1
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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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2
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Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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3
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Chen H, Liu R, Cai S, Zhang Y, Zhu C, Yu H, Li S. Intermediate product control in cascade reaction for one-pot production of ε-caprolactone by Escherichia coli. Biotechnol J 2024; 19:e2300210. [PMID: 38403458 DOI: 10.1002/biot.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/11/2023] [Accepted: 12/25/2023] [Indexed: 02/27/2024]
Abstract
ε-Caprolactone is an important non-toxic compound for polymer synthesis like polycaprolactone which has been widely used in drug delivery and degradable plastics. To meet the demand for a green economy, a bi-enzymatic cascade, consisting of an alcohol dehydrogenase (ADH) and a cyclohexanone monooxygenase (CHMO), was designed and introduced into Escherichia coli to synthesize ε-caprolactone from cyclohexanol with a self-sufficient NADPH-cofactor regeneration system. To further improve the catalytic efficiency, a carbonyl group-dependent colorimetric method using inexpensive 2,4-dinitrophenylhydrazine (DNPH) was developed for assay of cyclohexanone, an intermediate production of cascade reaction. It can be used to screen mutant strains with high catalytic efficiency from high-throughput library by detecting the absorbance value in microtiter plates (MTP) instead of gas chromatography (GC) analysis. Moreover, an RBS combinatorial library was constructed for balancing the expression of ADH and CHMO from two independent transcriptional units. After the high-throughput screening based on intermediate product control, an optimal variant with higher substrate tolerance and long-term stability was obtained from RBS combinatorial library. Through a fed-batch process, ε-caprolactone production reached 148.2 mM after 70 h of reaction under the optimized conditions, which was the highest yield achieved to date.
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Affiliation(s)
- Hefeng Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ran Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shengliang Cai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yingjiao Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chaoyi Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hao Yu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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4
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Wang M, Cui H, Gu C, Li A, Qiao J, Schwaneberg U, Zhang L, Wei J, Li X, Huang H. Engineering All-Round Cellulase for Bioethanol Production. ACS Synth Biol 2023; 12:2187-2197. [PMID: 37403343 DOI: 10.1021/acssynbio.3c00289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
One strategy to decrease both the consumption of crude oil and environmental damage is through the production of bioethanol from biomass. Cellulolytic enzyme stability and enzymatic hydrolysis play important roles in the bioethanol process. However, the gradually increased ethanol concentration often reduces enzyme activity and leads to inactivation, thereby limiting the final ethanol yield. Herein, we employed an optimized Two-Gene Recombination Process (2GenReP) approach to evolve the exemplary cellulase CBHI for practical bioethanol fermentation. Two all-round CBHI variants (named as R2 and R4) were obtained with simultaneously improved ethanol resistance, organic solvent inhibitor tolerance, and enzymolysis stability in simultaneous saccharification and fermentation (SSF). Notably, CBHI R4 had a 7.0- to 34.5-fold enhanced catalytic efficiency (kcat/KM) in the presence/absence of ethanol. Employing the evolved CBHI R2 and R4 in the 1G bioethanol process resulted in up to 10.27% (6.7 g/L) improved ethanol yield (ethanol concentration) than non-cellulase, which was far more beyond than other optimization strategies. Besides bioenergy fields, this transferable protein engineering routine holds the potential to generate all-round enzymes that meet the requirement in biotransformation and bioenergy fields.
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Affiliation(s)
- Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Chenlei Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Lihui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Junnan Wei
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, China
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5
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Huttanus HM, Triola EKH, Velasquez-Guzman JC, Shin SM, Granja-Travez RS, Singh A, Dale T, Jha RK. Targeted mutagenesis and high-throughput screening of diversified gene and promoter libraries for isolating gain-of-function mutations. Front Bioeng Biotechnol 2023; 11:1202388. [PMID: 37545889 PMCID: PMC10400447 DOI: 10.3389/fbioe.2023.1202388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/25/2023] [Indexed: 08/08/2023] Open
Abstract
Targeted mutagenesis of a promoter or gene is essential for attaining new functions in microbial and protein engineering efforts. In the burgeoning field of synthetic biology, heterologous genes are expressed in new host organisms. Similarly, natural or designed proteins are mutagenized at targeted positions and screened for gain-of-function mutations. Here, we describe methods to attain complete randomization or controlled mutations in promoters or genes. Combinatorial libraries of one hundred thousands to tens of millions of variants can be created using commercially synthesized oligonucleotides, simply by performing two rounds of polymerase chain reactions. With a suitably engineered reporter in a whole cell, these libraries can be screened rapidly by performing fluorescence-activated cell sorting (FACS). Within a few rounds of positive and negative sorting based on the response from the reporter, the library can rapidly converge to a few optimal or extremely rare variants with desired phenotypes. Library construction, transformation and sequence verification takes 6-9 days and requires only basic molecular biology lab experience. Screening the library by FACS takes 3-5 days and requires training for the specific cytometer used. Further steps after sorting, including colony picking, sequencing, verification, and characterization of individual clones may take longer, depending on number of clones and required experiments.
