MA. Using a barcoded AAV capsid library to select for clinically relevant gene therapy vectors. JCI Insight 2019; 4:131610. [PMID: 31723052 PMCID: PMC6948855 DOI: 10.1172/jci.insight.131610] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
While gene transfer using recombinant adeno-associated viral (rAAV) vectors has shown success in some clinical trials, there remain many tissues that are not well transduced. Because of the recent success in reprogramming islet-derived cells into functional β cells in animal models, we constructed 2 highly complex barcoded replication competent capsid shuffled libraries and selected for high-transducing variants on primary human islets. We describe the generation of a chimeric AAV capsid (AAV-KP1) that facilitates transduction of primary human islet cells and human embryonic stem cell-derived β cells with up to 10-fold higher efficiency compared with previously studied best-in-class AAV vectors. Remarkably, this chimeric capsid also enabled transduction of both mouse and human hepatocytes at very high levels in a humanized chimeric mouse model, thus providing a versatile vector that has the potential to be used in both preclinical testing and human clinical trials for liver-based diseases and diabetes.
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Affiliation(s)
- Katja Pekrun
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Gustavo De Alencastro
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Qing-Jun Luo
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Jun Liu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Youngjin Kim
- UCSF Diabetes Center, UCSF, San Francisco, California, USA
| | - Sean Nygaard
- Oregon Stem Cell Center, Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Feorillo Galivo
- Oregon Stem Cell Center, Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Ren Song
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Matthew R. Tiffany
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | - Jianpeng Xu
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
| | | | - Markus Grompe
- Oregon Stem Cell Center, Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Mark A. Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California, USA
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7
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Al-Qahtani AD, Bashraheel SS, Rashidi FB, O'Connor CD, Romero AR, Domling A, Goda SK. Production of "biobetter" variants of glucarpidase with enhanced enzyme activity. Biomed Pharmacother 2019; 112:108725. [PMID: 30970523 DOI: 10.1016/j.biopha.2019.108725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/13/2019] [Accepted: 02/21/2019] [Indexed: 01/21/2023] Open
Abstract
Glucarpidase, also known as carboxypeptidase G2, is a Food and Drug Administration-approved enzyme used in targeted cancer strategies such as antibody-directed enzyme prodrug therapy (ADEPT). It is also used in drug detoxification when cancer patients have excessive levels of the anti-cancer agent methotrexate. The application of glucarpidase is limited by its potential immunogenicity and limited catalytic efficiency. To overcome these pitfalls, mutagenesis was applied to the glucarpidase gene of Pseudomonas sp. strain RS-16 to isolate three novels "biobetter" variants with higher specific enzyme activity. DNA sequence analysis of the genes for the variants showed that each had a single point mutation, resulting in the amino acid substitutions: I100 T, G123S and T239 A. Km, Vmax and Kcat measurements confirmed that each variant had increased catalytic efficiency relative to wild type glucarpidase. Additionally, circular dichroism studies indicated that they had a higher alpha-helical content relative to the wild type enzyme. However, three different software packages predicted that they had reduced protein stability, which is consistent with having higher activities as a tradeoff. The novel glucarpidase variants presented in this work could pave the way for more efficient drug detoxification and might allow dose escalation during chemotherapy. They also have the potential to increase the efficiency of ADEPT and to reduce the number of treatment cycles, thereby reducing the risk that patients will develop antibodies to glucarpidase.
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Affiliation(s)
- Alanod D Al-Qahtani
- Protein Engineering Unit, Life and Science Research Department, Anti-Doping Lab-Qatar (ADLQ), Doha, Qatar; Drug Design Group, Department of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Sara S Bashraheel
- Protein Engineering Unit, Life and Science Research Department, Anti-Doping Lab-Qatar (ADLQ), Doha, Qatar; Drug Design Group, Department of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Fatma B Rashidi
- Cairo University, Faculty of Science, Chemistry Department, Giza, Egypt
| | - C David O'Connor
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Science and Education Innovation District, Suzhou 215123, China
| | - Atilio Reyes Romero
- Drug Design Group, Department of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Alexander Domling
- Drug Design Group, Department of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Sayed K Goda
- Protein Engineering Unit, Life and Science Research Department, Anti-Doping Lab-Qatar (ADLQ), Doha, Qatar; Cairo University, Faculty of Science, Chemistry Department, Giza, Egypt.
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8
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Tian J, Long X, Tian Y, Shi B. Enhanced extracellular recombinant keratinase activity in Bacillus subtilis SCK6 through signal peptide optimization and site-directed mutagenesis. RSC Adv 2019; 9:33337-33344. [PMID: 35529123 PMCID: PMC9073338 DOI: 10.1039/c9ra07866e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 11/21/2022] Open
Abstract
The extracellular recombinant keratinase activity in Bacillus subtilis SCK6 was enhanced by signal peptide optimization and site-directed mutagenesis.
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Affiliation(s)
- Jiewei Tian
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University)
- Department of Biomass and Leather Engineering
- Ministry of Education
- College of Biomass Science and Engineering (Sichuan University)
- Sichuan University
| | - Xiufeng Long
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University)
- Department of Biomass and Leather Engineering
- Ministry of Education
- College of Biomass Science and Engineering (Sichuan University)
- Sichuan University
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University)
- Department of Biomass and Leather Engineering
- Ministry of Education
- College of Biomass Science and Engineering (Sichuan University)
- Sichuan University
| | - Bi Shi
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University)
- Department of Biomass and Leather Engineering
- Ministry of Education
- College of Biomass Science and Engineering (Sichuan University)
- Sichuan University
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9
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The state-of-the-art strategies of protein engineering for enzyme stabilization. Biotechnol Adv 2018; 37:530-537. [PMID: 31138425 DOI: 10.1016/j.biotechadv.2018.10.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 10/12/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022]
Abstract
Enzymes generated by natural recruitment and protein engineering have greatly contribute in various sets of applications. However, their insufficient stability is a bottleneck that limit the rapid development of biocatalysis. Novel approaches based on precise and global structural dissection, advanced gene manipulation, and combination with the multidisciplinary techniques open a new horizon to generate stable enzymes efficiently. Here, we comprehensively introduced emerging advances of protein engineering strategies for enzyme stabilization. Then, we highlighted practical cases to show importance of enzyme stabilization in pharmaceutical and industrial applications. Combining computational enzyme design with molecular evolution will hold considerable promise in this field.
