1
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Fernez MT, Hegde S, Hayes JA, Hoyt KO, Carrier RL, Woolston BM. Development of a Transcriptional Biosensor for Hydrogen Sulfide That Functions under Aerobic and Anaerobic Conditions. ACS Synth Biol 2025. [PMID: 40358934 DOI: 10.1021/acssynbio.5c00124] [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: 05/15/2025]
Abstract
Hydrogen sulfide (H2S) is a gaseous gut metabolite with disputed effects on gastrointestinal health. Monitoring H2S concentration in the gut would provide insight into its role in disease but is complicated by sulfide's reactivity and volatility. Here we develop a transcriptional sulfide biosensor in Escherichiacoli. The sensor relies on enzymatic oxidation of sulfide catalyzed by a sulfide:quinone oxidoreductase (Sqr) to polysulfides, which interact with the repressor SqrR, triggering unbinding from the promoter and transcription of the reporter. Through promoter engineering and improved soluble SqrR expression, we optimized the system to provide an operational range of 50-750 μM and a dynamic range of 18 aerobically. To enable sensing in anaerobic environments, we identified an Sqr from Wolinella succinogenes that uses menaquinone, facilitating reoxidation through the anaerobic electron transport chain by fumarate or nitrate. Use of this homologue resulted in an anaerobic H2S response up to 750 μM. This sensor could ultimately enable spatially and temporally resolved measurements of H2S in the gastrointestinal tract to elucidate the role of this metabolite in disease and potentially as a noninvasive diagnostic.
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Affiliation(s)
- Matthew T Fernez
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Shanthi Hegde
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Justin A Hayes
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Kathryn O Hoyt
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rebecca L Carrier
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Benjamin M Woolston
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
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2
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Yang L, Zhang J, Andon JS, Li L, Wang T. Rapid discovery of cyclic peptide protein aggregation inhibitors by continuous selection. Nat Chem Biol 2025; 21:588-597. [PMID: 39806068 PMCID: PMC12019813 DOI: 10.1038/s41589-024-01823-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/10/2024] [Indexed: 01/16/2025]
Abstract
Protein aggregates are associated with numerous diseases. Here we report a platform for the rapid phenotypic selection of protein aggregation inhibitors from genetically encoded cyclic peptide libraries in Escherichia coli based on phage-assisted continuous evolution (PACE). We developed a new PACE-compatible selection for protein aggregation inhibition and used it to identify cyclic peptides that suppress amyloid-β42 and human islet amyloid polypeptide aggregation. Additionally, we integrated a negative selection that removes false positives and off-target hits, greatly improving cyclic peptide selectivity. We show that selected inhibitors are active when chemically resynthesized in in vitro assays. Our platform provides a powerful approach for the rapid discovery of cyclic peptide inhibitors of protein aggregation and may serve as the basis for the future evolution of cyclic peptides with a broad spectrum of inhibitory activities.
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Affiliation(s)
- Linwei Yang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jingwei Zhang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - James S Andon
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Tina Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Vasudhevan P, Ruoyu Z, Ma H, Singh S, Varshney D, Pu S. Biocatalytic enzymes in food packaging, biomedical, and biotechnological applications: A comprehensive review. Int J Biol Macromol 2025; 300:140069. [PMID: 39832587 DOI: 10.1016/j.ijbiomac.2025.140069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 12/27/2024] [Accepted: 01/17/2025] [Indexed: 01/22/2025]
Abstract
The increasing environmental concerns and health risks associated with synthetic chemicals have driven the demand for sustainable and eco-friendly solutions. Biocatalysis, employing enzymes or whole cells as biocatalysts, has emerged as a powerful alternative. This review provides a comprehensive analysis of the applications of biocatalytic enzymes in food packaging, biomedical sciences, and biotechnology. We highlight the potential of enzymes like laccase, glucose oxidase, lysozyme, protease, lipase, cellulase, and asparaginase to replace traditional chemical methods, driving innovation and sustainability. The global enzyme market is also analyzed, including current trends, emerging demands, and the impact of the COVID-19 pandemic. This review aims to bridge knowledge gaps, emphasize recent technological breakthroughs, and showcase the potential of biocatalytic enzymes to address critical industrial challenges while supporting environmental sustainability and economic growth.
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Affiliation(s)
- Palanisamy Vasudhevan
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu 610059, China.
| | - Zhang Ruoyu
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu 610059, China
| | - Hui Ma
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu 610059, China
| | - Subhav Singh
- Chitkara Centre for Research and Development, Chitkara University, Himachal Pradesh 174103, India; Division of research and development, Lovely Professional University, Phagwara, Punjab, India
| | - Deekshant Varshney
- Centre of Research Impact and Outcome, Chitkara University, Rajpura 140417, Punjab, India; Division of Research & innovation, Uttaranchal University, Dehradun, India
| | - Shengyan Pu
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu 610059, China.
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4
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Jiang W, Newell W, Liu J, Coppens L, Borah Slater K, Peng H, Bell D, Liu L, Haritos V, Ledesma-Amaro R. Insights into the methanol utilization capacity of Y. lipolytica and improvements through metabolic engineering. Metab Eng 2025; 91:30-43. [PMID: 40158687 DOI: 10.1016/j.ymben.2025.03.014] [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: 10/27/2024] [Revised: 02/19/2025] [Accepted: 03/21/2025] [Indexed: 04/02/2025]
Abstract
Methanol is a promising sustainable alternative feedstock for green biomanufacturing. The yeast Yarrowia lipolytica offers a versatile platform for producing a wide range of products but it cannot use methanol efficiently. In this study, we engineered Y. lipolytica to utilize methanol by overexpressing a methanol dehydrogenase, followed by the incorporation of methanol assimilation pathways from methylotrophic yeasts and bacteria. We also overexpressed the ribulose monophosphate (RuMP) and xylulose monophosphate (XuMP) pathways, which led to significant improvements in growth with methanol, reaching a consumption rate of 2.35 g/L in 24 h and a 2.68-fold increase in biomass formation. Metabolomics and Metabolite Flux Analysis confirmed methanol assimilation and revealed an increase in reducing power. The strains were further engineered to produce the valuable heterologous product resveratrol from methanol as a co-substrate. Unlike traditional methanol utilization processes, which are often resource-intensive and environmentally damaging, our findings represent a significant advance in green chemistry by demonstrating the potential of Y. lipolytica for efficient use of methanol as a co-substrate for energy, biomass, and product formation. This work not only contributes to our understanding of methanol metabolism in non-methylotrophic organisms but also paves the way for achieving efficient synthetic methylotrophy towards green biomanufacturing.
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Affiliation(s)
- Wei Jiang
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, SW7 2AZ, United Kingdom; Department of Chemical Engineering, Monash University, Clayton, VIC, 3800, Australia
| | - William Newell
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jingjing Liu
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, SW7 2AZ, United Kingdom; College of Life Sciences, Linyi University, Linyi, 276000, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Lucas Coppens
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Khushboo Borah Slater
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | - Huadong Peng
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, SW7 2AZ, United Kingdom; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Queensland, 4067, Australia
| | - David Bell
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Victoria Haritos
- Department of Chemical Engineering, Monash University, Clayton, VIC, 3800, Australia
| | - Rodrigo Ledesma-Amaro
- Bezos Centre for Sustainable Protein, Imperial College London, London SW7 2AZ, UK; UKRI Engineering Biology Mission Hub on Microbial Food, Imperial College London, London SW7 2AZ, UK.
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5
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Fernez MT, Hegde S, Hayes JA, Hoyt KO, Carrier RL, Woolston BM. Development of a Transcriptional Biosensor for Hydrogen Sulfide that Functions under Aerobic and Anaerobic Conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.639182. [PMID: 40027654 PMCID: PMC11870579 DOI: 10.1101/2025.02.19.639182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Hydrogen sulfide (H2S) is a gaseous gut metabolite with disputed effects on gastrointestinal health. Monitoring H2S concentration in the gut would provide insight into its role in disease, but is complicated by sulfide's reactivity and volatility. Here we develop a transcriptional sulfide biosensor in E. coli. The sensor relies on enzymatic oxidation of sulfide catalyzed by a sulfide:quinone reductase (Sqr) to polysulfides, which bind to the repressor SqrR, triggering unbinding from the promoter and transcription of the reporter. Through promoter engineering and improving soluble SqrR expression, we optimized the system to provide an operational range of 50 μM - 750 μM and dynamic range of 18 aerobically. To enable sensing in anaerobic environments, we identified an Sqr from Wolinella succinogenes that uses menaquinone, facilitating reoxidation through the anaerobic electron transport chain by fumarate or nitrate. Use of this homolog resulted in an anaerobic H2S response up to 750 μM. This sensor could ultimately enable spatially and temporally resolved measurements of H2S in the gastrointestinal tract to elucidate the role of this metabolite in disease, and potentially as a non-invasive diagnostic.