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Affiliation(s)
- Herbert M. Huttanus
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
| | - Ellin-Kristina H. Triola
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
| | - Jeanette C. Velasquez-Guzman
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
| | - Sang-Min Shin
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- BOTTLE Consortium, Golden, CO, United States
| | - Rommel S. Granja-Travez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- BOTTLE Consortium, Golden, CO, United States
| | - Anmoldeep Singh
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Taraka Dale
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
- BOTTLE Consortium, Golden, CO, United States
| | - Ramesh K. Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
- Agile BioFoundry, Emeryville, CA, United States
- BOTTLE Consortium, Golden, CO, United States
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6
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Pourhassan ZN, Cui H, Muckhoff N, Davari MD, Smits SHJ, Schwaneberg U, Schmitt L. A step forward to the optimized HlyA type 1 secretion system through directed evolution. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12653-7. [PMID: 37405436 PMCID: PMC10386944 DOI: 10.1007/s00253-023-12653-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
Secretion of proteins into the extracellular space has great advantages for the production of recombinant proteins. Type 1 secretion systems (T1SS) are attractive candidates to be optimized for biotechnological applications, as they have a relatively simple architecture compared to other classes of secretion systems. A paradigm of T1SS is the hemolysin A type 1 secretion system (HlyA T1SS) from Escherichia coli harboring only three membrane proteins, which makes the plasmid-based expression of the system easy. Although for decades the HlyA T1SS has been successfully applied for secretion of a long list of heterologous proteins from different origins as well as peptides, but its utility at commercial scales is still limited mainly due to low secretion titers of the system. To address this drawback, we engineered the inner membrane complex of the system, consisting of HlyB and HlyD proteins, following KnowVolution strategy. The applied KnowVolution campaign in this study provided a novel HlyB variant containing four substitutions (T36L/F216W/S290C/V421I) with up to 2.5-fold improved secretion for two hydrolases, a lipase and a cutinase. KEY POINTS: • An improvement in protein secretion via the use of T1SS • Reaching almost 400 mg/L of soluble lipase into the supernatant • A step forward to making E. coli cells more competitive for applying as a secretion host.
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Affiliation(s)
- Zohreh N Pourhassan
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
- Present Address: Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Neele Muckhoff
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225, Düsseldorf, Germany.
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7
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Qiao J, Sheng Y, Wang M, Li A, Li X, Huang H. Evolving Robust and Interpretable Enzymes for the Bioethanol Industry. Angew Chem Int Ed Engl 2023; 62:e202300320. [PMID: 36701239 DOI: 10.1002/anie.202300320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 01/27/2023]
Abstract
Obtaining a robust and applicable enzyme for bioethanol production is a dream for biorefinery engineers. Herein, we describe a general method to evolve an all-round and interpretable enzyme that can be directly employed in the bioethanol industry. By integrating the transferable protein evolution strategy InSiReP 2.0 (In Silico guided Recombination Process), enzymatic characterization for actual production, and computational molecular understanding, the model cellulase PvCel5A (endoglucanase II Cel5A from Penicillium verruculosum) was successfully evolved to overcome the remaining challenges of low ethanol and temperature tolerance, which primarily limited biomass transformation and bioethanol yield. Remarkably, application of the PvCel5A variants in both first- and second-generation bioethanol production processes (i. Conventional corn ethanol fermentation combined with the in situ pretreatment process; ii. cellulosic ethanol fermentation process) resulted in a 5.7-10.1 % increase in the ethanol yield, which was unlikely to be achieved by other optimization techniques.