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10
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Liu MD, Warner EA, Morrissey CE, Fick CW, Wu TS, Ornelas MY, Ochoa GV, Zhang B, Rathbun CM, Porterfield WB, Prescher JA, Leconte AM. Statistical Coupling Analysis-Guided Library Design for the Discovery of Mutant Luciferases. Biochemistry 2018; 57:663-671. [PMID: 29224332 PMCID: PMC6192264 DOI: 10.1021/acs.biochem.7b01014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Directed evolution has proven to be an invaluable tool for protein engineering; however, there is still a need for developing new approaches to continue to improve the efficiency and efficacy of these methods. Here, we demonstrate a new method for library design that applies a previously developed bioinformatic method, Statistical Coupling Analysis (SCA). SCA uses homologous enzymes to identify amino acid positions that are mutable and functionally important and engage in synergistic interactions between amino acids. We use SCA to guide a library of the protein luciferase and demonstrate that, in a single round of selection, we can identify luciferase mutants with several valuable properties. Specifically, we identify luciferase mutants that possess both red-shifted emission spectra and improved stability relative to those of the wild-type enzyme. We also identify luciferase mutants that possess a >50-fold change in specificity for modified luciferins. To understand the mutational origin of these improved mutants, we demonstrate the role of mutations at N229, S239, and G246 in altered function. These studies show that SCA can be used to guide library design and rapidly identify synergistic amino acid mutations from a small library.
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Affiliation(s)
- Mira D. Liu
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711, United States of America
| | - Elliot A. Warner
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711, United States of America
| | - Charlotte E. Morrissey
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711, United States of America
| | - Caitlyn W. Fick
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711, United States of America
| | - Taia S. Wu
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711, United States of America
| | - Marya Y. Ornelas
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711, United States of America
| | - Gabriela V. Ochoa
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711, United States of America
| | - Brendan Zhang
- Department of Chemistry, University of California – Irvine, Irvine, California, 92697, United States of America
| | - Colin M. Rathbun
- Department of Chemistry, University of California – Irvine, Irvine, California, 92697, United States of America
| | - William B. Porterfield
- Department of Chemistry, University of California – Irvine, Irvine, California, 92697, United States of America
| | - Jennifer A. Prescher
- Department of Chemistry, University of California – Irvine, Irvine, California, 92697, United States of America
- Department of Molecular Biology and Biochemistry, University of California – Irvine, Irvine, California, 92697, United States of America
- Department of Pharmaceutical Sciences, University of California – Irvine, Irvine, California, 92697, United States of America
| | - Aaron M. Leconte
- W.M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711, United States of America
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11
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Abstract
The last decade has seen a dramatic increase in the utilization of enzymes as green and sustainable (bio)catalysts in pharmaceutical and industrial applications. This trend has to a significant degree been fueled by advances in scientists' and engineers' ability to customize native enzymes by protein engineering. A review of the literature quickly reveals the tremendous success of this approach; protein engineering has generated enzyme variants with improved catalytic activity, broadened or altered substrate specificity, as well as raised or reversed stereoselectivity. Enzymes have been tailored to retain activity at elevated temperatures and to function in the presence of organic solvents, salts and pH values far from physiological conditions. However, readers unfamiliar with the field will soon encounter the confusingly large number of experimental techniques that have been employed to accomplish these engineering feats. Herein, we use history to guide a brief overview of the major strategies for protein engineering-past, present, and future.
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Affiliation(s)
- Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA.
| | - Samantha M Iamurri
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA
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12
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Abstract
One of the greatest sources of metabolic and enzymatic diversity are microorganisms. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly, and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
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Affiliation(s)
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CDMX, México
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13
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Hosseini SR, Wagner A. Constraint and Contingency Pervade the Emergence of Novel Phenotypes in Complex Metabolic Systems. Biophys J 2017; 113:690-701. [PMID: 28793223 DOI: 10.1016/j.bpj.2017.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/25/2017] [Accepted: 06/19/2017] [Indexed: 01/23/2023] Open
Abstract
An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. We know examples of such constraints, but we have no systematic understanding about their extent and causes for any one biological system. We here study metabolisms, genomically encoded complex networks of enzyme-catalyzed biochemical reactions, and the constraints they experience in bringing forth novel phenotypes that allow survival on novel carbon sources. Our computational approach does not limit us to analyzing constrained variation in any one organism, but allows us to quantify constraints experienced by any metabolism. Specifically, we study metabolisms that are viable on one of 50 different carbon sources, and quantify how readily alterations of their chemical reactions create the ability to survive on a novel carbon source. We find that some metabolic phenotypes are much less likely to originate than others. For example, metabolisms viable on D-glucose are 1835 times more likely to give rise to metabolisms viable on D-fructose than on acetate. Likewise, we observe that some novel metabolic phenotypes are more contingent on parental phenotypes than others. Biochemical similarities among carbon sources can help explain the causes of these constraints. In addition, we study metabolisms that can be produced by recombination among 55 metabolisms of different bacterial strains or species, and show that their novel phenotypes are also contingent on and constrained by parental genotypes. To our knowledge, our analysis is the first to systematically quantify the incidence of constrained evolution in a broad class of biological system that is central to life and its evolution.
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Affiliation(s)
- Sayed-Rzgar Hosseini
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland; The Swiss Institute of Bioinformatics, Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland; The Swiss Institute of Bioinformatics, Bioinformatics, Lausanne, Switzerland; The Santa Fe Institute, Santa Fe, New Mexico.
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14
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Hosseini SR, Martin OC, Wagner A. Phenotypic innovation through recombination in genome-scale metabolic networks. Proc Biol Sci 2016; 283:rspb.2016.1536. [PMID: 27683361 DOI: 10.1098/rspb.2016.1536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/06/2016] [Indexed: 12/17/2022] Open
Abstract
Recombination is an important source of metabolic innovation, especially in prokaryotes, which have evolved the ability to survive on many different sources of chemical elements and energy. Metabolic systems have a well-understood genotype-phenotype relationship, which permits a quantitative and biochemically principled understanding of how recombination creates novel phenotypes. Here, we investigate the power of recombination to create genome-scale metabolic reaction networks that enable an organism to survive in new chemical environments. To this end, we use flux balance analysis, an experimentally validated computational method that can predict metabolic phenotypes from metabolic genotypes. We show that recombination is much more likely to create novel metabolic abilities than random changes in chemical reactions of a metabolic network. We also find that phenotypic innovation is more likely when recombination occurs between parents that are genetically closely related, phenotypically highly diverse, and viable on few rather than many carbon sources. Survival on a new carbon source preferentially involves reactions that are superessential, that is, essential in many metabolic networks. We validate our observations with data from 61 reconstructed prokaryotic metabolic networks. Our systematic and quantitative analysis of metabolic systems helps understand how recombination creates innovation.