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Affiliation(s)
| | | | - Justin A Hayes
- Department of Chemical Engineering, Northeastern University
| | - Kathryn O Hoyt
- Department of Chemical Engineering, Northeastern University
| | - Rebecca L Carrier
- Department of Chemical Engineering, Northeastern University
- Department of Bioengineering, Northeastern University
| | - Benjamin M Woolston
- Department of Chemical Engineering, Northeastern University
- Department of Bioengineering, Northeastern University
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6
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Tang J, Du K. Mitochondrial base editing: from principle, optimization to application. Cell Biosci 2025; 15:9. [PMID: 39856740 PMCID: PMC11762502 DOI: 10.1186/s13578-025-01351-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Accepted: 01/13/2025] [Indexed: 01/27/2025] Open
Abstract
In recent years, mitochondrial DNA (mtDNA) base editing systems have emerged as bioengineering tools. DddA-derived cytosine base editors (DdCBEs) have been developed to specifically induce C-to-T conversion in mtDNA by the fusion of sequence-programmable transcription activator-like effector nucleases (TALENs) or zinc-finger nucleases (ZFNs), and split deaminase derived from interbacterial toxins. Similar to DdCBEs, mtDNA adenine base editors have been developed with the ability to introduce targeted A-to-G conversions into human mtDNA. In this review, we summarize the principles of mtDNA base-editing systems and elaborate on the evolution of different platforms of mtDNA base editors, including their deaminase replacement, engineering of DddAtox variants, structure optimization and editing outcomes. Finally, we highlight their applications in animal models and human embroys and discuss the future developmental direction and challenges of mtDNA base editors.
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Affiliation(s)
- Jinling Tang
- Clinical Laboratory Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Kunzhao Du
- Jinshan Hospital Center for Neurosurgery, Jinshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 201508, China.
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7
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Wen H, Deng H, Li B, Chen J, Zhu J, Zhang X, Yoshida S, Zhou Y. Mitochondrial diseases: from molecular mechanisms to therapeutic advances. Signal Transduct Target Ther 2025; 10:9. [PMID: 39788934 PMCID: PMC11724432 DOI: 10.1038/s41392-024-02044-3] [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: 07/02/2024] [Revised: 09/28/2024] [Accepted: 10/31/2024] [Indexed: 01/12/2025] Open
Abstract
Mitochondria are essential for cellular function and viability, serving as central hubs of metabolism and signaling. They possess various metabolic and quality control mechanisms crucial for maintaining normal cellular activities. Mitochondrial genetic disorders can arise from a wide range of mutations in either mitochondrial or nuclear DNA, which encode mitochondrial proteins or other contents. These genetic defects can lead to a breakdown of mitochondrial function and metabolism, such as the collapse of oxidative phosphorylation, one of the mitochondria's most critical functions. Mitochondrial diseases, a common group of genetic disorders, are characterized by significant phenotypic and genetic heterogeneity. Clinical symptoms can manifest in various systems and organs throughout the body, with differing degrees and forms of severity. The complexity of the relationship between mitochondria and mitochondrial diseases results in an inadequate understanding of the genotype-phenotype correlation of these diseases, historically making diagnosis and treatment challenging and often leading to unsatisfactory clinical outcomes. However, recent advancements in research and technology have significantly improved our understanding and management of these conditions. Clinical translations of mitochondria-related therapies are actively progressing. This review focuses on the physiological mechanisms of mitochondria, the pathogenesis of mitochondrial diseases, and potential diagnostic and therapeutic applications. Additionally, this review discusses future perspectives on mitochondrial genetic diseases.
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Affiliation(s)
- Haipeng Wen
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Hui Deng
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Bingyan Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Junyu Chen
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Junye Zhu
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Xian Zhang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Shigeo Yoshida
- Department of Ophthalmology, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China.
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8
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Pandey S, Gao XD, Krasnow NA, McElroy A, Tao YA, Duby JE, Steinbeck BJ, McCreary J, Pierce SE, Tolar J, Meissner TB, Chaikof EL, Osborn MJ, Liu DR. Efficient site-specific integration of large genes in mammalian cells via continuously evolved recombinases and prime editing. Nat Biomed Eng 2025; 9:22-39. [PMID: 38858586 PMCID: PMC11754103 DOI: 10.1038/s41551-024-01227-1] [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: 12/06/2023] [Accepted: 05/09/2024] [Indexed: 06/12/2024]
Abstract
Methods for the targeted integration of genes in mammalian genomes suffer from low programmability, low efficiencies or low specificities. Here we show that phage-assisted continuous evolution enhances prime-editing-assisted site-specific integrase gene editing (PASSIGE), which couples the programmability of prime editing with the ability of recombinases to precisely integrate large DNA cargoes exceeding 10 kilobases. Evolved and engineered Bxb1 recombinase variants (evoBxb1 and eeBxb1) mediated up to 60% donor integration (3.2-fold that of wild-type Bxb1) in human cell lines with pre-installed recombinase landing sites. In single-transfection experiments at safe-harbour and therapeutically relevant sites, PASSIGE with eeBxb1 led to an average targeted-gene-integration efficiencies of 23% (4.2-fold that of wild-type Bxb1). Notably, integration efficiencies exceeded 30% at multiple sites in primary human fibroblasts. PASSIGE with evoBxb1 or eeBxb1 outperformed PASTE (for 'programmable addition via site-specific targeting elements', a method that uses prime editors fused to recombinases) on average by 9.1-fold and 16-fold, respectively. PASSIGE with continuously evolved recombinases is an unusually efficient method for the targeted integration of genes in mammalian cells.
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Affiliation(s)
- Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Nicholas A Krasnow
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Amber McElroy
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Y Allen Tao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jordyn E Duby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Benjamin J Steinbeck
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Julia McCreary
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Sarah E Pierce
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Torsten B Meissner
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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9
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Xu B, Liu LH, Lin H, Zhang Y, Huang Y, He Q, Wang F, Wu YR, Zhang Z, Jiang A. A cell-free bacteriophage synthesis system for directed evolution. Trends Biotechnol 2025; 43:248-261. [PMID: 39462751 DOI: 10.1016/j.tibtech.2024.10.005] [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] [Received: 05/13/2024] [Revised: 10/05/2024] [Accepted: 10/08/2024] [Indexed: 10/29/2024]
Abstract
Efficient phage production has always been an urgent need in fields such as drug discovery, disease treatment, and gene evolution. To meet this demand, we constructed a robust cell-free synthesis system for generating M13 phage by simplifying its genome, enabling a three-times faster efficiency compared with the traditional method in vivo. We further developed a cell-free directed evolution system in droplets, comprising a modified helper plasmid (ΔPS-ΔgIII-ΔgVI) and the simplified M13 genome-carrying gene mutation library. This system was greatly improved when coupled with fluorescence-activated droplet sorting (FADS). We successfully evolved the T7 RNA polymerase (RNAP), achieving a twofold higher activity to read through the T7 terminator. Moreover, we evolved the tryptophan tRNA into a suppressor tRNA with an eightfold increase in activity to read through the stop codon UAG.
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Affiliation(s)
- Bo Xu
- School of Basic Medical Sciences, Hubei University of Science and Technology, Xianning 437100, PR China.
| | - Li-Hua Liu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China
| | - Houliang Lin
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China
| | - Yang Zhang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China
| | - Ying Huang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China
| | - Qing He
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China
| | - Fan Wang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China
| | - Yi-Rui Wu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China
| | - Zhiqian Zhang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China.
| | - Ao Jiang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd, Guangzhou Qianxiang Bioworks Co., Ltd., Guangzhou, Guangdong 510000, PR China.
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10
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Guo F, Liu K, Qiao Y, Zheng Y, Liu C, Wu Y, Zhang Z, Jiang W, Jiang Y, Xin F, Jiang M, Zhang W. Evolutionary engineering of Saccharomyces cerevisiae: Crafting a synthetic methylotroph via self-reprogramming. SCIENCE ADVANCES 2024; 10:eadq3484. [PMID: 39705340 DOI: 10.1126/sciadv.adq3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 11/18/2024] [Indexed: 12/22/2024]
Abstract
Methanol, as a non-edible feedstock, offers a promising sustainable alternative to sugar-based substrates in biochemical production. Despite progress in engineering methanol assimilation in nonmethylotrophs, the full transformation into methanol-dependent synthetic methylotrophs remains a formidable challenge. Here, moving beyond the conventional rational design principle, we engineered a synthetic methylotrophic Saccharomyces cerevisiae through genome rearrangement and adaptive laboratory evolution. This evolutionarily advanced strain unexpectedly shed the heterologous methanol assimilation pathway and demonstrated the robust growth on sole methanol. We discovered that the evolved strain likely realized methanol assimilation through a previously unidentified Adh2-Sfa1-rGly (ASrG) pathway, facilitating the concurrent assimilation of formate and CO2. Furthermore, the incorporation of electron transfer material C3N4 quantum dots obviously enhanced methanol-dependent growth, emphasizing the role of energy availability in the ASrG pathway. This breakthrough introduces a previously unidentified C1 utilization pathway and highlights the exceptional adaptability and self-evolving capacity of the S. cerevisiae metabolic network.