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Affiliation(s)
- Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Yijie Sheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China.,School of Pharmaceutical Science, Nanjing Tech University, Nanjing, 211816, China
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8
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Kumar M, Bandi CK, Chundawat SPS. High-throughput screening of glycosynthases using azido sugars for oligosaccharides synthesis. Methods Enzymol 2023; 682:211-245. [PMID: 36948703 DOI: 10.1016/bs.mie.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Glycosynthases are mutant glycosyl hydrolases that can synthesize glycosidic bonds between acceptor glycone/aglycone groups and activated donor sugars with suitable leaving groups (e.g., azido, fluoro). However, it has been challenging to rapidly detect glycosynthase reaction products involving azido sugars as donor sugars. This has limited our ability to apply rational engineering and directed evolution methods to rapidly screen for improved glycosynthases that are capable of synthesizing bespoke glycans. Here, we outline our recently developed screening methodologies for rapidly detecting glycosynthase activity using a model fucosynthase enzyme engineered to be active on fucosyl azide as donor sugar. We created a diverse library of fucosynthase mutants using semi-random and random error prone mutagenesis and then identified improved fucosynthase mutants with desired activity using two distinct screening methods developed by our group to detect glycosynthase activity (i.e., by detecting azide formed upon completion of fucosynthase reaction); (a) pCyn-GFP regulon method, and (b) Click chemistry method. Finally, we provide some proof-of-concept results illustrating the utility of both these screening methods to rapidly detect products of glycosynthase reactions involving azido sugars as donor groups.
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Affiliation(s)
- Mohit Kumar
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Chandra Kanth Bandi
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, United States.
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9
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Körfer G, Besirlioglu V, Davari MD, Martinez R, Vojcic L, Schwaneberg U. Combinatorial InVitroFlow-assisted Mutagenesis (CombIMut) yields a 41-fold improved CelA2 cellulase. Biotechnol Bioeng 2022; 119:2076-2087. [PMID: 35451061 DOI: 10.1002/bit.28110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/21/2022] [Accepted: 04/03/2022] [Indexed: 11/11/2022]
Abstract
The combination of diversity generation methods and ultrahigh-throughput screening (uHTS) technologies is key to efficiently explore nature's sequence space and elucidate structure-function relationships of enzymes. Beneficial substitutions often cluster in a few regions and simultaneous amino acid substitutions at multiple positions (e.g., by OmniChange) will likely lead to further improved enzyme variants. An extensive screening effort is required to identify such variants, as the simultaneous randomization of four codons can easily yield over 105 potential enzyme variants. The combination of flow cytometer-based uHTS with cell-free compartmentalization technology using (w/o/w) double emulsions (InVitroFlow), provides analysis capabilities of up to 107 events per hour, thus enabling efficient screening. InVitroFlow is an elegant solution since diversity loss through a transformation of host cells is omitted and emulsion compartments provide a genotype-phenotype linkage through a fluorescence readout. In this work, a multi-site saturation mutagenesis (mSSM) and an OmniChange library with four simultaneously saturated positions in the active site of CelA2 cellulase were screened using InVitroFlow. Screening of over 36 million events, yielded a significantly improved cellulase variant CelA2-M3 (H288F/H524Q) with an 8-fold increase in specific activity compared to the parent CelA2-H288F (83.9 U/mg) and a 41-fold increased specific activity (674.5 U/mg) compared to wildtype CelA2 (16.6 U/mg) for the substrate 4-MUC (4-methylumbelliferyl-β D-cellobioside). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Georgette Körfer
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany
| | - Volkan Besirlioglu
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Ronny Martinez
- Universidad de La Serena, Departamento de Ingeniería en Alimentos, Av. Raúl Bitrán 1305, 1720010, La Serena, Chile
| | - Ljubica Vojcic
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany.,Current address: Codexis Inc., 200 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, D-52074, Aachen, Germany.,DWI an der RWTH Aachen e.V, Forckenbeckstraße 50, 52056, Aachen, Germany
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10
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Pourhassan N. Z, Cui H, Khosa S, Davari MD, Jaeger K, Smits SHJ, Schwaneberg U, Schmitt L. Optimized Hemolysin Type 1 Secretion System in Escherichia coli by Directed Evolution of the Hly Enhancer Fragment and Including a Terminator Region. Chembiochem 2022; 23:e202100702. [PMID: 35062047 PMCID: PMC9306574 DOI: 10.1002/cbic.202100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Indexed: 11/26/2022]
Abstract
Type 1 secretion systems (T1SS) have a relatively simple architecture compared to other classes of secretion systems and therefore, are attractive to be optimized by protein engineering. Here, we report a KnowVolution campaign for the hemolysin (Hly) enhancer fragment, an untranslated region upstream of the hlyA gene, of the hemolysin T1SS of Escherichia coli to enhance its secretion efficiency. The best performing variant of the Hly enhancer fragment contained five nucleotide mutations at five positions (A30U, A36U, A54G, A81U, and A116U) resulted in a 2-fold increase in the secretion level of a model lipase fused to the secretion carrier HlyA1. Computational analysis suggested that altered affinity to the generated enhancer fragment towards the S1 ribosomal protein contributes to the enhanced secretion levels. Furthermore, we demonstrate that involving a native terminator region along with the generated Hly enhancer fragment increased the secretion levels of the Hly system up to 5-fold.