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Affiliation(s)
- Sayed-Rzgar Hosseini
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Building Y27, Winterthurerstrasse 190, 8057 Zurich, Switzerland The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, 1015 Lausanne, Switzerland
| | - Olivier C Martin
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Building Y27, Winterthurerstrasse 190, 8057 Zurich, Switzerland The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, 1015 Lausanne, Switzerland The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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15
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Baweja M, Nain L, Kawarabayasi Y, Shukla P. Current Technological Improvements in Enzymes toward Their Biotechnological Applications. Front Microbiol 2016; 7:965. [PMID: 27379087 PMCID: PMC4909775 DOI: 10.3389/fmicb.2016.00965] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
Enzymes from extremophiles are creating interest among researchers due to their unique properties and the enormous power of catalysis at extreme conditions. Since community demands are getting more intensified, therefore, researchers are applying various approaches viz. metagenomics to increase the database of extremophilic species. Furthermore, the innovations are being made in the naturally occurring enzymes utilizing various tools of recombinant DNA technology and protein engineering, which allows redesigning of the enzymes for its better fitment into the process. In this review, we discuss the biochemical constraints of psychrophiles during survival at the lower temperature. We summarize the current knowledge about the sources of such enzymes and their in vitro modification through mutagenesis to explore their biotechnological potential. Finally, we recap the microbial cell surface display to enhance the efficiency of the process in cost effective way.
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Affiliation(s)
- Mehak Baweja
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi India
| | - Yutaka Kawarabayasi
- National Institute of Advanced Industrial Science and Technology, Tsukuba Japan
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
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16
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Chen J, Jiang N, Wang T, Xie G, Zhang Z, Li H, Yuan J, Sun Z, Chen J. DNA shuffling of uricase gene leads to a more "human like" chimeric uricase with increased uricolytic activity. Int J Biol Macromol 2015; 82:522-9. [PMID: 26526169 DOI: 10.1016/j.ijbiomac.2015.10.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/17/2015] [Accepted: 10/19/2015] [Indexed: 10/22/2022]
Abstract
Urate oxidase (Uox) is the enzyme involved in purine metabolism. Pseudogenization of Uox gene is the underlying mechanism of hyperuricemia and gout in human. Although Uox from various microorganisms has been used in clinical practice for many years, its application is limited by potential immunogenicity. In order to develop a more "human like" uricase, DNA shuffling was used to create chimeric uricase with both improved enzymatic activity and increased homology with deduced human uricase (dHU) gene. By using wild porcine uricase (wPU) gene and dhu as parental genes, a diverse chimeric library was generated. After preliminary screening by a "homebrew" high throughput protocol, approximately 100 chimeras with relatively high enzymatic activity were obtained. By further activity comparison of the purified enzymes, chimera-62 with increase in both activity and homology with dHU compared with wPU was selected. Its Km and catalytic efficiency were determined as 9.43±0.04μM and 2.67s(-1)μM(-1) respectively. There were 33 amino acid substitutions in chimera-62 when compared with dHU and 5 substitutions when compared with wPU. By homology modeling and 3-D structure analysis, it was speculated that mutations G248S and L266F contributed to the increased activity of chimera-62 by increasing the stability of α-helix and surface polarity respectively.
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Affiliation(s)
- Jing Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Nan Jiang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Tao Wang
- Department of Neurosurgery, Shanghai 5th People's Hospital, Shanghai Medical College, Fudan University, Shanghai 200240, China
| | - Guangrong Xie
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Zhilai Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hui Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Jing Yuan
- School of life science, Faculty of Health and Life science, University of Liverpool, Liverpool, L69 3BX, UK
| | - Zengxian Sun
- Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang 222002, China.
| | - Jianhua Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
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17
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Kapoor S, Rafiq A, Sharma S. Protein engineering and its applications in food industry. Crit Rev Food Sci Nutr 2015; 57:2321-2329. [DOI: 10.1080/10408398.2014.1000481] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Swati Kapoor
- Department of Food Science and Technology, Punjab Agricultural University, Ludhiana, India
| | - Aasima Rafiq
- Department of Food Science and Technology, Punjab Agricultural University, Ludhiana, India
| | - Savita Sharma
- Department of Food Science and Technology, Punjab Agricultural University, Ludhiana, India
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McCormick K, Jiang Z, Zhu L, Lawson SR, Langenhorst R, Ransburgh R, Brunick C, Tracy MC, Hurtig HR, Mabee LM, Mingo M, Li Y, Webby RJ, Huber VC, Fang Y. Construction and Immunogenicity Evaluation of Recombinant Influenza A Viruses Containing Chimeric Hemagglutinin Genes Derived from Genetically Divergent Influenza A H1N1 Subtype Viruses. PLoS One 2015; 10:e0127649. [PMID: 26061265 PMCID: PMC4465703 DOI: 10.1371/journal.pone.0127649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 04/17/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Influenza A viruses cause highly contagious diseases in a variety of hosts, including humans and pigs. To develop a vaccine that can be broadly effective against genetically divergent strains of the virus, in this study we employed molecular breeding (DNA shuffling) technology to create a panel of chimeric HA genes. METHODS AND RESULTS Each chimeric HA gene contained genetic elements from parental swine influenza A viruses that had a history of zoonotic transmission, and also from a 2009 pandemic virus. Each parental virus represents a major phylogenetic clade of influenza A H1N1 viruses. Nine shuffled HA constructs were initially screened for immunogenicity in mice by DNA immunization, and one chimeric HA (HA-129) was expressed on both a A/Puerto Rico/8/34 backbone with mutations associated with a live, attenuated phenotype (PR8LAIV-129) and a A/swine/Texas/4199-2/98 backbone (TX98-129). When delivered to mice, the PR8LAIV-129 induced antibodies against all four parental viruses, which was similar to the breadth of immunity observed when HA-129 was delivered as a DNA vaccine. This chimeric HA was then tested as a candidate vaccine in a nursery pig model, using inactivated TX98-129 virus as the backbone. The results demonstrate that pigs immunized with HA-129 developed antibodies against all four parental viruses, as well as additional primary swine H1N1 influenza virus field isolates. CONCLUSION This study established a platform for creating novel genes of influenza viruses using a molecular breeding approach, which will have important applications toward future development of broadly protective influenza virus vaccines.