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Affiliation(s)
- Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Kang Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Yangyi Qiao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - YongMin Zheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Chenguang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200241, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Zhonghai Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200240, China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
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11
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Chen A, Zhang XD, Đelmaš AĐ, Weitz DA, Milcic K. Systems and Methods for Continuous Evolution of Enzymes. Chemistry 2024; 30:e202400880. [PMID: 38780896 DOI: 10.1002/chem.202400880] [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: 03/01/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Directed evolution generates novel biomolecules with desired functions by iteratively diversifying the genetic sequence of wildtype biomolecules, relaying the genetic information to the molecule with function, and selecting the variants that progresses towards the properties of interest. While traditional directed evolution consumes significant labor and time for each step, continuous evolution seeks to automate all steps so directed evolution can proceed with minimum human intervention and dramatically shortened time. A major application of continuous evolution is the generation of novel enzymes, which catalyze reactions under conditions that are not favorable to their wildtype counterparts, or on altered substrates. The challenge to continuously evolve enzymes lies in automating sufficient, unbiased gene diversification, providing selection for a wide array of reaction types, and linking the genetic information to the phenotypic function. Over years of development, continuous evolution has accumulated versatile strategies to address these challenges, enabling its use as a general tool for enzyme engineering. As the capability of continuous evolution continues to expand, its impact will increase across various industries. In this review, we summarize the working mechanisms of recently developed continuous evolution strategies, discuss examples of their applications focusing on enzyme evolution, and point out their limitations and future directions.
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Affiliation(s)
- Anqi Chen
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, 02138, USA E-mail: Dr David A. Weitz: E-mail: Dr. Karla Milcic
| | - Xinge Diana Zhang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, 02138, USA E-mail: Dr David A. Weitz: E-mail: Dr. Karla Milcic
| | | | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, 02138, USA E-mail: Dr David A. Weitz: E-mail: Dr. Karla Milcic
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
| | - Karla Milcic
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, 02138, USA E-mail: Dr David A. Weitz: E-mail: Dr. Karla Milcic
- University of Belgrade-Faculty of Chemistry, Studentski trg 12-16, 11000, Belgrade, Serbia
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12
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Wu X, Yang J, Zhang J, Song Y. Gene editing therapy for cardiovascular diseases. MedComm (Beijing) 2024; 5:e639. [PMID: 38974714 PMCID: PMC11224995 DOI: 10.1002/mco2.639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 07/09/2024] Open
Abstract
The development of gene editing tools has been a significant area of research in the life sciences for nearly 30 years. These tools have been widely utilized in disease detection and mechanism research. In the new century, they have shown potential in addressing various scientific challenges and saving lives through gene editing therapies, particularly in combating cardiovascular disease (CVD). The rapid advancement of gene editing therapies has provided optimism for CVD patients. The progress of gene editing therapy for CVDs is a comprehensive reflection of the practical implementation of gene editing technology in both clinical and basic research settings, as well as the steady advancement of research and treatment of CVDs. This article provides an overview of the commonly utilized DNA-targeted gene editing tools developed thus far, with a specific focus on the application of these tools, particularly the clustered regularly interspaced short palindromic repeat/CRISPR-associated genes (Cas) (CRISPR/Cas) system, in CVD gene editing therapy. It also delves into the challenges and limitations of current gene editing therapies, while summarizing ongoing research and clinical trials related to CVD. The aim is to facilitate further exploration by relevant researchers by summarizing the successful applications of gene editing tools in the field of CVD.
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Affiliation(s)
- Xinyu Wu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious DiseasesKey Laboratory for Zoonosis Research of the Ministry of Educationand College of Veterinary MedicineJilin UniversityChangchunChina
| | - Jie Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious DiseasesKey Laboratory for Zoonosis Research of the Ministry of Educationand College of Veterinary MedicineJilin UniversityChangchunChina
| | - Jiayao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious DiseasesKey Laboratory for Zoonosis Research of the Ministry of Educationand College of Veterinary MedicineJilin UniversityChangchunChina
| | - Yuning Song
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious DiseasesKey Laboratory for Zoonosis Research of the Ministry of Educationand College of Veterinary MedicineJilin UniversityChangchunChina
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13
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Schann K, Bakker J, Boinot M, Kuschel P, He H, Nattermann M, Paczia N, Erb T, Bar‐Even A, Wenk S. Design, construction and optimization of formaldehyde growth biosensors with broad application in biotechnology. Microb Biotechnol 2024; 17:e14527. [PMID: 39031508 PMCID: PMC11259041 DOI: 10.1111/1751-7915.14527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 07/02/2024] [Indexed: 07/22/2024] Open
Abstract
Formaldehyde is a key metabolite in natural and synthetic one-carbon metabolism. To facilitate the engineering of formaldehyde-producing enzymes, the development of sensitive, user-friendly, and cost-effective detection methods is required. In this study, we engineered Escherichia coli to serve as a cellular biosensor capable of detecting a broad range of formaldehyde concentrations. Using both natural and promiscuous formaldehyde assimilation enzymes, we designed three distinct E. coli growth biosensor strains that depend on formaldehyde for cell growth. These strains were engineered to be auxotrophic for one or several essential metabolites that could be produced through formaldehyde assimilation. The respective assimilating enzyme was expressed from the genome to compensate the auxotrophy in the presence of formaldehyde. We first predicted the formaldehyde dependency of the biosensors by flux balance analysis and then analysed it experimentally. Subsequent to strain engineering, we enhanced the formaldehyde sensitivity of two biosensors either through adaptive laboratory evolution or modifications at metabolic branch points. The final set of biosensors demonstrated the ability to detect formaldehyde concentrations ranging approximately from 30 μM to 13 mM. We demonstrated the application of the biosensors by assaying the in vivo activity of different methanol dehydrogenases in the most sensitive strain. The fully genomic nature of the biosensors allows them to be deployed as "plug-and-play" devices for high-throughput screenings of extensive enzyme libraries. The formaldehyde growth biosensors developed in this study hold significant promise for advancing the field of enzyme engineering, thereby supporting the establishment of a sustainable one-carbon bioeconomy.
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Affiliation(s)
- Karin Schann
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Jenny Bakker
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Maximilian Boinot
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Pauline Kuschel
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Hai He
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | | | - Nicole Paczia
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Tobias Erb
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Arren Bar‐Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Sebastian Wenk
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
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14
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Jansen S, Mayer C. A Robust Growth-Based Selection Platform to Evolve an Enzyme via Dependency on Noncanonical Tyrosine Analogues. JACS AU 2024; 4:1583-1590. [PMID: 38665651 PMCID: PMC11040555 DOI: 10.1021/jacsau.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 04/28/2024]
Abstract
Growth-based selections evaluate the fitness of individual organisms at a population level. In enzyme engineering, such growth selections allow for the rapid and straightforward identification of highly efficient biocatalysts from extensive libraries. However, selection-based improvement of (synthetically useful) biocatalysts is challenging, as they require highly dependable strategies that artificially link their activities to host survival. Here, we showcase a robust and scalable growth-based selection platform centered around the complementation of noncanonical amino acid-dependent bacteria. Specifically, we demonstrate how serial passaging of populations featuring millions of carbamoylase variants autonomously selects biocatalysts with up to 90,000-fold higher initial rates. Notably, selection of replicate populations enriched diverse biocatalysts, which feature distinct amino acid motifs that drastically boost carbamoylase activity. As beneficial substitutions also originated from unintended copying errors during library preparation or cell division, we anticipate that our growth-based selection platform will be applicable to the continuous, autonomous evolution of diverse biocatalysts in the future.
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Affiliation(s)
- Suzanne
C. Jansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
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15
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Mercer JAM, DeCarlo SJ, Roy Burman SS, Sreekanth V, Nelson AT, Hunkeler M, Chen PJ, Donovan KA, Kokkonda P, Tiwari PK, Shoba VM, Deb A, Choudhary A, Fischer ES, Liu DR. Continuous evolution of compact protein degradation tags regulated by selective molecular glues. Science 2024; 383:eadk4422. [PMID: 38484051 PMCID: PMC11203266 DOI: 10.1126/science.adk4422] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/09/2024] [Indexed: 03/19/2024]
Abstract
Conditional protein degradation tags (degrons) are usually >100 amino acids long or are triggered by small molecules with substantial off-target effects, thwarting their use as specific modulators of endogenous protein levels. We developed a phage-assisted continuous evolution platform for molecular glue complexes (MG-PACE) and evolved a 36-amino acid zinc finger (ZF) degron (SD40) that binds the ubiquitin ligase substrate receptor cereblon in complex with PT-179, an orthogonal thalidomide derivative. Endogenous proteins tagged in-frame with SD40 using prime editing are degraded by otherwise inert PT-179. Cryo-electron microscopy structures of SD40 in complex with ligand-bound cereblon revealed mechanistic insights into the molecular basis of SD40's activity and specificity. Our efforts establish a system for continuous evolution of molecular glue complexes and provide ZF tags that overcome shortcomings associated with existing degrons.
