1
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024; 41:1113-1151. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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2
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Krappinger JC, Aguilar Gomez CM, Hönikl A, Schusterbauer V, Hatzl AM, Feichtinger J, Glieder A. dMAD7 is a Promising Tool for Targeted Gene Regulation in the Methylotrophic Yeast Komagataella phaffii. N Biotechnol 2024:S1871-6784(24)00029-3. [PMID: 38960022 DOI: 10.1016/j.nbt.2024.06.008] [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: 03/27/2024] [Revised: 06/07/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
The methylotrophic yeast Komagataella phaffii is a popular host system for the pharmaceutical and biotechnological production of recombinant proteins. CRISPR-Cas9 and its derivative CRISPR interference (CRISPRi) offer a promising avenue to further enhance and exploit the full capabilities of this host. MAD7 and its catalytically inactive variant "dead" MAD7 (dMAD7) represent an interesting alternative to established CRISPR-Cas9 systems and are free to use for industrial and academic research. CRISPRi utilizing dMAD7 does not introduce double-strand breaks but only binds to the DNA to regulate gene expression. Here, we report the first use of dMAD7 in K. phaffii to regulate the expression of the enhanced green fluorescent protein (eGFP). A reduction of eGFP fluorescence level (up to 88%) was achieved in random integration experiments using dMAD7 plasmids. Integration loci/events of investigated strains were assessed through whole genome sequencing. Additionally, RNA-sequencing experiments corroborated the whole genome sequencing results and showed a significantly reduced expression of eGFP in strains containing a dMAD7 plasmid, among others. Our findings conclusively demonstrate the utility of dMAD7 in K. phaffii through successfully regulating eGFP expression.
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Affiliation(s)
- Julian C Krappinger
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | - Carla M Aguilar Gomez
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Andrea Hönikl
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Anna-Maria Hatzl
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Julia Feichtinger
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria.
| | - Anton Glieder
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Graz, Austria; Bisy GmbH, Hofstaetten, Austria
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3
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Pietralla J, Capdeville N, Schindele P, Puchta H. Optimizing ErCas12a for efficient gene editing in Arabidopsis thaliana. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:401-412. [PMID: 37864303 PMCID: PMC10826985 DOI: 10.1111/pbi.14194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/24/2023] [Accepted: 09/23/2023] [Indexed: 10/22/2023]
Abstract
The ErCas12a nuclease, also known as MAD7, is part of a CRISPR/Cas system from Eubacterium rectale and distantly related to Cas12a nucleases. As it shares only 31% sequence homology with the commonly used AsCas12a, its intellectual property may not be covered by the granted patent rights for Cas12a nucleases. Thus, ErCas12a became an attractive alternative for practical applications. However, the editing efficiency of ErCas12a is strongly target sequence- and temperature-dependent. Therefore, optimization of the enzyme activity through protein engineering is especially attractive for its application in plants, as they are cultivated at lower temperatures. Based on the knowledge obtained from the optimization of Cas12a nucleases, we opted to improve the gene editing efficiency of ErCas12a by introducing analogous amino acid exchanges. Interestingly, neither of these mutations analogous to those in the enhanced or Ultra versions of AsCas12a resulted in significant editing enhancement of ErCas12a in Arabidopsis thaliana. However, two different mutations, V156R and K172R, in putative alpha helical structures of the enzyme showed a detectable improvement in editing. By combining these two mutations, we obtained an improved ErCas12a (imErCas12a) variant, showing several-fold increase in activity in comparison to the wild-type enzyme in Arabidopsis. This variant yields strong editing efficiencies at 22 °C which could be further increased by raising the cultivation temperature to 28 °C and even enabled editing of formerly inaccessible targets. Additionally, no enhanced off-site activity was detected. Thus, imErCas12a is an economically attractive and efficient alternative to other CRISPR/Cas systems for plant genome engineering.