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Affiliation(s)
- Kara McCormick
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, 57069, United States of America
| | - Zhiyong Jiang
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, United States of America
| | - Longchao Zhu
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, United States of America
| | - Steven R. Lawson
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, United States of America
| | - Robert Langenhorst
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, United States of America
| | - Russell Ransburgh
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, United States of America
| | - Colin Brunick
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, 57069, United States of America
| | - Miranda C. Tracy
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, 57069, United States of America
| | - Heather R. Hurtig
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, 57069, United States of America
| | - Leah M. Mabee
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, 57069, United States of America
| | - Mark Mingo
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, 57069, United States of America
| | - Yanhua Li
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, United States of America
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, 38105, United States of America
| | - Victor C. Huber
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, 57069, United States of America
| | - Ying Fang
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, United States of America
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Bayer T, Milker S, Wiesinger T, Rudroff F, Mihovilovic MD. Designer Microorganisms for Optimized Redox Cascade Reactions - Challenges and Future Perspectives. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Huang R, Yang Q, Feng H. Single amino acid mutation alters thermostability of the alkaline protease from Bacillus pumilus: thermodynamics and temperature dependence. Acta Biochim Biophys Sin (Shanghai) 2015; 47:98-105. [PMID: 25534779 DOI: 10.1093/abbs/gmu120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dehairing alkaline protease (DHAP) from Bacillus pumilus BA06 has been demonstrated to have high catalytic efficiency and good thermostability, with potential application in leather processing. In order to get insights into its catalytic mechanism, two mutants with single amino acid substitution according to the homology modeling and multiple sequence alignment were characterized in thermodynamics of thermal denaturation and temperature dependence of substrate hydrolysis. The results showed that both mutants of V149I and R249E have a systematic increase in catalytic efficiency (kcat/Km) in a wide range of temperatures, mainly due to an increase of k1 (substrate diffusion) and k2 (acylation) for V149I and of k2 and k3 (deacylation) for R249E. In comparison with the wild-type DHAP, the thermostability is increased for V149I and decreased for R249E. Thermodynamic analysis indicated that the free energy (ΔGa°) of activation for thermal denaturation may govern the thermostability. The value of ΔGa° is increased for V149I and decreased for R249E. Based on these data and the structural modeling, it is suggested that substitution of Val149 with Ile may disturb the local flexibility in the substrate-binding pocket, leading to enhancement of binding affinity for the substrate. In contrast, substitution of Arg249 with Glu leads to interruption of interaction with the C-terminal of enzyme, thus resulting in less thermostability. This study indicates that amino acid residues in the active center or in the substrate-binding pocket may disturb the catalytic process and can be selected as the target for protein engineering in the bacterial alkaline proteases.
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Affiliation(s)
- Rong Huang
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Qingjun Yang
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Hong Feng
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China
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21
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Jemli S, Ayadi-Zouari D, Hlima HB, Bejar S. Biocatalysts: application and engineering for industrial purposes. Crit Rev Biotechnol 2014; 36:246-58. [DOI: 10.3109/07388551.2014.950550] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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22
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Adrio JL, Demain AL. Microbial enzymes: tools for biotechnological processes. Biomolecules 2014; 4:117-39. [PMID: 24970208 PMCID: PMC4030981 DOI: 10.3390/biom4010117] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 11/29/2022] Open
Abstract
Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today there is a need for new, improved or/and more versatile enzymes in order to develop more novel, sustainable and economically competitive production processes. Microbial diversity and modern molecular techniques, such as metagenomics and genomics, are being used to discover new microbial enzymes whose catalytic properties can be improved/modified by different strategies based on rational, semi-rational and random directed evolution. Most industrial enzymes are recombinant forms produced in bacteria and fungi.
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Affiliation(s)
- Jose L Adrio
- Neol Biosolutions SA, BIC Granada, Granada 18016, Spain.
| | - Arnold L Demain
- Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ 07940, USA.
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23
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Shi J, Zhang M, Zhang L, Wang P, Jiang L, Deng H. Xylose-fermenting Pichia stipitis by genome shuffling for improved ethanol production. Microb Biotechnol 2014; 7:90-9. [PMID: 24393385 PMCID: PMC3937714 DOI: 10.1111/1751-7915.12092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 09/04/2013] [Accepted: 09/09/2013] [Indexed: 11/27/2022] Open
Abstract
Xylose fermentation is necessary for the bioconversion of lignocellulose to ethanol as fuel, but wild-type Saccharomyces cerevisiae strains cannot fully metabolize xylose. Several efforts have been made to obtain microbial strains with enhanced xylose fermentation. However, xylose fermentation remains a serious challenge because of the complexity of lignocellulosic biomass hydrolysates. Genome shuffling has been widely used for the rapid improvement of industrially important microbial strains. After two rounds of genome shuffling, a genetically stable, high-ethanol-producing strain was obtained. Designated as TJ2-3, this strain could ferment xylose and produce 1.5 times more ethanol than wild-type Pichia stipitis after fermentation for 96 h. The acridine orange and propidium iodide uptake assays showed that the maintenance of yeast cell membrane integrity is important for ethanol fermentation. This study highlights the importance of genome shuffling in P. stipitis as an effective method for enhancing the productivity of industrial strains.