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Affiliation(s)
- Jaron A. M. Mercer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
| | - Stephan J. DeCarlo
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
| | - Shourya S. Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA 02115
| | - Andrew T. Nelson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Peter J. Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Praveen K. Tiwari
- Chemical Biology and Therapeutics Science, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA 02115
| | - Veronika M. Shoba
- Chemical Biology and Therapeutics Science, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Arghya Deb
- Chemical Biology and Therapeutics Science, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA 02115
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
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16
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Hwang HG, Ye DY, Jung GY. Biosensor-guided discovery and engineering of metabolic enzymes. Biotechnol Adv 2023; 69:108251. [PMID: 37690614 DOI: 10.1016/j.biotechadv.2023.108251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.
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Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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17
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Li Z, Deng Y, Yang GY. Growth-coupled high throughput selection for directed enzyme evolution. Biotechnol Adv 2023; 68:108238. [PMID: 37619825 DOI: 10.1016/j.biotechadv.2023.108238] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Directed enzyme evolution has revolutionized the rapid development of enzymes with desired properties. However, the lack of a high-throughput method to identify the most suitable variants from a large pool of genetic diversity poses a major bottleneck. To overcome this challenge, growth-coupled in vivo high-throughput selection approaches (GCHTS) have emerged as a novel selection system for enzyme evolution. GCHTS links the survival of the host cell with the properties of the target protein, resulting in a screening system that is easily measurable and has a high throughput-scale limited only by transformation efficiency. This allows for the rapid identification of desired variants from a pool of >109 variants in each experiment. In recent years, GCHTS approaches have been extensively utilized in the directed evolution of multiple enzymes, demonstrating success in catalyzing non-native substrates, enhancing catalytic activity, and acquiring novel functions. This review introduces three main strategies employed to achieve GCHTS: the elimination of toxic compounds via desired variants, enabling host cells to thrive in hazardous conditions; the complementation of an auxotroph with desired variants, where essential genes for cell growth have been eliminated; and the control of the transcription or expression of a reporter gene related to host cell growth, regulated by the desired variants. Additionally, we highlighted the recent developments in the in vivo continuous evolution of enzyme technology, including phage-assisted continuous evolution (PACE) and orthogonal DNA Replication (OrthoRep). Furthermore, this review discusses the challenges and future prospects in the field of growth-coupled selection for protein engineering.
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Affiliation(s)
- Zhengqun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuting Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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18
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Jewel D, Pham Q, Chatterjee A. Virus-assisted directed evolution of biomolecules. Curr Opin Chem Biol 2023; 76:102375. [PMID: 37542745 PMCID: PMC10870257 DOI: 10.1016/j.cbpa.2023.102375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 08/07/2023]
Abstract
Directed evolution is a powerful technique that uses principles of natural evolution to enable the development of biomolecules with novel functions. However, the slow pace of natural evolution does not support the demand for rapidly generating new biomolecular functions in the laboratory. Viruses offer a unique path to design fast laboratory evolution experiments, owing to their innate ability to evolve much more rapidly than most living organisms, facilitated by a smaller genome size that tolerate a high frequency of mutations, as well as a fast rate of replication. These attributes offer a great opportunity to evolve various biomolecules by linking their activity to the replication of a suitable virus. This review highlights the recent advances in the application of virus-assisted directed evolution of designer biomolecules in both prokaryotic and eukaryotic cells.
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Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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19
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Gan Y, Meng X, Gao C, Song W, Liu L, Chen X. Metabolic engineering strategies for microbial utilization of methanol. ENGINEERING MICROBIOLOGY 2023; 3:100081. [PMID: 39628934 PMCID: PMC11611044 DOI: 10.1016/j.engmic.2023.100081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/19/2023] [Accepted: 02/25/2023] [Indexed: 12/06/2024]
Abstract
The increasing shortage of fossil resources and environmental pollution has renewed interest in the synthesis of value-added biochemicals from methanol. However, most of native or synthetic methylotrophs are unable to assimilate methanol at a sufficient rate to produce biochemicals. Thus, the performance of methylotrophs still needs to be optimized to meet the demands of industrial applications. In this review, we provide an in-depth discussion on the properties of natural and synthetic methylotrophs, and summarize the natural and synthetic methanol assimilation pathways. Further, we discuss metabolic engineering strategies for enabling microbial utilization of methanol for the bioproduction of value-added chemicals. Finally, we highlight the potential of microbial engineering for methanol assimilation and offer guidance for achieving a low-carbon footprint for the biosynthesis of chemicals.
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Affiliation(s)
- Yamei Gan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xin Meng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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20
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Qian J, Fan L, Yang J, Feng J, Gao N, Cheng G, Pu W, Zhou W, Cai T, Li S, Zheng P, Sun J, Wang D, Wang Y. Directed evolution of a neutrophilic and mesophilic methanol dehydrogenase based on high-throughput and accurate measurement of formaldehyde. Synth Syst Biotechnol 2023; 8:386-395. [PMID: 37342805 PMCID: PMC10277290 DOI: 10.1016/j.synbio.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/01/2023] [Accepted: 05/21/2023] [Indexed: 06/23/2023] Open
Abstract
Methanol is a promising one-carbon feedstock for biomanufacturing, which can be sustainably produced from carbon dioxide and natural gas. However, the efficiency of methanol bioconversion is limited by the poor catalytic properties of nicotinamide adenine dinucleotide (NAD+)-dependent methanol dehydrogenase (Mdh) that oxidizes methanol to formaldehyde. Herein, the neutrophilic and mesophilic NAD+-dependent Mdh from Bacillus stearothermophilus DSM 2334 (MdhBs) was subjected to directed evolution for enhancing the catalytic activity. The combination of formaldehyde biosensor and Nash assay allowed high-throughput and accurate measurement of formaldehyde and facilitated efficient selection of desired variants. MdhBs variants with up to 6.5-fold higher Kcat/KM value for methanol were screened from random mutation libraries. The T153 residue that is spatially proximal to the substrate binding pocket has significant influence on enzyme activity. The beneficial T153P mutation changes the interaction network of this residue and breaks the α-helix important for substrate binding into two short α-helices. Reconstructing the interaction network of T153 with surrounding residues may represent a promising strategy to further improve MdhBs, and this study provides an efficient strategy for directed evolution of Mdh.
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Affiliation(s)
- Jin Qian
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Liwen Fan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jinxing Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jinhui Feng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ning Gao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guimin Cheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wei Pu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wenjuan Zhou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Cai
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ping Zheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
| | - Yu Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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21
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Doman JL, Pandey S, Neugebauer ME, An M, Davis JR, Randolph PB, McElroy A, Gao XD, Raguram A, Richter MF, Everette KA, Banskota S, Tian K, Tao YA, Tolar J, Osborn MJ, Liu DR. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 2023; 186:3983-4002.e26. [PMID: 37657419 PMCID: PMC10482982 DOI: 10.1016/j.cell.2023.07.039] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/07/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023]
Abstract
Prime editing enables a wide variety of precise genome edits in living cells. Here we use protein evolution and engineering to generate prime editors with reduced size and improved efficiency. Using phage-assisted evolution, we improved editing efficiencies of compact reverse transcriptases by up to 22-fold and generated prime editors that are 516-810 base pairs smaller than the current-generation editor PEmax. We discovered that different reverse transcriptases specialize in different types of edits and used this insight to generate reverse transcriptases that outperform PEmax and PEmaxΔRNaseH, the truncated editor used in dual-AAV delivery systems. Finally, we generated Cas9 domains that improve prime editing. These resulting editors (PE6a-g) enhance therapeutically relevant editing in patient-derived fibroblasts and primary human T-cells. PE6 variants also enable longer insertions to be installed in vivo following dual-AAV delivery, achieving 40% loxP insertion in the cortex of the murine brain, a 24-fold improvement compared to previous state-of-the-art prime editors.
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Affiliation(s)
- Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Monica E Neugebauer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Peyton B Randolph
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Amber McElroy
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Michelle F Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kelcee A Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kathryn Tian
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Y Allen Tao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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22
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Krüsemann JL, Rainaldi V, Cotton CA, Claassens NJ, Lindner SN. The cofactor challenge in synthetic methylotrophy: bioengineering and industrial applications. Curr Opin Biotechnol 2023; 82:102953. [PMID: 37320962 DOI: 10.1016/j.copbio.2023.102953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/03/2023] [Accepted: 05/14/2023] [Indexed: 06/17/2023]
Abstract
Methanol is a promising feedstock for industrial bioproduction: it can be produced renewably and has high solubility and limited microbial toxicity. One of the key challenges for its bio-industrial application is the first enzymatic oxidation step to formaldehyde. This reaction is catalysed by methanol dehydrogenases (MDH) that can use NAD+, O2 or pyrroloquinoline quinone (PQQ) as an electron acceptor. While NAD-dependent MDH are simple to express and have the highest energetic efficiency, they exhibit mediocre kinetics and poor thermodynamics at ambient temperatures. O2-dependent methanol oxidases require high oxygen concentrations, do not conserve energy and thus produce excessive heat as well as toxic H2O2. PQQ-dependent MDH provide a good compromise between energy efficiency and good kinetics that support fast growth rates without any drawbacks for process engineering. Therefore, we argue that this enzyme class represents a promising solution for industry and outline engineering strategies for the implementation of these complex systems in heterologous hosts.