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Affiliation(s)
- Zohreh Pourhassan N.
- Institute of BiochemistryHeinrich Heine UniversityUniversitätsstrasse 140225DüsseldorfGermany
| | - Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstraße 5052056AachenGermany
- Present address: Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 West Gregory DriveUrbanaIl 61801USA
| | - Sakshi Khosa
- Institute of BiochemistryHeinrich Heine UniversityUniversitätsstrasse 140225DüsseldorfGermany
| | - Mehdi D. Davari
- Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryWeinberg 306120HalleGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine University and Institute of Bio- and Geosciences IBG-1Biotechnology, Forschungszentrum Jülich GmbH52426JülichGermany
| | - Sander H. J. Smits
- Institute of BiochemistryHeinrich Heine UniversityUniversitätsstrasse 140225DüsseldorfGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstraße 5052056AachenGermany
| | - Lutz Schmitt
- Institute of BiochemistryHeinrich Heine UniversityUniversitätsstrasse 140225DüsseldorfGermany
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11
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Jakočiūnas T, Jensen MK, Keasling JD. CasPER: A CRISPR/Cas9-Based Method for Directed Evolution in Genomic Loci in Saccharomyces cerevisiae. Methods Mol Biol 2022; 2513:23-37. [PMID: 35781198 DOI: 10.1007/978-1-0716-2399-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, in this chapter, we describe a detailed protocol for the method named Cas9-mediated protein evolution reaction or short CasPER. CasPER is based on the generation of large 300-600-bp mutagenized linear DNA fragments by error-prone PCR which are used as a donor for repair of double-strand break mediated by Cas9 and subsequently integrated to the genome. This method can be efficiently used for directed evolution of desired essential or nonessential genes in the genome and most importantly can be multiplexed. Altogether, the described method allows for heterogeneous DNA integration with successful transformation efficiencies of 98-100% for both single and multiplex targeting.
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Affiliation(s)
- Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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12
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Pourhassan N Z, Smits SHJ, Ahn JH, Schmitt L. Biotechnological applications of type 1 secretion systems. Biotechnol Adv 2021; 53:107864. [PMID: 34767962 DOI: 10.1016/j.biotechadv.2021.107864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 02/06/2023]
Abstract
Bacteria have evolved a diverse range of secretion systems to export different substrates across their cell envelope. Although secretion of proteins into the extracellular space could offer advantages for recombinant protein production, the low secretion titers of the secretion systems for some heterologous proteins remain a clear drawback of their utility at commercial scales. Therefore, a potential use of most of secretion systems as production platforms at large scales are still limited. To overcome this limitation, remarkable efforts have been made toward improving the secretion efficiency of different bacterial secretion systems in recent years. Here, we review the progress with respect to biotechnological applications of type I secretion system (T1SS) of Gram-negative bacteria. We will also focus on the applicability of T1SS for the secretion of heterologous proteins as well as vaccine development. Last but not least, we explore the employed engineering strategies that have enhanced the secretion efficiencies of T1SS. Attention is also paid to directed evolution approaches that may offer a more versatile approach to optimize secretion efficiency of T1SS.
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Affiliation(s)
- Zohreh Pourhassan N
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Jung Hoon Ahn
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, South Korea
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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13
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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14
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Abstract
Enzymes are widely used in the food industry. Their use as a supplement to the raw material for animal feed is a current research topic. Although there are several studies on the application of enzyme additives in the animal feed industry, it is necessary to search for new enzymes, as well as to utilize bioinformatics tools for the design of specific enzymes that work in certain environmental conditions and substrates. This will allow the improvement of the productive parameters in animals, reducing costs and making the processes more efficient. Technological needs have considered these catalysts as essential in many industrial sectors and research is constantly being carried out to optimize their use in those processes. This review describes the enzymes used in animal nutrition, their mode of action, their production and new sources of production as well as studies on different animal models to evaluate their effect on the productive performance intended for the production of animal feed.