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Affiliation(s)
- Jun Shi
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, China
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24
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Protein Engineering as an Enabling Tool for Synthetic Biology. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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25
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Abstract
Microorganisms are one of the greatest sources of metabolic and enzymatic diversity. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
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26
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Zhang W, Geng A. Improved ethanol production by a xylose-fermenting recombinant yeast strain constructed through a modified genome shuffling method. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:46. [PMID: 22809265 PMCID: PMC3463424 DOI: 10.1186/1754-6834-5-46] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 01/11/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Xylose is the second most abundant carbohydrate in the lignocellulosic biomass hydrolysate. The fermentation of xylose is essential for the bioconversion of lignocelluloses to fuels and chemicals. However the wild-type strains of Saccharomyces cerevisiae are unable to utilize xylose. Many efforts have been made to construct recombinant yeast strains to enhance xylose fermentation over the past few decades. Xylose fermentation remains challenging due to the complexity of lignocellulosic biomass hydrolysate. In this study, a modified genome shuffling method was developed to improve xylose fermentation by S. cerevisiae. Recombinant yeast strains were constructed by recursive DNA shuffling with the recombination of entire genome of P. stipitis with that of S. cerevisiae. RESULTS After two rounds of genome shuffling and screening, one potential recombinant yeast strain ScF2 was obtained. It was able to utilize high concentration of xylose (100 g/L to 250 g/L xylose) and produced ethanol. The recombinant yeast ScF2 produced ethanol more rapidly than the naturally occurring xylose-fermenting yeast, P. stipitis, with improved ethanol titre and much more enhanced xylose tolerance. CONCLUSION The modified genome shuffling method developed in this study was more effective and easier to operate than the traditional protoplast-fusion-based method. Recombinant yeast strain ScF2 obtained in this study was a promising candidate for industrial cellulosic ethanol production. In order to further enhance its xylose fermentation performance, ScF2 needs to be additionally improved by metabolic engineering and directed evolution.
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Affiliation(s)
- Wei Zhang
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, 535 Clementi Road, Singapore, 599489, Singapore
| | - Anli Geng
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, 535 Clementi Road, Singapore, 599489, Singapore
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27
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Abstract
BACKGROUND DNA shuffling generates combinatorial libraries of chimeric genes by stochastically recombining parent genes. The resulting libraries are subjected to large-scale genetic selection or screening to identify those chimeras with favorable properties (e.g., enhanced stability or enzymatic activity). While DNA shuffling has been applied quite successfully, it is limited by its homology-dependent, stochastic nature. Consequently, it is used only with parents of sufficient overall sequence identity, and provides no control over the resulting chimeric library. RESULTS This paper presents efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents and to generate more predictable, optimized libraries. Our CODNS (cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic programming algorithms to select codons for the parental amino acids, allowing for zero or a fixed number of conservative substitutions. We first present efficient algorithms to optimize the local sequence identity or the nearest-neighbor approximation of the change in free energy upon annealing, objectives that were previously optimized by computationally-expensive integer programming methods. We then present efficient algorithms for more powerful objectives that seek to localize and enhance the frequency of recombination by producing "runs" of common nucleotides either overall or according to the sequence diversity of the resulting chimeras. We demonstrate the effectiveness of CODNS in choosing codons and allocating substitutions to promote recombination between parents targeted in earlier studies: two GAR transformylases (41% amino acid sequence identity), two very distantly related DNA polymerases, Pol X and β (15%), and beta-lactamases of varying identity (26-47%). CONCLUSIONS Our methods provide the protein engineer with a new approach to DNA shuffling that supports substantially more diverse parents, is more deterministic, and generates more predictable and more diverse chimeric libraries.
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Affiliation(s)
- Lu He
- Dept of Computer Science, Dartmouth College, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA
| | - Alan M Friedman
- Dept of Biological Sciences, Markey Center for Structural Biology, Purdue Cancer Center, and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Chris Bailey-Kellogg
- Dept of Computer Science, Dartmouth College, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA
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Yongjun C, Wei B, Shujun J, Meizhi W, Yan J, Yan Y, Zhongliang Z, Goulin Z. Directed evolution improves the fibrinolytic activity of nattokinase from Bacillus natto. FEMS Microbiol Lett 2011; 325:155-61. [DOI: 10.1111/j.1574-6968.2011.02423.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Cai Yongjun
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Bao Wei
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Jiang Shujun
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Weng Meizhi
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Jia Yan
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Yin Yan
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Zheng Zhongliang
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
| | - Zou Goulin
- State Key Laboratory of Virology; Department of Biochemistry and Molecular Biology; College of Life Sciences; Wuhan University; Wuhan; China
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Jones DD. Recombining low homology, functionally rich regions of bacterial subtilisins by combinatorial fragment exchange. PLoS One 2011; 6:e24319. [PMID: 21915310 PMCID: PMC3168465 DOI: 10.1371/journal.pone.0024319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/08/2011] [Indexed: 11/19/2022] Open
Abstract
Combinatorial fragment exchange was utilised to recombine key structural and functional low homology regions of bacilli subtilisins to generate new active hybrid proteases with altered substrate profiles. Up to six different regions comprising mostly of loop residues from the commercially important subtilisin Savinase were exchanged with the structurally equivalent regions of six other subtilisins. The six additional subtilisins derive from diverse origins and included thermophilic and intracellular subtilisins as well as other academically and commercially relevant subtilisins. Savinase was largely tolerant to fragment exchange; rational replacement of all six regions with 5 of 6 donating subtilisin sequences preserved activity, albeit reduced compared to Savinase. A combinatorial approach was used to generate hybrid Savinase variants in which the sequences derived from all seven subtilisins at each region were recombined to generate new region combinations. Variants with different substrate profiles and with greater apparent activity compared to Savinase and the rational fragment exchange variants were generated with the substrate profile exhibited by variants dependent on the sequence combination at each region.
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Affiliation(s)
- D Dafydd Jones
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.