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Affiliation(s)
- Jan L Krüsemann
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry and Synthetic Metabolism, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Vittorio Rainaldi
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Steffen N Lindner
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Charitéplatz 1, 10117 Berlin, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.
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23
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Neugebauer ME, Hsu A, Arbab M, Krasnow NA, McElroy AN, Pandey S, Doman JL, Huang TP, Raguram A, Banskota S, Newby GA, Tolar J, Osborn MJ, Liu DR. Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity. Nat Biotechnol 2023; 41:673-685. [PMID: 36357719 PMCID: PMC10188366 DOI: 10.1038/s41587-022-01533-6] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/28/2022] [Indexed: 11/12/2022]
Abstract
Cytosine base editors (CBEs) are larger and can suffer from higher off-target activity or lower on-target editing efficiency than current adenine base editors (ABEs). To develop a CBE that retains the small size, low off-target activity and high on-target activity of current ABEs, we evolved the highly active deoxyadenosine deaminase TadA-8e to perform cytidine deamination using phage-assisted continuous evolution. Evolved TadA cytidine deaminases contain mutations at DNA-binding residues that alter enzyme selectivity to strongly favor deoxycytidine over deoxyadenosine deamination. Compared to commonly used CBEs, TadA-derived cytosine base editors (TadCBEs) offer similar or higher on-target activity, smaller size and substantially lower Cas-independent DNA and RNA off-target editing activity. We also identified a TadA dual base editor (TadDE) that performs equally efficient cytosine and adenine base editing. TadCBEs support single or multiplexed base editing at therapeutically relevant genomic loci in primary human T cells and primary human hematopoietic stem and progenitor cells. TadCBEs expand the utility of CBEs for precision gene editing.
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Affiliation(s)
- Monica E Neugebauer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Alvin Hsu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Mandana Arbab
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Nicholas A Krasnow
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Amber N McElroy
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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24
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Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more suitable for specific applications. Since the first in vitro evolution experiments performed by Sol Spiegelman in 1967, a wide range of techniques have been developed to tackle the main two steps of directed evolution: genetic diversification (library generation), and isolation of the variants of interest. This review covers the main modern methodologies, discussing the advantages and drawbacks of each, and hence the considerations for designing directed evolution experiments. Furthermore, the most recent developments are discussed, showing how advances in the handling of ever larger library sizes are enabling new research questions to be tackled.
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Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- School of Life Sciences, The University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
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25
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Kar B, Castillo SR, Sabharwal A, Clark KJ, Ekker SC. Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities. Int J Mol Sci 2023; 24:5798. [PMID: 36982871 PMCID: PMC10056815 DOI: 10.3390/ijms24065798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are critical organelles that form networks within our cells, generate energy dynamically, contribute to diverse cell and organ function, and produce a variety of critical signaling molecules, such as cortisol. This intracellular microbiome can differ between cells, tissues, and organs. Mitochondria can change with disease, age, and in response to the environment. Single nucleotide variants in the circular genomes of human mitochondrial DNA are associated with many different life-threatening diseases. Mitochondrial DNA base editing tools have established novel disease models and represent a new possibility toward personalized gene therapies for the treatment of mtDNA-based disorders.
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Affiliation(s)
- Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Santiago R. Castillo
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Mayo Clinic, Rochester, MN 55905, USA
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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26
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Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
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Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
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27
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Keller P, Reiter MA, Kiefer P, Gassler T, Hemmerle L, Christen P, Noor E, Vorholt JA. Generation of an Escherichia coli strain growing on methanol via the ribulose monophosphate cycle. Nat Commun 2022; 13:5243. [PMID: 36068201 PMCID: PMC9448777 DOI: 10.1038/s41467-022-32744-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Methanol is a liquid with high energy storage capacity that holds promise as an alternative substrate to replace sugars in the biotechnology industry. It can be produced from CO2 or methane and its use does not compete with food and animal feed production. However, there are currently only limited biotechnological options for the valorization of methanol, which hinders its widespread adoption. Here, we report the conversion of the industrial platform organism Escherichia coli into a synthetic methylotroph that assimilates methanol via the energy efficient ribulose monophosphate cycle. Methylotrophy is achieved after evolution of a methanol-dependent E. coli strain over 250 generations in continuous chemostat culture. We demonstrate growth on methanol and biomass formation exclusively from the one-carbon source by 13C isotopic tracer analysis. In line with computational modeling, the methylotrophic E. coli strain optimizes methanol oxidation by upregulation of an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway and downregulating tricarboxylic acid cycle enzymes. En route towards sustainable bioproduction processes, our work lays the foundation for the efficient utilization of methanol as the dominant carbon and energy resource. Using one carbon compounds as feedstock is a promising approach in abating climate change. Here, the authors report the conversion of E. coli into a synthetic methylotroph that assimilates methanol via the ribulose monophosphate cycle and a set of distinctive mutations.
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Affiliation(s)
- Philipp Keller
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Michael A Reiter
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Thomas Gassler
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland.,Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Philipp Christen
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland.
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28
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Andon JS, Lee B, Wang T. Enzyme directed evolution using genetically encodable biosensors. Org Biomol Chem 2022; 20:5891-5906. [PMID: 35437559 DOI: 10.1039/d2ob00443g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Directed evolution has been remarkably successful in identifying enzyme variants with new or improved properties, such as altered substrate scope or novel reactivity. Genetically encodable biosensors (GEBs), which convert the concentration of a small molecule ligand into an easily detectable output signal, have seen increasing application to enzyme directed evolution in the last decade. GEBs enable the use of high-throughput methods to assess enzyme activity of very large libraries, which can accelerate the search for variants with desirable activity. Here, we review different classes of GEBs and their properties in the context of enzyme evolution, how GEBs have been integrated into directed evolution workflows, and recent examples of enzyme evolution efforts utilizing GEBs. Finally, we discuss the advantages, challenges, and opportunities for using GEBs in the directed evolution of enzymes.
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Affiliation(s)
- James S Andon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - ByungUk Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Tina Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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29
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Peiro C, Vicente CM, Jallet D, Heux S. From a Hetero- to a Methylotrophic Lifestyle: Flash Back on the Engineering Strategies to Create Synthetic Methanol-User Strains. Front Bioeng Biotechnol 2022; 10:907861. [PMID: 35757790 PMCID: PMC9214030 DOI: 10.3389/fbioe.2022.907861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/16/2022] [Indexed: 12/31/2022] Open
Abstract
Engineering microorganisms to grow on alternative feedstocks is crucial not just because of the indisputable biotechnological applications but also to deepen our understanding of microbial metabolism. One-carbon (C1) substrate metabolism has been the focus of extensive research for the prominent role of C1 compounds in establishing a circular bioeconomy. Methanol in particular holds great promise as it can be produced directly from greenhouse gases methane and carbon dioxide using renewable resources. Synthetic methylotrophy, i.e. introducing a non-native methanol utilization pathway into a model host, has therefore been the focus of long-time efforts and is perhaps the pinnacle of metabolic engineering. It entails completely changing a microorganism's lifestyle, from breaking up multi-carbon nutrients for growth to building C-C bonds from a single-carbon molecule to obtain all metabolites necessary to biomass formation as well as energy. The frontiers of synthetic methylotrophy have been pushed further than ever before and in this review, we outline the advances that paved the way for the more recent accomplishments. These include optimizing the host's metabolism, "copy and pasting" naturally existing methylotrophic pathways, "mixing and matching" enzymes to build new pathways, and even creating novel enzymatic functions to obtain strains that are able to grow solely on methanol. Finally, new approaches are contemplated to further advance the field and succeed in obtaining a strain that efficiently grows on methanol and allows C1-based production of added-value compounds.
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Affiliation(s)
- Camille Peiro
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Denis Jallet
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Stephanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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30
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CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat Biotechnol 2022; 40:1378-1387. [PMID: 35379961 PMCID: PMC9463067 DOI: 10.1038/s41587-022-01256-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/08/2022] [Indexed: 12/21/2022]
Abstract
The all-protein cytosine base editor DdCBE uses TALE proteins and a double-stranded DNA-specific cytidine deaminase (DddA) to mediate targeted C•G-to-T•A editing. To improve editing efficiency and overcome the strict TC sequence-context constraint of DddA, we used phage-assisted non-continuous and continuous evolution to evolve DddA variants with improved activity and expanded targeting scope. Compared to canonical DdCBEs, base editors with evolved DddA6 improved mitochondrial DNA (mtDNA) editing efficiencies at TC by 3.3-fold on average. DdCBEs containing evolved DddA11 offered a broadened HC (H = A, C or T) sequence compatibility for both mitochondrial and nuclear base editing, increasing average editing efficiencies at AC and CC targets from less than 10% for canonical DdCBE to 15-30% and up to 50% in cell populations sorted to express both halves of DdCBE. We used these evolved DdCBEs to efficiently install disease-associated mtDNA mutations in human cells at non-TC target sites. DddA6 and DddA11 substantially increase the effectiveness and applicability of all-protein base editing.