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15
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Yang J, Tu R, Yuan H, Wang Q, Zhu L. Recent advances in droplet microfluidics for enzyme and cell factory engineering. Crit Rev Biotechnol 2021; 41:1023-1045. [PMID: 33730939 DOI: 10.1080/07388551.2021.1898326] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Enzymes and cell factories play essential roles in industrial biotechnology for the production of chemicals and fuels. The properties of natural enzymes and cells often cannot meet the requirements of different industrial processes in terms of cost-effectiveness and high durability. To rapidly improve their properties and performances, laboratory evolution equipped with high-throughput screening methods and facilities is commonly used to tailor the desired properties of enzymes and cell factories, addressing the challenges of achieving high titer and the yield of the target products at high/low temperatures or extreme pH, in unnatural environments or in the presence of unconventional media. Droplet microfluidic screening (DMFS) systems have demonstrated great potential for exploring vast genetic diversity in a high-throughput manner (>106/h) for laboratory evolution and have been increasingly used in recent years, contributing to the identification of extraordinary mutants. This review highlights the recent advances in concepts and methods of DMFS for library screening, including the key factors in droplet generation and manipulation, signal sources for sensitive detection and sorting, and a comprehensive summary of success stories of DMFS implementation for engineering enzymes and cell factories during the past decade.
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Affiliation(s)
- Jianhua Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Huiling Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
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16
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Ji Y, Lu Y, Puetz H, Schwaneberg U. Anchor peptides promote degradation of mixed plastics for recycling. Methods Enzymol 2021; 648:271-292. [PMID: 33579408 DOI: 10.1016/bs.mie.2020.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Resource stewardship and sustainable use of natural resources is mandatory for a circular plastic economy. The discovery of microbes and enzymes that can selectively degrade mixed-plastic waste enables to recycle plastics. Knowledge on how to achieve efficient and selective enzymatic plastic degradation is a key prerequisite for biocatalytic recycling of plastics. Wild-type natural polymer degrading enzymes such as cellulases pose often selective non-catalytic binding domains that facilitate a targeting and efficient degradation of polymeric substrates. Recently identified polyester hydrolases with synthetic polymer degrading activities, however, lack in general such selective domains. Inspired by nature, we herein report a protocol for the identification and engineering of anchor peptides which serve as non-catalytic binding domains specifically toward synthetic plastics. The identified anchor peptides hold the promise to be fused to known plastic degrading enzymes and thereby enhance the efficiency of biocatalytic plastic recycling processes.
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Affiliation(s)
- Yu Ji
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Yi Lu
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Hendrik Puetz
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany; DWI-Leibniz Institute for Interactive Materials, Aachen, Germany.
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17
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Rodríguez-Núñez K, Bernal C, Martínez R. Immobilized Biocatalyst Engineering: High throughput enzyme immobilization for the integration of biocatalyst improvement strategies. Int J Biol Macromol 2020; 170:61-70. [PMID: 33358947 DOI: 10.1016/j.ijbiomac.2020.12.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/05/2020] [Accepted: 12/12/2020] [Indexed: 10/22/2022]
Abstract
The increasing use of sustainable manufacturing technologies in the industry presents a constant challenge for the development of suitable biocatalysts. Traditionally, improved biocatalysts are developed either using protein engineering (PE) or enzyme immobilization (EI). However, these approaches are usually not simultaneously applied. In this work, we designed and validated an enzyme improvement platform, Immobilized Biocatalyst Engineering (IBE), which simultaneously integrates PE and EI, with a unique combination of improvement through amino acid substitutions and attachment to a support material, allowing to select variants that would not be found through single or subsequent PE and EI improvement strategies. Our results show that there is a significant difference on the best performing variants identified through IBE, when compared to those that could be identified as soluble enzymes and then immobilized, especially when evaluating variants with low enzyme as soluble enzymes and high activity when immobilized. IBE allows evaluating thousands of variants in a short time through an integrated screening, and selection can be made with more information, resulting in the detection of highly stable and active heterogeneous biocatalysts. This novel approach can translate into a higher probability of finding suitable biocatalysts for highly demanding processes.
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Affiliation(s)
- Karen Rodríguez-Núñez
- Laboratorio de Tecnología de Enzimas para Bioprocesos, Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, 1720010 La Serena, Chile
| | - Claudia Bernal
- Laboratorio de Tecnología de Enzimas para Bioprocesos, Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, 1720010 La Serena, Chile; Instituto de Investigación Multidisciplinario en Ciencia y Tecnología, Universidad de La Serena, Benavente 980, 1720010 La Serena, Chile.
| | - Ronny Martínez
- Laboratorio de Tecnología de Enzimas para Bioprocesos, Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, 1720010 La Serena, Chile.