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Phrommao E, Yongsawatdigul J, Rodtong S, Yamabhai M. A novel subtilase with NaCl-activated and oxidant-stable activity from Virgibacillus sp. SK37. BMC Biotechnol 2011; 11:65. [PMID: 21658261 PMCID: PMC3135529 DOI: 10.1186/1472-6750-11-65] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 06/09/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial proteases are one of the most commercially valuable enzymes, of which the largest market share has been taken by subtilases or alkaline proteases of the Bacillus species. Despite a large amount of information on microbial proteases, a search for novel proteases with unique properties is still of interest for both basic and applied aspects of this highly complex class of enzymes. Oxidant stable proteases (OSPs) have been shown to have a wide application in the detergent and bleaching industries and recently have become one of the most attractive enzymes in various biotechnological applications. RESULTS A gene encoding a novel member of the subtilase superfamily was isolated from Virgibacillus sp. SK37, a protease-producing bacterium isolated from Thai fish sauce fermentation. The gene was cloned by an activity-based screening of a genomic DNA expression library on Luria-Bertani (LB) agar plates containing 1 mM IPTG and 3% skim milk. Of the 100,000 clones screened, all six isolated positive clones comprised one overlapping open reading frame of 45% identity to the aprX gene from Bacillus species. This gene, designated aprX-sk37 was cloned into pET21d(+) and over-expressed in E. coli BL21(DE3). The enzyme product, designated AprX-SK37, was purified by an immobilized metal ion affinity chromatography to apparent homogeneity and characterized. The AprX-SK37 enzyme showed optimal catalytic conditions at pH 9.5 and 55°C, based on the azocasein assay containing 5 mM CaCl2. Maximum catalytic activity was found at 1 M NaCl with residual activity of 30% at 3 M NaCl. Thermal stability of the enzyme was also enhanced by 1 M NaCl. The enzyme was absolutely calcium-dependent, with optimal concentration of CaCl2 at 15 mM. Inhibitory effects by phenylmethanesulfonyl fluoride and ethylenediaminetetraacetic acid indicated that this enzyme is a metal-dependent serine protease. The enzyme activity was sensitive towards reducing agents, urea, and SDS, but relatively stable up to 5% of H2O2. Phylogenetic analysis suggested that AprX-SK37 belongs to a novel family of the subtilase superfamily. We propose the name of this new family as alkaline serine protease-X (AprX). CONCLUSIONS The stability towards H2O2 and moderately halo- and thermo-tolerant properties of the AprX-SK37 enzyme are attractive for various biotechnological applications.
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Affiliation(s)
- Ekkarat Phrommao
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Nakhon Ratchasima, 30000, Thailand
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Wagner A. The low cost of recombination in creating novel phenotypes: Recombination can create new phenotypes while disrupting well-adapted phenotypes much less than mutation. Bioessays 2011; 33:636-46. [PMID: 21633964 DOI: 10.1002/bies.201100027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recombination is often considered a disruptive force for well-adapted phenotypes, but recent evidence suggests that this cost of recombination can be small. A key benefit of recombination is that it can help create proteins and regulatory circuits with novel and useful phenotypes more efficiently than point mutation. Its effectiveness stems from the large-scale reorganization of genotypes that it causes, which can help explore far-flung regions in genotype space. Recent work on complex phenotypes in model gene regulatory circuits and proteins shows that the disruptive effects of recombination can be very mild compared to the effects of mutation. Recombination thus can have great benefits at a modest cost, but we do not understand the reasons well. A better understanding might shed light on the evolution of recombination and help improve evolutionary strategies in biochemical engineering.
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Affiliation(s)
- Andreas Wagner
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Zurich, Switzerland.
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Blagodatski A, Katanaev VL. Technologies of directed protein evolution in vivo. Cell Mol Life Sci 2011; 68:1207-14. [PMID: 21190058 PMCID: PMC11115086 DOI: 10.1007/s00018-010-0610-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 12/07/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
Abstract
Directed evolution of proteins for improved or modified functionality is an important branch of modern biotechnology. It has traditionally been performed using various in vitro methods, but more recently, methods of in vivo artificial evolution come into play. In this review, we discuss and compare prokaryotic and eukaryotic-based systems of directed protein evolution in vivo, highlighting their benefits and current limitations and focusing on the biotechnological potential of vertebrate immune cells for the generation of protein diversity by means of the immunoglobulin diversification machinery.
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Affiliation(s)
- Artem Blagodatski
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya St. 4, 142290 Pushchino, Russian Federation
| | - Vladimir L. Katanaev
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya St. 4, 142290 Pushchino, Russian Federation
- University of Konstanz, Universitätsstrasse 10, Box 643, 78457 Konstanz, Germany
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Wang Q, Wu H, Wang A, Du P, Pei X, Li H, Yin X, Huang L, Xiong X. Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach. J Biol Chem 2010; 285:41509-16. [PMID: 20962349 DOI: 10.1074/jbc.m110.139659] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA family shuffling is a powerful method for enzyme engineering, which utilizes recombination of naturally occurring functional diversity to accelerate laboratory-directed evolution. However, the use of this technique has been hindered by the scarcity of family genes with the required level of sequence identity in the genome database. We describe here a strategy for collecting metagenomic homologous genes for DNA shuffling from environmental samples by truncated metagenomic gene-specific PCR (TMGS-PCR). Using identified metagenomic gene-specific primers, twenty-three 921-bp truncated lipase gene fragments, which shared 64-99% identity with each other and formed a distinct subfamily of lipases, were retrieved from 60 metagenomic samples. These lipase genes were shuffled, and selected active clones were characterized. The chimeric clones show extensive functional and genetic diversity, as demonstrated by functional characterization and sequence analysis. Our results indicate that homologous sequences of genes captured by TMGS-PCR can be used as suitable genetic material for DNA family shuffling with broad applications in enzyme engineering.
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Affiliation(s)
- Qiuyan Wang
- Center for Biomedicine and Health, Hangzhou Normal University, Hangzhou 310012, China
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34
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Glasner ME, Gerlt JA, Babbitt PC. Mechanisms of protein evolution and their application to protein engineering. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2010; 75:193-239, xii-xiii. [PMID: 17124868 DOI: 10.1002/9780471224464.ch3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein engineering holds great promise for the development of new biosensors, diagnostics, therapeutics, and agents for bioremediation. Despite some remarkable successes in experimental and computational protein design, engineered proteins rarely achieve the efficiency or specificity of natural enzymes. Current protein design methods utilize evolutionary concepts, including mutation, recombination, and selection, but the inability to fully recapitulate the success of natural evolution suggests that some evolutionary principles have not been fully exploited. One aspect of protein engineering that has received little attention is how to select the most promising proteins to serve as templates, or scaffolds, for engineering. Two evolutionary concepts that could provide a rational basis for template selection are the conservation of catalytic mechanisms and functional promiscuity. Knowledge of the catalytic motifs responsible for conserved aspects of catalysis in mechanistically diverse superfamilies could be used to identify promising templates for protein engineering. Second, protein evolution often proceeds through promiscuous intermediates, suggesting that templates which are naturally promiscuous for a target reaction could enhance protein engineering strategies. This review explores these ideas and alternative hypotheses concerning protein evolution and engineering. Future research will determine if application of these principles will lead to a protein engineering methodology governed by predictable rules for designing efficient, novel catalysts.