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Affiliation(s)
- Janine Pietralla
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP)Department of Molecular BiologyKarlrsruheGermany
| | - Niklas Capdeville
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP)Department of Molecular BiologyKarlrsruheGermany
| | - Patrick Schindele
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP)Department of Molecular BiologyKarlrsruheGermany
| | - Holger Puchta
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP)Department of Molecular BiologyKarlrsruheGermany
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4
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Vlassis A, Jensen TL, Mohr M, Jedrzejczyk DJ, Meng X, Kovacs G, Morera-Gómez M, Barghetti A, Muyo Abad S, Baumgartner RF, Natarajan KN, Nielsen LK, Warnecke T, Gill RT. CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells. iScience 2023; 26:108287. [PMID: 38034357 PMCID: PMC10682145 DOI: 10.1016/j.isci.2023.108287] [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: 09/19/2022] [Revised: 04/23/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023] Open
Abstract
Discovery of genomic safe harbor sites (SHSs) is fundamental for multiple transgene integrations, such as reporter genes, chimeric antigen receptors (CARs), and safety switches, which are required for safe cell products for regenerative cell therapies and immunotherapies. Here we identified and characterized potential SHS in human cells. Using the CRISPR-MAD7 system, we integrated transgenes at these sites in induced pluripotent stem cells (iPSCs), primary T and natural killer (NK) cells, and Jurkat cell line, and demonstrated efficient and stable expression at these loci. Subsequently, we validated the differentiation potential of engineered iPSC toward CD34+ hematopoietic stem and progenitor cells (HSPCs), lymphoid progenitor cells (LPCs), and NK cells and showed that transgene expression was perpetuated in these lineages. Finally, we demonstrated that engineered iPSC-derived NK cells retained expression of a non-virally integrated anti-CD19 CAR, suggesting that several of the investigated SHSs can be used to engineer cells for adoptive immunotherapies.
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Affiliation(s)
- Arsenios Vlassis
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Tanja L. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Marina Mohr
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Dominika J. Jedrzejczyk
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Xiangyou Meng
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Gergo Kovacs
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Martí Morera-Gómez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Andrea Barghetti
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Sergi Muyo Abad
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Roland F. Baumgartner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Kedar N. Natarajan
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Lars K. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tanya Warnecke
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Ryan T. Gill
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
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5
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Lv X, Li Y, Xiu X, Liao C, Xu Y, Liu Y, Li J, Du G, Liu L. CRISPR genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnol Adv 2023; 69:108261. [PMID: 37741424 DOI: 10.1016/j.biotechadv.2023.108261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Production of food-related products using microorganisms in an environmentally friendly manner is a crucial solution to global food safety and environmental pollution issues. Traditional microbial modification methods rely on artificial selection or natural mutations, which require time for repeated screening and reproduction, leading to unstable results. Therefore, it is imperative to develop rapid, efficient, and precise microbial modification technologies. This review summarizes recent advances in the construction of gene editing and metabolic regulation toolkits based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) systems and their applications in reconstructing food microorganism metabolic networks. The development and application of gene editing toolkits from single-site gene editing to multi-site and genome-scale gene editing was also introduced. Moreover, it presented a detailed introduction to CRISPR interference, CRISPR activation, and logic circuit toolkits for metabolic network regulation. Moreover, the current challenges and future prospects for developing CRISPR genetic toolkits were also discussed.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yang Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xiang Xiu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chao Liao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yameng Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Food Laboratory of Zhongyuan, Jiangnan University, Wuxi 214122, China.
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6
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Mund M, Weber W, Degreif D, Schiklenk C. A MAD7-based genome editing system for Escherichia coli. Microb Biotechnol 2023; 16:1000-1010. [PMID: 36929689 PMCID: PMC10128132 DOI: 10.1111/1751-7915.14234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 03/18/2023] Open
Abstract
A broad variety of biomolecules is industrially produced in bacteria and yeasts. These microbial expression hosts can be optimized through genetic engineering using CRISPR tools. Here, we designed and characterized such a modular genome editing system based on the Cas12a-like RNA-guided nuclease MAD7 in Escherichia coli. This system enables the efficient generation of single nucleotide polymorphisms (SNPs) or gene deletions and can directly be used with donor DNA from benchtop DNA assembly to increase throughput. We combined multiple edits to engineer an E. coli strain with reduced overflow metabolism and increased plasmid yield, highlighting the versatility and industrial applicability of this approach.