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18
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Csörgő B, Nyerges A, Pál C. Targeted mutagenesis of multiple chromosomal regions in microbes. Curr Opin Microbiol 2020; 57:22-30. [PMID: 32599531 PMCID: PMC7613694 DOI: 10.1016/j.mib.2020.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/20/2022]
Abstract
Directed evolution allows the effective engineering of proteins, biosynthetic pathways, and cellular functions. Traditional plasmid-based methods generally subject one or occasionally multiple genes-of-interest to mutagenesis, require time-consuming manual interventions, and the genes that are subjected to mutagenesis are outside of their native genomic context. Other methods mutagenize the whole genome unselectively which may distort the outcome. Recent recombineering- and CRISPR-based technologies radically change this field by allowing exceedingly high mutation rates at multiple, predefined loci in their native genomic context. In this review, we focus on recent technologies that potentially allow accelerated tunable mutagenesis at multiple genomic loci in the native genomic context of these target sequences. These technologies will be compared by four main criteria, including the scale of mutagenesis, portability to multiple microbial species, off-target mutagenesis, and cost-effectiveness. Finally, we discuss how these technical advances open new avenues in basic research and biotechnology.
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Affiliation(s)
- Bálint Csörgő
- Department of Microbiology and Immunology, University of California, San Francisco, 94143, San Francisco, CA, USA; Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Akos Nyerges
- Synthetic and Systems Biology Unit, Biological Research Centre, 6726, Szeged, Hungary; Department of Genetics, Harvard Medical School, 02115, Boston, MA, USA
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Biological Research Centre, 6726, Szeged, Hungary.
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19
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Shen S, Zhang X, Li Z. Development of an engineered carbamoyl phosphate synthetase with released sensitivity to feedback inhibition by site-directed mutation and casting error-prone PCR. Enzyme Microb Technol 2019; 129:109354. [PMID: 31307577 DOI: 10.1016/j.enzmictec.2019.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/30/2019] [Accepted: 05/26/2019] [Indexed: 12/26/2022]
Abstract
Carbamoyl phosphate synthetase (CPS) is a key enzyme in both pyrimidine and arginine biosynthesis. However, it is inhibited strongly by uridine monophosphate (UMP), which is an intermediate of the de-novo synthesis of pyrimidine nucleoside. In this study, the native carbamoyl phosphate synthetase, from Escherichia coli, was evolved by site-directed mutation and casting error-prone PCR. Compared with the wild-type, the variant N1015 F had released sensitivity to UMP and exhibited 100% of the initial activity in the presence of UMP. Variant K1006A exhibited 0.14-fold improvement in initial activity and kept above 65% of relative activity under the saturated concentration of inhibitor. Structure analysis of variants demonstrated that the reduced sensitivity to inhibitor was largely attributed to the decreased hydrogen bonds, which could reduce the binding affinity with UMP. Also, Phe with large side chain could narrow the binding pocket and generate more steric hindrance. Based on the results in this study, N1015F was an ideal alternative catalyst for the wild-type CPS for pyrimidine biosynthesis.
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Affiliation(s)
- Su Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China.
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20
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Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives. Mol Biotechnol 2019; 61:579-601. [DOI: 10.1007/s12033-019-00187-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Zhong Z, Liu CC. Probing pathways of adaptation with continuous evolution. CURRENT OPINION IN SYSTEMS BIOLOGY 2019; 14:18-24. [PMID: 31608311 PMCID: PMC6788780 DOI: 10.1016/j.coisb.2019.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ziwei Zhong
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
- Lead Contact
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22
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Zhang L, Cui H, Zou Z, Garakani TM, Novoa-Henriquez C, Jooyeh B, Schwaneberg U. Directed Evolution of a Bacterial Laccase (CueO) for Enzymatic Biofuel Cells. Angew Chem Int Ed Engl 2019; 58:4562-4565. [PMID: 30689276 DOI: 10.1002/anie.201814069] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Indexed: 11/10/2022]
Abstract
Escherichia coli's copper efflux oxidase (CueO) has rarely been employed in the cathodic compartment of enzymatic biofuel cells (EBFCs) due to its low redox potential (0.36 V vs. Ag/AgCl, pH 5.5) towards O2 reduction. Herein, directed evolution of CueO towards a more positive onset potential was performed in an electrochemical screening system. An improved CueO variant (D439T/L502K) was obtained with a significantly increased onset potential (0.54 V), comparable to that of high-redox-potential fungal laccases. Upon coupling with an anodic compartment, the EBFC exhibited an open-circuit voltage (Voc ) of 0.56 V. Directed enzyme evolution by tailoring enzymes to application conditions in EBFCs has been validated and might, in combination with molecular understanding, enable future breakthroughs in EBFC performance.