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Affiliation(s)
- Margaret E Glasner
- Department of Biopharmaceutical Sciences, University of California-San Francisco, San Francisco, CA 94143, USA
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35
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Schmidt M, Böttcher D, Bornscheuer UT. Directed Evolution of Industrial Biocatalysts. Ind Biotechnol (New Rochelle N Y) 2010. [DOI: 10.1002/9783527630233.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Ramsay N, Jemth AS, Brown A, Crampton N, Dear P, Holliger P. CyDNA: synthesis and replication of highly Cy-dye substituted DNA by an evolved polymerase. J Am Chem Soc 2010; 132:5096-104. [PMID: 20235594 PMCID: PMC2850551 DOI: 10.1021/ja909180c] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Indexed: 11/28/2022]
Abstract
DNA not only transmits genetic information but can also serve as a versatile supramolecular scaffold. Here we describe a strategy for the synthesis and replication of DNA displaying hundreds of substituents using directed evolution of polymerase function by short-patch compartmentalized self-replication (spCSR) and the widely used fluorescent dye labeled deoxinucleotide triphosphates Cy3-dCTP and Cy5-dCTP as substrates. In just two rounds of spCSR selection, we have isolated a polymerase that allows the PCR amplification of double stranded DNA fragments up to 1kb, in which all dC bases are substituted by its fluorescent dye-labeled equivalent Cy3- or Cy5-dC. The resulting "CyDNA" displays hundreds of aromatic heterocycles on the outside of the DNA helix and is brightly colored and highly fluorescent. CyDNA also exhibits significantly altered physicochemical properties compared to standard B-form DNA, including loss of silica and intercalating dye binding, resistance to cleavage by some endonucleases, an up to 40% increased apparent diameter as judged by atomic force microscopy and organic phase partitioning during phenol extraction. CyDNA also displays very bright fluorescence enabling significant signal gains in microarray and microfluidic applications. CyDNA represents a step toward a long-term goal of the encoded synthesis of DNA-based polymers of programmable and evolvable sequence and properties.
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37
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Adrio JL, Demain AL. Recombinant organisms for production of industrial products. Bioeng Bugs 2009; 1:116-31. [PMID: 21326937 DOI: 10.4161/bbug.1.2.10484] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 11/19/2022] Open
Abstract
A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products.
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Affiliation(s)
- Jose-Luis Adrio
- NeuronBioPharma, S.A., Parque Tecnologico de Ciencias de la Salud, Edificio BIC, Armilla, Granada, Spain
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Gong J, Zheng H, Wu Z, Chen T, Zhao X. Genome shuffling: Progress and applications for phenotype improvement. Biotechnol Adv 2009; 27:996-1005. [DOI: 10.1016/j.biotechadv.2009.05.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kiss C, Temirov J, Chasteen L, Waldo GS, Bradbury AR. Directed evolution of an extremely stable fluorescent protein. Protein Eng Des Sel 2009; 22:313-23. [DOI: 10.1093/protein/gzp006] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Schweiker KL, Makhatadze GI. Protein stabilization by the rational design of surface charge-charge interactions. Methods Mol Biol 2009; 490:261-83. [PMID: 19157087 DOI: 10.1007/978-1-59745-367-7_11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The design of proteins with increased stability has many important applications in biotechnology. In recent years, strategies involving directed evolution, sequence-based design, or computational design have proven successful for generating stabilized proteins. A brief overview of the various methods that have been used to increase protein stability is presented, followed by a detailed example of how the rational design of surface charge-charge interactions has provided a robust method for protein stabilization.
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Affiliation(s)
- Katrina L Schweiker
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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Kumar D, . S, Thakur N, Verma R, Bhalla TC. Microbial Proteases and Application as Laundry Detergent Additive. ACTA ACUST UNITED AC 2008. [DOI: 10.3923/jm.2008.661.672] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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43
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Kurtovic S, Shokeer A, Mannervik B. Diverging catalytic capacities and selectivity profiles with haloalkane substrates of chimeric alpha class glutathione transferases. Protein Eng Des Sel 2008; 21:329-41. [DOI: 10.1093/protein/gzn010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Abstract
Life on earth is not possible without microorganisms. Microbes have contributed to industrial science for over 100 years. They have given us diversity in enzymatic content and metabolic pathways. The advent of recombinant DNA brought many changes to industrial microbiology. New expression systems have been developed, biosynthetic pathways have been modified by metabolic engineering to give new metabolites, and directed evolution has provided enzymes with modified selectability, improved catalytic activity and stability. More and more genomes of industrial microorganisms are being sequenced giving valuable information about the genetic and enzymatic makeup of these valuable forms of life. Major tools such as functional genomics, proteomics, and metabolomics are being exploited for the discovery of new valuable small molecules for medicine and enzymes for catalysis.
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Affiliation(s)
- Arnold L Demain
- Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ 07940, USA.