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Affiliation(s)
- Markus Mund
- Sanofi-Aventis Deutschland GmbH, Global CMC Microbial Platform, USP Development - Molecular Biology, Frankfurt am Main, Germany
| | - Wadim Weber
- Sanofi-Aventis Deutschland GmbH, Global CMC Microbial Platform, USP Development - Molecular Biology, Frankfurt am Main, Germany
| | - Daniel Degreif
- Sanofi-Aventis Deutschland GmbH, Global CMC Microbial Platform, USP Development - Molecular Biology, Frankfurt am Main, Germany
| | - Christoph Schiklenk
- Sanofi-Aventis Deutschland GmbH, Global CMC Microbial Platform, USP Development - Molecular Biology, Frankfurt am Main, Germany
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7
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Mohr M, Damas N, Gudmand-Høyer J, Zeeberg K, Jedrzejczyk D, Vlassis A, Morera-Gómez M, Pereira-Schoning S, Puš U, Oliver-Almirall A, Lyholm Jensen T, Baumgartner R, Tate Weinert B, Gill RT, Warnecke T. The CRISPR-Cas12a Platform for Accurate Genome Editing, Gene Disruption, and Efficient Transgene Integration in Human Immune Cells. ACS Synth Biol 2023; 12:375-389. [PMID: 36750230 PMCID: PMC9942205 DOI: 10.1021/acssynbio.2c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
CRISPR-Cas12a nucleases have expanded the toolbox for targeted genome engineering in a broad range of organisms. Here, using a high-throughput engineering approach, we explored the potential of a novel CRISPR-MAD7 system for genome editing in human cells. We evaluated several thousand optimization conditions and demonstrated accurate genome reprogramming with modified MAD7. We identified crRNAs that allow for ≤95% non-homologous end joining (NHEJ) and 66% frameshift mutations in various genes and observed the high-cleavage fidelity of MAD7 resulting in undetectable off-target activity. We explored the dsDNA delivery efficiency of CRISPR-MAD7, and by using our optimized transfection protocol, we obtained ≤85% chimeric antigen receptor (CAR) insertions in primary T cells, thus exceeding the baseline integration efficiencies of therapeutically relevant transgenes using currently available virus-free technologies. Finally, we evaluated multiplex editing efficiency with CRISPR-MAD7 and demonstrated simultaneous ≤35% CAR transgene insertions and ≤80% gene disruption efficiencies. Both the platform and our transfection procedure are easily adaptable for further preclinical studies and could potentially be used for clinical manufacturing of CAR T cells.
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Affiliation(s)
- Marina Mohr
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Nkerorema Damas
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Johanne Gudmand-Høyer
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Katrine Zeeberg
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Dominika Jedrzejczyk
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Arsenios Vlassis
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Martí Morera-Gómez
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Sara Pereira-Schoning
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Urška Puš
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Anna Oliver-Almirall
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Tanja Lyholm Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Roland Baumgartner
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Brian Tate Weinert
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Ryan T. Gill
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark,Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States,
| | - Tanya Warnecke
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States,
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8
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Bennis NX, Anderson JP, Kok SMC, Daran JMG. Expanding the genome editing toolbox of Saccharomyces cerevisiae with the endonuclease ErCas12a. FEMS Yeast Res 2023; 23:foad043. [PMID: 37791490 PMCID: PMC10583194 DOI: 10.1093/femsyr/foad043] [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: 07/04/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023] Open
Abstract
ErCas12a is a class 2 type V CRISPR-Cas nuclease isolated from Eubacterium rectale with attractive fundamental characteristics, such as RNA self-processing capability, and lacks reach-through royalties typical for Cas nucleases. This study aims to develop a ErCas12a-mediated genome editing tool applicable in the model yeast Saccharomyces cerevisiae. The optimal design parameters for ErCas12a editing in S. cerevisiae were defined as a 21-nt spacer flanked by 19 nt direct repeats expressed from either RNApolII or III promoters, achieving near 100% editing efficiencies in commonly targeted genomic locations. To be able to transfer the ErCas12a genome editing tool to different strain lineages, a transportable platform plasmid was constructed and evaluated for its genome editing efficiency. Using an identical crRNA expression design, the transportable ErCas12a genome editing tool showed lower efficiency when targeting the ADE2 gene. In contrast to genomic Ercas12a expression, episomal expression of Ercas12a decreases maximum specific growth rate on glucose, indicating ErCas12a toxicity at high expression levels. Moreover, ErCas12a processed a multispacer crRNA array using the RNA self-processing capability, which allowed for simultaneous editing of multiple chromosomal locations. ErCas12a is established as a valuable addition to the genetic toolbox for S. cerevisiae.
