Article
Chemistry, Multidisciplinary
Ross Thyer, Simon d'Oelsnitz, Molly S. Blevins, Dustin R. Klein, Jennifer S. Brodbelt, Andrew D. Ellington
Summary: The study developed new technology to site-specifically incorporate L-DOPA into recombinant proteins, providing a new approach for protein engineering applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Saurabh Rajendra Nirantar
Summary: Enzymes play a crucial role in biotransformations, however, they often need to be engineered for better performance in biotechnological applications. Researchers have developed a variety of wet-lab methods over the years to achieve this goal, which are examined in this review.
Article
Biochemical Research Methods
Jing Liang, Huibin Zhang, Yee Ling Tan, Huimin Zhao, Ee Lui Ang
Summary: Bacteriophages are a promising alternative to antibiotics in combating antimicrobial resistance. This study presents a strategy for generating large libraries of phage variants, allowing for engineering of phage specificity and improved qualities. The findings demonstrate the potential of directed evolution in enhancing phage therapy for therapeutic applications.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Konstantinos Voskarides
Summary: This article comments on a paper by Frances Arnold and Kentaro Miyazaki from 1999, discussing the pros and cons of random and saturation mutagenesis, as well as important results from directed evolution. The author concludes that molecular evolution is finding new applications in science and is an integral part of the genomic era's revolution.
JOURNAL OF MOLECULAR EVOLUTION
(2021)
Article
Chemistry, Multidisciplinary
Philipp Stephan, Chloe Langley, Daniela Winkler, Jerome Basquin, Lorenzo Caputi, Sarah E. E. O'Connor, Hajo Kries
Summary: Engineering of biosynthetic enzymes is used to synthesize antibiotics analogues. This study focuses on nonribosomal peptide synthetases (NRPSs) responsible for producing antimicrobial peptides. By directed evolution, the substrate specificity of an adenylation domain of a Pro-specific NRPS module was completely switched to a non-standard amino acid. This achievement was made through screening of mutant libraries and can be replicated with different substrates and NRPS modules. New possibilities for modifying NRPS specificity in a biosynthetically useful way are presented.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Multidisciplinary
Ariane Stucki, Jaicy Vallapurackal, Thomas R. Ward, Petra S. Dittrich
Summary: Evolution is crucial for the generation of complexity and life, shaping the world over billions of years. While natural evolution is slow and gradual, directed evolution allows for faster optimization of phenotype. The development of versatile tools based on droplet microfluidics has improved the efficiency of enzyme discovery and optimization.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Agriculture, Multidisciplinary
Zhihua Nie, Pi Liu, Yu Wang, Xuan Guo, Zijian Tan, Jie Shen, Zijing Tang, Jianping Lin, Jibin Sun, Ping Zheng, Leilei Zhu
Summary: This study focused on protein engineering of the mechanosensitive glutamate exporter MscCG2 to improve glutamate excretion efficiency, using directed evolution and computer-assisted design. The engineered variants showed increased levels of glutamate excretion and enhanced efflux of 4-fluoroglutamate, with structural analysis revealing changes in the size of MscCG2 portals and inner channel. These findings demonstrate the potential of protein engineering in enhancing bioproduction through improved secretion efficiency of exporters.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemical Research Methods
Josephin M. Holstein, Christian Gylstorff, Florian Hollfelder
Summary: Compartmentalization of single genes in water-in-oil emulsion droplets is a powerful method to create numerous reactors for enzyme library selections. This study introduces a three-step workflow that overcomes previously incompatible steps, potentially enabling the first in vitro evolution in droplets.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Plant Sciences
Jorge D. Garcia-Garcia, Kristen Van Gelder, Jaya Joshi, Ulschan Bathe, Bryan J. Leong, Steven D. Bruner, Chang C. Liu, Andrew D. Hanson
Summary: Continuous directed evolution of enzymes and other proteins in microbial hosts is a powerful method to improve enzymes for use in plant engineering. By simultaneously performing hypermutation and selection in vivo, the activity of target enzymes can be improved through growth selection, without requiring prior mechanistic knowledge. The yeast OrthoRep system is an effective tool for continuous directed evolution, enabling the modification of plant enzymes and adaptation of enzymes from prokaryotes for plant-like conditions.