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45
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Characterisation of mutagenised acid-resistant alpha-amylase expressed in Bacillus subtilis WB600. Appl Microbiol Biotechnol 2008; 78:85-94. [DOI: 10.1007/s00253-007-1287-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 11/11/2007] [Accepted: 11/14/2007] [Indexed: 10/22/2022]
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46
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Chaparro-Riggers JF, Loo BL, Polizzi KM, Gibbs PR, Tang XS, Nelson MJ, Bommarius AS. Revealing biases inherent in recombination protocols. BMC Biotechnol 2007; 7:77. [PMID: 18001472 PMCID: PMC2203992 DOI: 10.1186/1472-6750-7-77] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 11/14/2007] [Indexed: 11/23/2022] Open
Abstract
Background The recombination of homologous genes is an effective protein engineering tool to evolve proteins. DNA shuffling by gene fragmentation and reassembly has dominated the literature since its first publication, but this fragmentation-based method is labor intensive. Recently, a fragmentation-free PCR based protocol has been published, termed recombination-dependent PCR, which is easy to perform. However, a detailed comparison of both methods is still missing. Results We developed different test systems to compare and reveal biases from DNA shuffling and recombination-dependent PCR (RD-PCR), a StEP-like recombination protocol. An assay based on the reactivation of β-lactamase was developed to simulate the recombination of point mutations. Both protocols performed similarly here, with slight advantages for RD-PCR. However, clear differences in the performance of the recombination protocols were observed when applied to homologous genes of varying DNA identities. Most importantly, the recombination-dependent PCR showed a less pronounced bias of the crossovers in regions with high sequence identity. We discovered that template variations, including engineered terminal truncations, have significant influence on the position of the crossovers in the recombination-dependent PCR. In comparison, DNA shuffling can produce higher crossover numbers, while the recombination-dependent PCR frequently results in one crossover. Lastly, DNA shuffling and recombination-dependent PCR both produce counter-productive variants such as parental sequences and have chimeras that are over-represented in a library, respectively. Lastly, only RD-PCR yielded chimeras in the low homology situation of GFP/mRFP (45% DNA identity level). Conclusion By comparing different recombination scenarios, this study expands on existing recombination knowledge and sheds new light on known biases, which should improve library-creation efforts. It could be shown that the recombination-dependent PCR is an easy to perform alternative to DNA shuffling.
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Affiliation(s)
- Javier F Chaparro-Riggers
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute of Bioengineering and Bioscience, 315 Ferst Drive, Atlanta, GA 30332-0363, USA.
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47
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Knight ZA, Garrison JL, Chan K, King DS, Shokat KM. A remodelled protease that cleaves phosphotyrosine substrates. J Am Chem Soc 2007; 129:11672-3. [PMID: 17803306 PMCID: PMC2932698 DOI: 10.1021/ja073875n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zachary A. Knight
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94107
| | - Jennifer L. Garrison
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94107
| | - Karina Chan
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94107
| | - David S. King
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, California 94720
| | - Kevan M. Shokat
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94107
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48
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Beltrametti F, Barucco D, Rossi R, Selva E, Marinelli F. Protoplast Fusion and Gene Recombination in the Uncommon Actinomycete Planobispora rosea Producing GE2270. J Antibiot (Tokyo) 2007; 60:447-54. [PMID: 17721003 DOI: 10.1038/ja.2007.57] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An efficient method for protoplast generation for the uncommon actinomycete Planobispora rosea, the producer of the thiazolylpeptide antibiotic GE2270, was developed using a combination of hen egg white lysozyme and Streptomyces globisporus mutanolysin. This method converted more than 70% of vegetative mycelium to protoplasts, which were then regenerated with 50% efficiency in an optimized medium. When P. rosea protoplasts were efficiently fused, recombination between different antibiotic (streptomycin and gentamicin) resistance markers originated sensitive strains (str(s)gen(s)) at frequencies as high as 18% and double resistant fusants (str(r)gen(r)) at frequencies as high as 29%. Double resistant fusants showed GE2270 productivity intermediate between the productivity of the parental strains. Protoplast generation and fusion in P. rosea makes whole genome shuffling feasible as an approach to be used alternately with classical random mutagenesis in industrial strain improvement programs.
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49
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Sheedy C, MacKenzie CR, Hall JC. Isolation and affinity maturation of hapten-specific antibodies. Biotechnol Adv 2007; 25:333-52. [PMID: 17383141 DOI: 10.1016/j.biotechadv.2007.02.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Revised: 02/05/2007] [Accepted: 02/05/2007] [Indexed: 11/16/2022]
Abstract
More and more recombinant antibodies specific for haptens such as drugs of abuse, dyes and pesticides are being isolated from antibody libraries. Thereby isolated antibodies tend to possess lower affinity than their parental, full-size counterparts, and therefore the isolation techniques must be optimized or the antibody genes must be affinity-matured in order to reach high affinities and specificities required for practical applications. Several strategies have been explored to obtain high-affinity recombinant antibodies from antibody libraries: At the selection level, biopanning optimization can be performed through elution with free hapten, analogue pre-incubation and subtractive panning. At the mutagenesis level, techniques such as random mutagenesis, bacterial mutator strains passaging, site-directed mutagenesis, mutational hotspots targeting, parsimonious mutagenesis, antibody shuffling (chain, DNA and staggered extension process) have been used with various degrees of success to affinity mature or modify hapten-specific antibodies. These techniques are reviewed, illustrated and compared.
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Affiliation(s)
- Claudia Sheedy
- Department of Environmental Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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50
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Kurtovic S, Runarsdottir A, Emrén LO, Larsson AK, Mannervik B. Multivariate-activity mining for molecular quasi-species in a glutathione transferase mutant library. Protein Eng Des Sel 2007; 20:243-56. [PMID: 17468114 DOI: 10.1093/protein/gzm017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A library of recombinant glutathione transferases (GSTs) generated by shuffling of DNA encoding human GST M1-1 and GST M2-2 was screened with eight alternative substrates, and the activities were subjected to multivariate analysis. Assays were made in lysates of bacteria in which the GST variants had been expressed. The primary data showed clustering of the activities in eight-dimensional substrate-activity space. For an incisive analysis, the rows of the data matrix, corresponding to the different enzyme variants, were individually scaled to unit length, thus accounting for different expression levels of the enzymes. The columns representing the activities with alternative substrates were subsequently individually normalized to unit variance and a zero mean. By this standardization, the data were adjusted to comparable orders of magnitude. Three molecular quasi-species were recognized by multivariate K-means and principal component analyses. Two of them encompassed the parental GST M1-1 and GST M2-2. A third one diverged functionally by displaying enhanced activities with some substrates and suppressed activities with signature substrates for GST M1-1 and GST M2-2. A fourth cluster contained mutants with impaired functions and was not regarded as a quasi-species. Sequence analysis of representatives of the mutant clusters demonstrated that the majority of the variants in the diverging novel quasi-species were structurally similar to the M1-like GSTs, but distinguished themselves from GST M1-1 by a Ser to Thr substitution in the active site. The data show that multivariate analysis of functional profiles can identify small structural changes influencing the evolution of enzymes with novel substrate-activity profiles.
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Affiliation(s)
- Sanela Kurtovic
- Department of Biochemistry and Organic Chemistry, Uppsala University, BMC, Box 576, SE-75123 Uppsala, Sweden
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