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Affiliation(s)
- Nicole X Bennis
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627 HZ Delft, The Netherlands
| | - Jonah P Anderson
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627 HZ Delft, The Netherlands
| | - Siebe M C Kok
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627 HZ Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627 HZ Delft, The Netherlands
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9
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Vanegas KG, Rendsvig JKH, Jarczynska ZD, Cortes MVDCB, van Esch AP, Morera-Gómez M, Contesini FJ, Mortensen UH. A Mad7 System for Genetic Engineering of Filamentous Fungi. J Fungi (Basel) 2022; 9:jof9010016. [PMID: 36675838 PMCID: PMC9865164 DOI: 10.3390/jof9010016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The introduction of CRISPR technologies has revolutionized strain engineering in filamentous fungi. However, its use in commercial applications has been hampered by concerns over intellectual property (IP) ownership, and there is a need for implementing Cas nucleases that are not limited by complex IP constraints. One promising candidate in this context is the Mad7 enzyme, and we here present a versatile Mad7-CRISPR vector-set that can be efficiently used for the genetic engineering of four different Aspergillus species: Aspergillus nidulans, A. niger, A. oryzae and A. campestris, the latter being a species that has never previously been genetically engineered. We successfully used Mad7 to introduce unspecific as well as specific template-directed mutations including gene disruptions, gene insertions and gene deletions. Moreover, we demonstrate that both single-stranded oligonucleotides and PCR fragments equipped with short and long targeting sequences can be used for efficient marker-free gene editing. Importantly, our CRISPR/Mad7 system was functional in both non-homologous end-joining (NHEJ) proficient and deficient strains. Therefore, the newly implemented CRISPR/Mad7 was efficient to promote gene deletions and integrations using different types of DNA repair in four different Aspergillus species, resulting in the expansion of CRISPR toolboxes in fungal cell factories.
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Affiliation(s)
- Katherina Garcia Vanegas
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Jakob Kræmmer Haar Rendsvig
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Zofia Dorota Jarczynska
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | | | - Abel Peter van Esch
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Martí Morera-Gómez
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Fabiano Jares Contesini
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Uffe Hasbro Mortensen
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
- Correspondence:
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10
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Song Y, He S, Jopkiewicz A, Setroikromo R, van Merkerk R, Quax WJ. Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages. J Appl Microbiol 2022; 133:2280-2298. [PMID: 35797344 PMCID: PMC9796756 DOI: 10.1111/jam.15704] [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: 03/24/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been developed into a precise and efficient genome editing tool. Since its discovery as an adaptive immune system in prokaryotes, it has been applied in many different research fields including biotechnology and medical sciences. The high demand for rapid, highly efficient and versatile genetic tools to thrive in bacteria-based cell factories accelerates this process. This review mainly focuses on significant advancements of the CRISPR system in Bacillus subtilis, including the achievements in gene editing, and on problems still remaining. Next, we comprehensively summarize this genetic tool's up-to-date development and utilization in other Bacillus species, including B. licheniformis, B. methanolicus, B. anthracis, B. cereus, B. smithii and B. thuringiensis. Furthermore, we describe the current application of CRISPR tools in phages to increase Bacillus hosts' resistance to virulent phages and phage genetic modification. Finally, we suggest potential strategies to further improve this advanced technique and provide insights into future directions of CRISPR technologies for rendering Bacillus species cell factories more effective and more powerful.
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Affiliation(s)
- Yafeng Song
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern ChinaInstitute of Microbiology, Guangdong Acadamy of SciencesGuangzhouChina
| | - Siqi He
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Anita Jopkiewicz
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
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11
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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12
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Zocca VFB, Corrêa GG, Lins MRDCR, de Jesus VN, Tavares LF, Amorim LADS, Kundlatsch GE, Pedrolli DB. The CRISPR toolbox for the gram-positive model bacterium Bacillus subtilis. Crit Rev Biotechnol 2021; 42:813-826. [PMID: 34719304 DOI: 10.1080/07388551.2021.1983516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
CRISPR has revolutionized the way we engineer genomes. Its simplicity and modularity have enabled the development of a great number of tools to edit genomes and to control gene expression. This powerful technology was first adapted to Bacillus subtilis in 2016 and has been intensely upgraded since then. Many tools have been successfully developed to build a CRISPR toolbox for this Gram-positive model and important industrial chassis. The toolbox includes tools, such as double-strand and single-strand cutting CRISPR for point mutation, gene insertion, and gene deletion up to 38 kb. Moreover, catalytic dead Cas proteins have been used for base editing, as well as for the control of gene expression (CRISPRi and CRISPRa). Many of these tools have been used for multiplex CRISPR with the most successful one targeting up to six loci simultaneously for point mutation. However, tools for efficient multiplex CRISPR for other functionalities are still missing in the toolbox. CRISPR engineering has already resulted in efficient protein and metabolite-producing strains, demonstrating its great potential. In this review, we cover all the important additions made to the B. subtilis CRISPR toolbox since 2016, and strain developments fomented by the technology.