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31
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Yu SY, Birkenshaw A, Thomson T, Carlaw T, Zhang LH, Ross CJD. Increasing the Targeting Scope of CRISPR Base Editing System Beyond NGG. CRISPR J 2022; 5:187-202. [PMID: 35238621 DOI: 10.1089/crispr.2021.0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genome editing provides a new therapeutic strategy to cure genetic diseases. The recently developed CRISPR-Cas9 base editing technology has shown great potential to repair the majority of pathogenic point mutations in the patient's DNA precisely. Base editor is the fusion of a Cas9 nickase with a base-modifying enzyme that can change a nucleotide on a single strand of DNA without generating double-stranded DNA breaks. However, a major limitation in applying such a system is the prerequisite of a protospacer adjacent motif sequence at the desired position relative to the target site. Progress has been made to increase the targeting scope of base editors by engineering SpCas9 protein variants, establishing systems with broadened editing windows, characterizing new SpCas9 orthologs, and developing prime editing technology. In this review, we discuss recent progress in the development of CRISPR base editing, focusing on its targeting scope, and we provide a workflow for selecting a suitable base editor based on the target nucleotide sequences.
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Affiliation(s)
- Si-Yue Yu
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Alexandra Birkenshaw
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Tyler Thomson
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Tiffany Carlaw
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Lin-Hua Zhang
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Colin J D Ross
- Faculty of Pharmaceutical Sciences, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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32
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McLure RJ, Radford SE, Brockwell DJ. High-throughput directed evolution: a golden era for protein science. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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33
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Al'Abri IS, Haller DJ, Li Z, Crook N. Inducible directed evolution of complex phenotypes in bacteria. Nucleic Acids Res 2022; 50:e58. [PMID: 35150576 PMCID: PMC9177967 DOI: 10.1093/nar/gkac094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 12/22/2021] [Accepted: 02/01/2022] [Indexed: 11/15/2022] Open
Abstract
Directed evolution is a powerful method for engineering biology in the absence of detailed sequence-function relationships. To enable directed evolution of complex phenotypes encoded by multigene pathways, we require large library sizes for DNA sequences >5–10 kb in length, elimination of genomic hitchhiker mutations, and decoupling of diversification and screening steps. To meet these challenges, we developed Inducible Directed Evolution (IDE), which uses a temperate bacteriophage to package large plasmids and transfer them to naive cells after intracellular mutagenesis. To demonstrate IDE, we evolved a 5-gene pathway from Bacillus licheniformis that accelerates tagatose catabolism in Escherichia coli, resulting in clones with 65% shorter lag times during growth on tagatose after only two rounds of evolution. Next, we evolved a 15.4 kb, 10-gene pathway from Bifidobacterium breve UC2003 that aids E. coli’s utilization of melezitose. After three rounds of IDE, we isolated evolved pathways that both reduced lag time by more than 2-fold and enabled 150% higher final optical density. Taken together, this work enhances the capacity and utility of a whole pathway directed evolution approach in E. coli.
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Affiliation(s)
- Ibrahim S Al'Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Daniel J Haller
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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34
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Trivedi VD, Mohan K, Chappell TC, Mays ZJS, Nair NU. Cheating the Cheater: Suppressing False-Positive Enrichment during Biosensor-Guided Biocatalyst Engineering. ACS Synth Biol 2022; 11:420-429. [PMID: 34914365 DOI: 10.1021/acssynbio.1c00506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Transcription factor (TF)-based biosensors are very desirable reagents for high-throughput enzyme and strain engineering campaigns. Despite their potential, they are often difficult to deploy effectively as the small molecules being detected can leak out of high-producer cells, into low-producer cells, and activate the biosensor therein. This crosstalk leads to the overrepresentation of false-positive/cheater cells in the enriched population. While the host cell can be engineered to minimize crosstalk (e.g., by deleting responsible transporters), this is not easily applicable to all molecules of interest, particularly those that can diffuse passively. One such biosensor recently reported for trans-cinnamic acid (tCA) suffers from crosstalk when used for phenylalanine ammonia-lyase (PAL) enzyme engineering by directed evolution. We report that desensitizing the biosensor (i.e., increasing the limit of detection) suppresses cheater population enrichment. Furthermore, we show that, if we couple the biosensor-based screen with an orthogonal prescreen that eliminates a large fraction of true negatives, we can successfully reduce the cheater population during the fluorescence-activated cell sorting. Using the approach developed here, we were successfully able to isolate PAL variants with ∼70% higher kcat after a single sort. These mutants have tremendous potential in phenylketonuria (PKU) treatment and flavonoid production.
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Affiliation(s)
- Vikas D. Trivedi
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Karishma Mohan
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Todd C. Chappell
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Zachary J. S. Mays
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Nikhil U. Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
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35
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Le TK, Lee YJ, Han GH, Yeom SJ. Methanol Dehydrogenases as a Key Biocatalysts for Synthetic Methylotrophy. Front Bioeng Biotechnol 2022; 9:787791. [PMID: 35004648 PMCID: PMC8741260 DOI: 10.3389/fbioe.2021.787791] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
One-carbon (C1) chemicals are potential building blocks for cheap and sustainable re-sources such as methane, methanol, formaldehyde, formate, carbon monoxide, and more. These resources have the potential to be made into raw materials for various products used in our daily life or precursors for pharmaceuticals through biological and chemical processes. Among the soluble C1 substrates, methanol is regarded as a biorenewable platform feedstock because nearly all bioresources can be converted into methanol through syngas. Synthetic methylotrophy can be exploited to produce fuels and chemicals using methanol as a feedstock that integrates natural or artificial methanol assimilation pathways in platform microorganisms. In the methanol utilization in methylotrophy, methanol dehydrogenase (Mdh) is a primary enzyme that converts methanol to formaldehyde. The discovery of new Mdhs and engineering of present Mdhs have been attempted to develop synthetic methylotrophic bacteria. In this review, we describe Mdhs, including in terms of their enzyme properties and engineering for desired activity. In addition, we specifically focus on the application of various Mdhs for synthetic methylotrophy.
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Affiliation(s)
- Thien-Kim Le
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Yu-Jin Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea.,School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju, South Korea
| | - Gui Hwan Han
- Center for Industrialization of Agricultural and Livestock Microorganisms (CIALM), Jeollabuk-do, South Korea
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea.,School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju, South Korea
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36
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Morrison MS, Wang T, Raguram A, Hemez C, Liu DR. Disulfide-compatible phage-assisted continuous evolution in the periplasmic space. Nat Commun 2021; 12:5959. [PMID: 34645844 PMCID: PMC8514426 DOI: 10.1038/s41467-021-26279-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/27/2021] [Indexed: 11/18/2022] Open
Abstract
The directed evolution of antibodies has yielded important research tools and human therapeutics. The dependence of many antibodies on disulfide bonds for stability has limited the application of continuous evolution technologies to antibodies and other disulfide-containing proteins. Here we describe periplasmic phage-assisted continuous evolution (pPACE), a system for continuous evolution of protein-protein interactions in the disulfide-compatible environment of the E. coli periplasm. We first apply pPACE to rapidly evolve novel noncovalent and covalent interactions between subunits of homodimeric YibK protein and to correct a binding-defective mutant of the anti-GCN4 Ω-graft antibody. We develop an intein-mediated system to select for soluble periplasmic expression in pPACE, leading to an eight-fold increase in soluble expression of the Ω-graft antibody. Finally, we evolve disulfide-containing trastuzumab antibody variants with improved binding to a Her2-like peptide and improved soluble expression. Together, these results demonstrate that pPACE can rapidly optimize proteins containing disulfide bonds, broadening the applicability of continuous evolution.
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Affiliation(s)
- Mary S Morrison
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Tina Wang
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Colin Hemez
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.
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37
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Jones K, Snodgrass HM, Belsare K, Dickinson BC, Lewis JC. Phage-Assisted Continuous Evolution and Selection of Enzymes for Chemical Synthesis. ACS CENTRAL SCIENCE 2021; 7:1581-1590. [PMID: 34584960 PMCID: PMC8461764 DOI: 10.1021/acscentsci.1c00811] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 05/04/2023]
Abstract
Ligand-dependent biosensors are valuable tools for coupling the intracellular concentrations of small molecules to easily detectable readouts such as absorbance, fluorescence, or cell growth. While ligand-dependent biosensors are widely used for monitoring the production of small molecules in engineered cells and for controlling or optimizing biosynthetic pathways, their application to directed evolution for biocatalysts remains underexplored. As a consequence, emerging continuous evolution technologies are rarely applied to biocatalyst evolution. Here, we develop a panel of ligand-dependent biosensors that can detect a range of small molecules. We demonstrate that these biosensors can link enzymatic activity to the production of an essential phage protein to enable biocatalyst-dependent phage-assisted continuous evolution (PACE) and phage-assisted continuous selection (PACS). By combining these phage-based evolution and library selection technologies, we demonstrate that we can evolve enzyme variants with improved and expanded catalytic properties. Finally, we show that the genetic diversity resulting from a highly mutated PACS library is enriched for active enzyme variants with altered substrate scope. These results lay the foundation for using phage-based continuous evolution and selection technologies to engineer biocatalysts with novel substrate scope and reactivity.