Article
Biochemistry & Molecular Biology
Daisylyn Senna Tan, Yanpu Chen, Ya Gao, Anastasia Bednarz, Yuanjie Wei, Vikas Malik, Derek Hoi-Hang Ho, Mingxi Weng, Sik Yin Ho, Yogesh Srivastava, Sergiy Velychko, Xiaoxiao Yang, Ligang Fan, Johnny Kim, Johannes Graumann, Gary D. Stormo, Thomas Braun, Jian Yan, Hans R. Schoeler, Ralf Jauch
Summary: Transcription factor-driven cell fate engineering requires efficiency, speed, and maturity for clinical translation. Directed evolution led to the discovery of an artificially evolved POU factor (ePOU) that surpasses Oct4 in reprogramming efficacy. ePOU can induce pluripotency with or without Sox2, has altered DNA binding preferences, and accelerates pluripotency network establishment.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Food Science & Technology
Anshula Sharma, Gaganjot Gupta, Tawseef Ahmad, Sheikh Mansoor, Baljinder Kaur
Summary: Enzyme engineering techniques, such as directed evolution and site-directed mutagenesis, play a crucial role in enhancing catalytic properties, improving industrial efficiency, and producing novel metabolites. These strategies offer excellent opportunities to tailor existing enzymes and construct highly efficient industrial enzymes for cost-effective production of value-added products.
FOOD REVIEWS INTERNATIONAL
(2021)
Article
Biotechnology & Applied Microbiology
Zohreh N. Pourhassan, Haiyang Cui, Neele Muckhoff, Mehdi D. Davari, Sander H. J. Smits, Ulrich Schwaneberg, Lutz Schmitt
Summary: Protein secretion is advantageous for recombinant protein production. Type 1 secretion systems (T1SS) have a simple architecture and are attractive for biotechnological applications. The hemolysin A type 1 secretion system (HlyA T1SS) from Escherichia coli has been used for secretion of heterologous proteins, but its commercial utility is limited by low secretion titers. To improve this, we engineered the inner membrane complex of the system using KnowVolution strategy, resulting in a novel HlyB variant with improved secretion for two hydrolases.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yaojie Gao, Yuchun Zhao, Jie Zhou, Maohua Yang, Lin Lin, Wenning Wang, Meifeng Tao, Zixin Deng, Ming Jiang
Summary: The study investigated the biosynthetic pathway of type II polyketide murayaquinone, focusing on the role of MrqM in the second polyketide ring cyclization. Results from gene deletion experiments and structural elucidation of intermediates showed that MrqM is essential for the proper biosynthesis of murayaquinone. Additionally, it was suggested that MrqD, previously thought to be involved in ring cyclization, might actually play a different role in the chain releasing step of murayaquinone biosynthesis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Food Science & Technology
Ankita Kataria, Rajan Sharma, Savita Sharma, Baljit Singh, Gurkirat Kaur, Caleb Maina Yakubu
Summary: Protein engineering is a biotechnological tool used to construct new protein structures to enhance biological activities, playing a key role in food applications. Optimizing enzyme functionality is crucial for the food industry.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Amy E. Fraley, Cora L. Dieterich, Mathijs F. J. Mabesoone, Hannah A. Minas, Roy A. Meoded, Franziska Hemmerling, Joern Piel
Summary: This study provides the first structural insights into a distinct group of TEs (TE(B)s) that have diverse acylation roles in polyketide and peptide biosynthesis. By analyzing and engineering the active site, the acyl-group acceptance can be modulated. Moreover, the production of longer chain branched oocydins was discovered, positioning this enzyme as a valuable synthetic biology tool for polyketide drug development.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Sean Lund, Rachael Hall, Gavin J. Williams
ACS SYNTHETIC BIOLOGY