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Affiliation(s)
- Lingling Zhang
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Zhi Zou
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.,DWI Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52074, Aachen, Germany
| | | | - Catalina Novoa-Henriquez
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.,DWI Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52074, Aachen, Germany
| | - Bahareh Jooyeh
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.,DWI Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52074, Aachen, Germany
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23
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Zhang L, Cui H, Zou Z, Garakani TM, Novoa‐Henriquez C, Jooyeh B, Schwaneberg U. Directed Evolution of a Bacterial Laccase (CueO) for Enzymatic Biofuel Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lingling Zhang
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Haiyang Cui
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Zhi Zou
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
| | | | - Catalina Novoa‐Henriquez
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
| | - Bahareh Jooyeh
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
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24
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Zou Z, Alibiglou H, Mate DM, Davari MD, Jakob F, Schwaneberg U. Directed sortase A evolution for efficient site-specific bioconjugations in organic co-solvents. Chem Commun (Camb) 2018; 54:11467-11470. [PMID: 30255876 DOI: 10.1039/c8cc06017g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Directed sortase A evolution yielded the variants R159G and D165Q/D186G/K196V with increased resistance (2.2-fold) and catalytic efficiency (6.3-fold) in 45% (v/v) dimethylsulfoxide. Interestingly, D165Q/D186G/K196V also showed an up to 4.7-fold increased activity for the conjugation of hydrophobic peptides/amines in co-solvents. MD simulations revealed that conformational mobilities are important for the gained resistance.
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Affiliation(s)
- Zhi Zou
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraβe 50, 52056 Aachen, Germany
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25
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Improvement of carbonyl reductase activity for the bioproduction of tert-butyl (3R,5S)-6-chloro-3,5-dihydroxyhexanoate. Bioorg Chem 2018; 80:733-740. [DOI: 10.1016/j.bioorg.2018.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/25/2022]
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26
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CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9. Metab Eng 2018; 48:288-296. [PMID: 29981865 DOI: 10.1016/j.ymben.2018.07.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 11/22/2022]
Abstract
Here we describe a method for robust directed evolution using mutagenesis of large sequence spaces in their genomic contexts. The method employs error-prone PCR and Cas9-mediated genome integration of mutant libraries of large-sized donor variants into single or multiple genomic sites with efficiencies reaching 98-99%. From sequencing of genome integrants, we determined that the mutation frequency along the donor fragments is maintained evenly and successfully integrated into the genomic target loci, indicating that there is no bias of mutational load towards the proximity of the double strand break. To validate the applicability of the method for directed evolution of metabolic gene products we engineered two essential enzymes in the mevalonate pathway of Saccharomyces cerevisiae with selected variants supporting up to 11-fold higher production of isoprenoids. Taken together, our method extends on existing CRISPR technologies by facilitating efficient mutagenesis of hundreds of nucleotides in cognate genomic contexts.
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27
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Ensari Y, Dhoke GV, Davari MD, Ruff AJ, Schwaneberg U. A Comparative Reengineering Study of cpADH5 through Iterative and Simultaneous Multisite Saturation Mutagenesis. Chembiochem 2018; 19:1563-1569. [DOI: 10.1002/cbic.201800159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Yunus Ensari
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
- Kafkas UniversityFaculty of Engineering and ArchitectureDepartment of Bioengineering 36100 Kars Turkey
| | - Gaurao V. Dhoke
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für BiotechnologieRWTH Aachen University Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institut für Interaktive Materialien Forckenbeckstrasse 50 52056 Aachen Germany
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28
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Rigoldi F, Donini S, Redaelli A, Parisini E, Gautieri A. Review: Engineering of thermostable enzymes for industrial applications. APL Bioeng 2018; 2:011501. [PMID: 31069285 PMCID: PMC6481699 DOI: 10.1063/1.4997367] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/14/2017] [Indexed: 01/19/2023] Open
Abstract
The catalytic properties of some selected enzymes have long been exploited to carry out efficient and cost-effective bioconversions in a multitude of research and industrial sectors, such as food, health, cosmetics, agriculture, chemistry, energy, and others. Nonetheless, for several applications, naturally occurring enzymes are not considered to be viable options owing to their limited stability in the required working conditions. Over the years, the quest for novel enzymes with actual potential for biotechnological applications has involved various complementary approaches such as mining enzyme variants from organisms living in extreme conditions (extremophiles), mimicking evolution in the laboratory to develop more stable enzyme variants, and more recently, using rational, computer-assisted enzyme engineering strategies. In this review, we provide an overview of the most relevant enzymes that are used for industrial applications and we discuss the strategies that are adopted to enhance enzyme stability and/or activity, along with some of the most relevant achievements. In all living species, many different enzymes catalyze fundamental chemical reactions with high substrate specificity and rate enhancements. Besides specificity, enzymes also possess many other favorable properties, such as, for instance, cost-effectiveness, good stability under mild pH and temperature conditions, generally low toxicity levels, and ease of termination of activity. As efficient natural biocatalysts, enzymes provide great opportunities to carry out important chemical reactions in several research and industrial settings, ranging from food to pharmaceutical, cosmetic, agricultural, and other crucial economic sectors.