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Affiliation(s)
- Krysten
A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Ketaki Belsare
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- E-mail:
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
- E-mail:
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38
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Gregory GJ, Bennett RK, Papoutsakis ET. Recent advances toward the bioconversion of methane and methanol in synthetic methylotrophs. Metab Eng 2021; 71:99-116. [PMID: 34547453 DOI: 10.1016/j.ymben.2021.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022]
Abstract
Abundant natural gas reserves, along with increased biogas production, have prompted recent interest in harnessing methane as an industrial feedstock for the production of liquid fuels and chemicals. Methane can either be used directly for fermentation or first oxidized to methanol via biological or chemical means. Methanol is advantageous due to its liquid state under normal conditions. Methylotrophy, defined as the ability of microorganisms to utilize reduced one-carbon compounds like methane and methanol as sole carbon and energy sources for growth, is widespread in bacterial communities. However, native methylotrophs lack the extensive and well-characterized synthetic biology toolbox of platform microorganisms like Escherichia coli, which results in slow and inefficient design-build-test cycles. If a heterologous production pathway can be engineered, the slow growth and uptake rates of native methylotrophs generally limit their industrial potential. Therefore, much focus has been placed on engineering synthetic methylotrophs, or non-methylotrophic platform microorganisms, like E. coli, that have been engineered with synthetic methanol utilization pathways. These platform hosts allow for rapid design-build-test cycles and are well-suited for industrial application at the current time. In this review, recent progress made toward synthetic methylotrophy (including methanotrophy) is discussed. Specifically, the importance of amino acid metabolism and alternative one-carbon assimilation pathways are detailed. A recent study that has achieved methane bioconversion to liquid chemicals in a synthetic E. coli methanotroph is also briefly discussed. We also discuss strategies for the way forward in order to realize the industrial potential of synthetic methanotrophs and methylotrophs.
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Affiliation(s)
- Gwendolyn J Gregory
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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39
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Dewey JA, Azizi SA, Lu V, Dickinson BC. A System for the Evolution of Protein-Protein Interaction Inducers. ACS Synth Biol 2021; 10:2096-2110. [PMID: 34319091 DOI: 10.1021/acssynbio.1c00276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecules that induce interactions between proteins, often referred to as "molecular glues", are increasingly recognized as important therapeutic modalities and as entry points for rewiring cellular signaling networks. Here, we report a new PACE-based method to rapidly select and evolve molecules that mediate interactions between otherwise noninteracting proteins: rapid evolution of protein-protein interaction glues (rePPI-G). By leveraging proximity-dependent split RNA polymerase-based biosensors, we developed E. coli-based detection and selection systems that drive gene expression outputs only when interactions between target proteins are induced. We then validated the system using engineered bivalent molecular glues, showing that rePPI-G robustly selects for molecules that induce the target interaction. Proof-of-concept evolutions demonstrated that rePPI-G reduces the "hook effect" of the engineered molecular glues, due at least in part to tuning the interaction affinities of each individual component of the bifunctional molecule. Altogether, this work validates rePPI-G as a continuous, phage-based evolutionary technology for optimizing molecular glues, providing a strategy for developing molecules that reprogram protein-protein interactions.
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Affiliation(s)
- Jeffrey A. Dewey
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Vivian Lu
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
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40
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Ho JML, Miller CA, Smith KA, Mattia JR, Bennett MR. Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway. Nat Commun 2021; 12:3914. [PMID: 34168131 PMCID: PMC8225853 DOI: 10.1038/s41467-021-24183-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Pyrrolysine (Pyl, O) exists in nature as the 22nd proteinogenic amino acid. Despite being a fundamental building block of proteins, studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, we improve Pyl biosynthesis via rational engineering and directed evolution of the entire biosynthetic pathway. To accommodate toxicity of Pyl biosynthetic genes in Escherichia coli, we also develop Alternating Phage Assisted Non-Continuous Evolution (Alt-PANCE) that alternates mutagenic and selective phage growths. The evolved pathway provides 32-fold improved yield of Pyl-containing reporter protein compared to the rationally engineered ancestor. Evolved PylB mutants are present at up to 4.5-fold elevated levels inside cells, and show up to 2.2-fold increased protease resistance. This study demonstrates that Alt-PANCE provides a general approach for evolving proteins exhibiting toxic side effects, and further provides an improved pathway capable of producing substantially greater quantities of Pyl-proteins in E. coli. Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.
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Affiliation(s)
- Joanne M L Ho
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Corwin A Miller
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Kathryn A Smith
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Jacob R Mattia
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA.
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41
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Zhan C, Li X, Yang Y, Nielsen J, Bai Z, Chen Y. Strategies and challenges with the microbial conversion of methanol to high-value chemicals. Biotechnol Bioeng 2021; 118:3655-3668. [PMID: 34133022 DOI: 10.1002/bit.27862] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/25/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023]
Abstract
As alternatives to traditional fermentation substrates, methanol (CH3 OH), carbon dioxide (CO2 ) and methane (CH4 ) represent promising one-carbon (C1) sources that are readily available at low-cost and share similar metabolic pathway. Of these C1 compounds, methanol is used as a carbon and energy source by native methylotrophs, and can be obtained from CO2 and CH4 by chemical catalysis. Therefore, constructing and rewiring methanol utilization pathways may enable the use of one-carbon sources for microbial fermentations. Recent bioengineering efforts have shown that both native and nonnative methylotrophic organisms can be engineered to convert methanol, together with other carbon sources, into biofuels and other commodity chemicals. However, many challenges remain and must be overcome before industrial-scale bioprocessing can be established using these engineered cell refineries. Here, we provide a comprehensive summary and comparison of methanol metabolic pathways from different methylotrophs, followed by a review of recent progress in engineering methanol metabolic pathways in vitro and in vivo to produce chemicals. We discuss the major challenges associated with establishing efficient methanol metabolic pathways in microbial cells, and propose improved designs for future engineering.
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Affiliation(s)
- Chunjun Zhan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.,BioInnovation Institute, Copenhagen N, Denmark
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
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42
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Qi H, Ma M, Lai D, Tao SC. Phage display: an ideal platform for coupling protein to nucleic acid. Acta Biochim Biophys Sin (Shanghai) 2021; 53:389-399. [PMID: 33537750 DOI: 10.1093/abbs/gmab006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Indexed: 01/07/2023] Open
Abstract
Display technology, especially phage display technology, has been widely applied in many fields. The theoretical core of display technology is the physical linkage between the protein/peptide on the surface of a phage and the coding DNA sequence inside the same phage. Starting from phage-displayed peptide/protein/antibody libraries and taking advantage of the ever-growing power of next-generation sequencing (NGS) for DNA sequencing/decoding, rich protein-related information can easily be obtained in a high-throughput way. Based on this information, many scientific and clinical questions can be readily addressed. In the past few years, aided by the development of NGS, droplet technology, and massive oligonucleotide synthesis, we have witnessed and continue to witness large advances of phage display technology, in both technology development and application. The aim of this review is to summarize and discuss these recent advances.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingliang Ma
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Danyun Lai
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
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43
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Systems for in vivo hypermutation: a quest for scale and depth in directed evolution. Curr Opin Chem Biol 2021; 64:20-26. [PMID: 33784581 DOI: 10.1016/j.cbpa.2021.02.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022]
Abstract
Traditional approaches to the directed evolution of genes of interest (GOIs) place constraints on the scale of experimentation and depth of evolutionary search reasonably achieved. Engineered genetic systems that dramatically elevate the mutation of target GOIs in vivo relieve these constraints by enabling continuous evolution, affording new strategies in the exploration of sequence space and fitness landscapes for GOIs. We describe various in vivo hypermutation systems for continuous evolution, discuss how different architectures for in vivo hypermutation facilitate evolutionary search scale and depth in their application to problems in protein evolution and engineering, and outline future opportunities for the field.
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44
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Blum TR, Liu H, Packer MS, Xiong X, Lee PG, Zhang S, Richter M, Minasov G, Satchell KJF, Dong M, Liu DR. Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity. Science 2021; 371:803-810. [PMID: 33602850 DOI: 10.1126/science.abf5972] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022]
Abstract
Although bespoke, sequence-specific proteases have the potential to advance biotechnology and medicine, generation of proteases with tailor-made cleavage specificities remains a major challenge. We developed a phage-assisted protease evolution system with simultaneous positive and negative selection and applied it to three botulinum neurotoxin (BoNT) light-chain proteases. We evolved BoNT/X protease into separate variants that preferentially cleave vesicle-associated membrane protein 4 (VAMP4) and Ykt6, evolved BoNT/F protease to selectively cleave the non-native substrate VAMP7, and evolved BoNT/E protease to cleave phosphatase and tensin homolog (PTEN) but not any natural BoNT protease substrate in neurons. The evolved proteases display large changes in specificity (218- to >11,000,000-fold) and can retain their ability to form holotoxins that self-deliver into primary neurons. These findings establish a versatile platform for reprogramming proteases to selectively cleave new targets of therapeutic interest.