(2019)
Article
Chemistry, Multidisciplinary
Edward Kalkreuter, Jared M. CroweTipton, Andrew N. Lowell, David H. Sherman, Gavin J. Williams
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Biochemistry & Molecular Biology
Sean Lund, Taylor Courtney, Gavin J. Williams
Article
Biochemical Research Methods
Edward Kalkreuter, Aaron M. Keeler, Alexandra A. Malico, Kyle S. Bingham, Anuran K. Gayen, Gavin J. Williams
ACS SYNTHETIC BIOLOGY
(2019)
Article
Chemistry, Multidisciplinary
Phyo Phyo Kyaw Zin, Gavin Williams, Denis Fourches
JOURNAL OF CHEMINFORMATICS
(2020)
Article
Multidisciplinary Sciences
Phyo Phyo Kyaw Zin, Gavin J. Williams, Sean Ekins
SCIENTIFIC REPORTS
(2020)
Editorial Material
Chemistry, Physical
Anuran K. Gayen, Lindsay Nichols, Gavin J. Williams
Review
Biochemistry & Molecular Biology
Alexandra A. Malico, Lindsay Nichols, Gavin J. Williams
CURRENT OPINION IN CHEMICAL BIOLOGY
(2020)
Review
Biotechnology & Applied Microbiology
Alexandra A. Malico, Miles A. Calzini, Anuran K. Gayen, Gavin J. Williams
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Edward Kalkreuter, Kyle S. Bingham, Aaron M. Keeler, Andrew N. Lowell, Jennifer J. Schmidt, David H. Sherman, Gavin J. Williams
Summary: This study utilized molecular dynamics simulations to identify mutations influencing AT domain selectivity and exchanged structural motifs to obtain chimeric PKS modules with expanded substrate specificity.
NATURE COMMUNICATIONS
(2021)
Review
Biochemical Research Methods
Melissa M. Mitchler, Jessie M. Garcia, Nichole E. Montero, Gavin J. Williams
Summary: Natural products and their derivatives are important sources of chemical and biological diversity, and improving their biosynthetic pathways can increase yields and access to different derivatives, but this requires a precise understanding of enzymatic processes. Biosensors based on allosteric transcription factors can help overcome screening bottlenecks, enabling searches through large libraries of pathway/strain variants.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Yiwei Li, Megan Reed, H. Tonie Wright, T. Ashton Cropp, Gavin J. Williams
Summary: Clarithromycin is an improved semisynthetic analogue of erythromycin, with enhanced acid stability. By evolving the effector specificity of MphR protein, selective recognition of clarithromycin was achieved, providing insights for the evolution of new metabolic functions using this biosensor.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Thaddeus Q. Paulsel, Gavin J. Williams
Summary: Polyketide natural products have great potential as pharmaceutical targets and molecular tools for human health and disease research. Despite the well-understood biosynthetic logic of polyketide synthases, the synthesis of designer polyketides remains challenging due to various issues. Chemical enzymatic synthesis of PKSs has provided valuable insights into enzymatic promiscuity and mechanistic activity and has successfully yielded natural product derivatives. Combining chemical synthesis and enzymology can further improve polyketide synthetic biology approaches.
Review
Biochemistry & Molecular Biology
Miles A. Calzini, Alexandra A. Malico, Melissa M. Mitchler, Gavin J. Williams
Summary: As protein engineering advances, various strategies have been developed to modify protein structure and function for redesigning and optimizing natural product biosynthesis. These strategies include computational tools, rational mutagenesis, directed evolution, and microenvironment engineering, along with novel high-throughput screening methods using designer protein-based biosensors.
PROTEIN ENGINEERING DESIGN & SELECTION
(2021)
Correction
Biotechnology & Applied Microbiology
Alexandra A. Malico, Miles A. Calzini, Anuran K. Gayen, Gavin J. Williams
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2020)