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Affiliation(s)
- Federica Rigoldi
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Stefano Donini
- Center for Nano Science and Technology at Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133 Milano, Italy
| | - Alberto Redaelli
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology at Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133 Milano, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
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Islam S, Mate DM, Martínez R, Jakob F, Schwaneberg U. A robust protocol for directed aryl sulfotransferase evolution toward the carbohydrate building block GlcNAc. Biotechnol Bioeng 2018; 115:1106-1115. [PMID: 29288579 DOI: 10.1002/bit.26535] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/18/2017] [Accepted: 12/26/2017] [Indexed: 12/17/2022]
Abstract
Bacterial aryl sulfotransferases (AST) utilize p-nitrophenylsulfate (pNPS) as a phenolic donor to sulfurylate typically a phenolic acceptor. Interest in aryl sulfotransferases is growing because of their broad variety of acceptors and cost-effective sulfuryl-donors. For instance, aryl sulfotransferase A (ASTA) from Desulfitobacterium hafniense was recently reported to sulfurylate d-glucose. In this study, a directed evolution protocol was developed and validated for aryl sulfotransferase B (ASTB). Thereby the well-known pNPS quantification system was advanced to operate efficiently as a continuous screening system in 96-well MTP format with a true coefficient of variation of 14.3%. A random mutagenesis library (SeSaM library) of ASTB was screened (1,760 clones) to improve sulfurylation of the carbohydrate building block N-acetylglucosamine (GlcNAc). The beneficial variant ASTB-V1 (Val579Asp) showed an up to 3.4-fold increased specific activity toward GlcNAc when compared to ASTB-WT. HPLC- and MS-analysis confirmed ASTB-V1's increased GlcNAc monosulfurylation (2.4-fold increased product formation) representing the validation of the first successful directed evolution round of an AST for a saccharide substrate.
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Affiliation(s)
- Shohana Islam
- DWI-Leibniz-Institut für Interaktive Materialien e.V., Aachen, Germany
| | - Diana M Mate
- DWI-Leibniz-Institut für Interaktive Materialien e.V., Aachen, Germany
| | - Ronny Martínez
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Felix Jakob
- DWI-Leibniz-Institut für Interaktive Materialien e.V., Aachen, Germany
| | - Ulrich Schwaneberg
- DWI-Leibniz-Institut für Interaktive Materialien e.V., Aachen, Germany.,Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
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Rübsam K, Weber L, Jakob F, Schwaneberg U. Directed evolution of polypropylene and polystyrene binding peptides. Biotechnol Bioeng 2017; 115:321-330. [DOI: 10.1002/bit.26481] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/12/2017] [Accepted: 10/15/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Kristin Rübsam
- RWTH Aachen University; Worringerweg 3; Aachen Germany
- DWI - Leibniz-Institute for Interactive Materials; Forckenbeckstraße 50; Aachen Germany
| | - Lina Weber
- DWI - Leibniz-Institute for Interactive Materials; Forckenbeckstraße 50; Aachen Germany
| | - Felix Jakob
- DWI - Leibniz-Institute for Interactive Materials; Forckenbeckstraße 50; Aachen Germany
| | - Ulrich Schwaneberg
- RWTH Aachen University; Worringerweg 3; Aachen Germany
- DWI - Leibniz-Institute for Interactive Materials; Forckenbeckstraße 50; Aachen Germany
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