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Affiliation(s)
- Travis R Blum
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Hao Liu
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Michael S Packer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Pyung-Gang Lee
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Sicai Zhang
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA. .,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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45
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Chan SI, Chuankhayan P, Reddy Nareddy PK, Tsai IK, Tsai YF, Chen KHC, Yu SSF, Chen CJ. Mechanism of Pyrroloquinoline Quinone-Dependent Hydride Transfer Chemistry from Spectroscopic and High-Resolution X-ray Structural Studies of the Methanol Dehydrogenase from Methylococcus capsulatus (Bath). J Am Chem Soc 2021; 143:3359-3372. [PMID: 33629832 DOI: 10.1021/jacs.0c11414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The active site of methanol dehydrogenase (MDH) contains a rare disulfide bridge between adjacent cysteine residues. As a vicinal disulfide, the structure is highly strained, suggesting it might work together with the pyrroloquinoline quinone (PQQ) prosthetic group and the Ca2+ ion in the catalytic turnover during methanol (CH3OH) oxidation. We purify MDH from Methylococcus capsulatus (Bath) with the disulfide bridge broken into two thiols. Spectroscopic and high-resolution X-ray crystallographic studies of this form of MDH indicate that the disulfide bridge is redox active. We observe an internal redox process within the holo-MDH that produces a disulfide radical anion concomitant with a companion PQQ radical, as evidenced by an optical absorption at 408 nm and a magnetically dipolar-coupled biradical in the EPR spectrum. These observations are corroborated by electron-density changes between the two cysteine sulfurs of the disulfide bridge as well as between the bound Ca2+ ion and the O5-C5 bond of the PQQ in the high-resolution X-ray structure. On the basis of these findings, we propose a mechanism for the controlled redistribution of the two electrons during hydride transfer from the CH3OH in the alcohol oxidation without formation of the reduced PQQ ethenediol, a biradical mechanism that allows for possible recovery of the hydride for transfer to an external NAD+ oxidant in the regeneration of the PQQ cofactor for multiple catalytic turnovers. In support of this mechanism, a steady-state level of the disulfide radical anion is observed during turnover of the MDH in the presence of CH3OH and NAD+.
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Affiliation(s)
- Sunney I Chan
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | | | - I-Kuen Tsai
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Yi-Fang Tsai
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Kelvin H-C Chen
- Department of Applied Chemistry, National Pingtung University, Pingtung 90003, Taiwan
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
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Bennett RK, Gregory GJ, Gonzalez JE, Har JRG, Antoniewicz MR, Papoutsakis ET. Improving the Methanol Tolerance of an Escherichia coli Methylotroph via Adaptive Laboratory Evolution Enhances Synthetic Methanol Utilization. Front Microbiol 2021; 12:638426. [PMID: 33643274 PMCID: PMC7904680 DOI: 10.3389/fmicb.2021.638426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/21/2021] [Indexed: 02/05/2023] Open
Abstract
There is great interest in developing synthetic methylotrophs that harbor methane and methanol utilization pathways in heterologous hosts such as Escherichia coli for industrial bioconversion of one-carbon compounds. While there are recent reports that describe the successful engineering of synthetic methylotrophs, additional efforts are required to achieve the robust methylotrophic phenotypes required for industrial realization. Here, we address an important issue of synthetic methylotrophy in E. coli: methanol toxicity. Both methanol, and its oxidation product, formaldehyde, are cytotoxic to cells. Methanol alters the fluidity and biological properties of cellular membranes while formaldehyde reacts readily with proteins and nucleic acids. Thus, efforts to enhance the methanol tolerance of synthetic methylotrophs are important. Here, adaptive laboratory evolution was performed to improve the methanol tolerance of several E. coli strains, both methylotrophic and non-methylotrophic. Serial batch passaging in rich medium containing toxic methanol concentrations yielded clones exhibiting improved methanol tolerance. In several cases, these evolved clones exhibited a > 50% improvement in growth rate and biomass yield in the presence of high methanol concentrations compared to the respective parental strains. Importantly, one evolved clone exhibited a two to threefold improvement in the methanol utilization phenotype, as determined via 13C-labeling, at non-toxic, industrially relevant methanol concentrations compared to the respective parental strain. Whole genome sequencing was performed to identify causative mutations contributing to methanol tolerance. Common mutations were identified in 30S ribosomal subunit proteins, which increased translational accuracy and provided insight into a novel methanol tolerance mechanism. This study addresses an important issue of synthetic methylotrophy in E. coli and provides insight as to how methanol toxicity can be alleviated via enhancing methanol tolerance. Coupled improvement of methanol tolerance and synthetic methanol utilization is an important advancement for the field of synthetic methylotrophy.
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Affiliation(s)
- R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.,Molecular Biotechnology Laboratory, The Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Gwendolyn J Gregory
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.,Molecular Biotechnology Laboratory, The Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Jacqueline E Gonzalez
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Jie Ren Gerald Har
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.,Molecular Biotechnology Laboratory, The Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
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Inamoto I, Sheoran I, Popa SC, Hussain M, Shin JA. Combining Rational Design and Continuous Evolution on Minimalist Proteins That Target the E-box DNA Site. ACS Chem Biol 2021; 16:35-44. [PMID: 33370105 DOI: 10.1021/acschembio.0c00684] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based therapeutics are part of the next-generation arsenal of drugs being developed against proto-oncoprotein Myc. We designed protein MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of Max and Myc, which bind to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. We used phage-assisted continuous evolution (PACE), which uncovered mutations at Arg12 that contact the DNA phosphodiester backbone. The Arg12 mutations improved ME47's stability. We replaced Cys29 with Ala to eliminate potential undesired disulfide formation and fused the designed FosW leucine zipper to mutated ME47 to increase the dimerization interface and E-box targeting activity. This "franken-protein" MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper. Compared with ME47, MEF gives 2-fold stronger binding to E-box and 4-fold increased specificity for E-box over nonspecific DNA. The synergistic combination of rational design and PACE allowed us to make MEF and demonstrates the power and utility of our two-pronged approach toward development of promising protein drugs with robust structure and DNA-binding function.
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Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Inder Sheoran
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Serban C. Popa
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Montdher Hussain
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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Katsimpouras C, Stephanopoulos G. Enzymes in biotechnology: Critical platform technologies for bioprocess development. Curr Opin Biotechnol 2021; 69:91-102. [PMID: 33422914 DOI: 10.1016/j.copbio.2020.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/09/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023]
Abstract
Enzymes are core elements of biosynthetic pathways employed in the synthesis of numerous bioproducts. Here, we review enzyme promiscuity, enzyme engineering, enzyme immobilization, and cell-free systems as fundamental strategies of bioprocess development. Initially, promiscuous enzymes are the first candidates in the quest for new activities to power new, artificial, or bypass pathways that expand substrate range and catalyze the production of new products. If the activity or regulation of available enzymes is unsuitable for a process, protein engineering can be applied to improve them to the required level. When cell toxicity and low productivity cannot be engineered away, cell-free systems are an attractive option, especially in combination with enzyme immobilization that allows extended enzyme use. Overall, the above methods support powerful platforms for bioprocess development and optimization.
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Affiliation(s)
- Constantinos Katsimpouras
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139 MA, USA.
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Miller SM, Wang T, Liu DR. Phage-assisted continuous and non-continuous evolution. Nat Protoc 2020; 15:4101-4127. [PMID: 33199872 PMCID: PMC7865204 DOI: 10.1038/s41596-020-00410-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022]
Abstract
Directed evolution, which applies the principles of Darwinian evolution to a laboratory setting, is a powerful strategy for generating biomolecules with diverse and tailored properties. This technique can be implemented in a highly efficient manner using continuous evolution, which enables the steps of directed evolution to proceed seamlessly over many successive generations with minimal researcher intervention. Phage-assisted continuous evolution (PACE) enables continuous directed evolution in bacteria by mapping the steps of Darwinian evolution onto the bacteriophage life cycle and allows directed evolution to occur on much faster timescales compared to conventional methods. This protocol provides detailed instructions on evolving proteins using PACE and phage-assisted non-continuous evolution (PANCE) and includes information on the preparation of selection phage and host cells, the assembly of a continuous flow apparatus and the performance and analysis of evolution experiments. This protocol can be performed in as little as 2 weeks to complete more than 100 rounds of evolution (complete cycles of mutation, selection and replication) in a single PACE experiment.
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Affiliation(s)
- Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Tina Wang
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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Abstract
The diversity of advanced genetic engineering techniques that have become available in recent years has enabled a more precise manipulation of genes and genomes. Among these, bacteriophage genomes stand out as an interesting target due to their dependence on a host for replication, which previously complicated their manipulation, and due as well to the many possible fields in which they can be used. In this review, we highlight recent applications for which genetically modified bacteriophages are being employed: as phage therapy in medicine, animal industries and agricultural settings; as a source of new antimicrobials; as biosensors for research, health and environmental purposes; and as genetic engineering tools themselves.
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Affiliation(s)
| | - Hiroki Ando
- Department of Microbiology, Graduate School of Medicine, Gifu University
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