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Affiliation(s)
- Vitoria Fernanda Bertolazzi Zocca
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Graciely Gomes Corrêa
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Milca Rachel da Costa Ribeiro Lins
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Victor Nunes de Jesus
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Leonardo Ferro Tavares
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Laura Araujo da Silva Amorim
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Guilherme Engelberto Kundlatsch
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
| | - Danielle Biscaro Pedrolli
- Department of Bioprocess Engineering and Biotechnology, School of Pharmaceutical Sciences, Universidade Estadual Paulista (UNESP), Araraquara, Brazil
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Sachla AJ, Alfonso AJ, Helmann JD. A Simplified Method for CRISPR-Cas9 Engineering of Bacillus subtilis. Microbiol Spectr 2021; 9:e0075421. [PMID: 34523974 PMCID: PMC8557940 DOI: 10.1128/spectrum.00754-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/16/2021] [Indexed: 11/20/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system from Streptococcus pyogenes has been widely deployed as a tool for bacterial strain construction. Conventional CRISPR-Cas9 editing strategies require design and molecular cloning of an appropriate guide RNA (gRNA) to target genome cleavage and a repair template for introduction of the desired site-specific genome modification. Here, we present a streamlined method that leverages the existing collection of nearly 4,000 Bacillus subtilis strains (the BKE collection) with individual genes replaced by an integrated erythromycin (erm) resistance cassette. A single plasmid (pAJS23) with a gRNA targeted to erm allows cleavage of the genome at any nonessential gene and at sites nearby to many essential genes. This plasmid can be engineered to include a repair template, or the repair template can be cotransformed with the plasmid as either a PCR product or genomic DNA. We demonstrate the utility of this system for generating gene replacements, site-specific mutations, modification of intergenic regions, and introduction of gene-reporter fusions. In sum, this strategy bypasses the need for gRNA design and allows the facile transfer of mutations and genetic constructions with no requirement for intermediate cloning steps. IMPORTANCE Bacillus subtilis is a well-characterized Gram-positive model organism and a popular platform for biotechnology. Although many different CRISPR-based genome editing strategies have been developed for B. subtilis, they generally involve the design and cloning of a specific guide RNA (gRNA) and repair template for each application. By targeting the erm resistance cassette with an anti-erm gRNA, genome editing can be directed to any of nearly 4,000 gene disruptants within the existing BKE collection of strains. Repair templates can be engineered as PCR products, or specific alleles and constructions can be transformed as chromosomal DNA, thereby bypassing the need for plasmid construction. The described method is rapid and facilitates a wide range of genome manipulations.
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Affiliation(s)
- Ankita J. Sachla
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | | | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Lin Q, Zhu Z, Liu G, Sun C, Lin D, Xue C, Li S, Zhang D, Gao C, Wang Y, Qiu JL. Genome editing in plants with MAD7 nuclease. J Genet Genomics 2021; 48:444-451. [PMID: 34120856 DOI: 10.1016/j.jgg.2021.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/03/2021] [Accepted: 04/11/2021] [Indexed: 12/31/2022]
Abstract
MAD7 is an engineered nuclease of the Class 2 type V-A CRISPR-Cas (Cas12a/Cpf1) family with a low level of homology to canonical Cas12a nucleases. It has been publicly released as a royalty-free nuclease for both academic and commercial use. Here, we demonstrate that the CRISPR-MAD7 system can be used for genome editing and recognizes T-rich PAM sequences (YTTN) in plants. Its editing efficiency in rice and wheat is comparable to that of the widely used CRISPR-LbCas12a system. We develop two variants, MAD7-RR and MAD7-RVR that increase the target range of MAD7, as well as an M-AFID (a MAD7-APOBEC fusion-induced deletion) system that creates predictable deletions from 5'-deaminated Cs to the MAD7-cleavage site. Moreover, we show that MAD7 can be used for multiplex gene editing and that it is effective in generating indels when combined with other CRISPR RNA orthologs. Using the CRISPR-MAD7 system, we have obtained regenerated mutant rice and wheat plants with up to 65.6% efficiency.
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Affiliation(s)
- Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zixu Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanwen Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dexing Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxiao Xue
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengnan Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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Bayarsaikhan D, Bayarsaikhan G, Lee B. Recent advances in stem cells and gene editing: Drug discovery and therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:231-269. [PMID: 34127195 DOI: 10.1016/bs.pmbts.2021.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recently introduced genome editing technology has had a remarkable impact on genetic medicine. Zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas nucleases are the three major platforms used for priming of stem cells or correction of mutated genes. Among these nucleases, CRISPR/Cas is the most easily applicable. Various CRISPR/Cas variants such as base editors, prime editors, mad7 nucleases, RESCUE, REPAIR, digenome sequencing, and SHERLOCK are being developed and considered as a promising tool for gene therapy and drug discovery. These advances in the CRISPR/Cas platform have enabled the correction of gene mutations from DNA to RNA level and validation of the safety of genome editing performance at a very precise level by allowing the detection of one base-pair mismatch. These promising alternatives of the CRISPR/Cas system can benefit millions of patients with intractable diseases. Although the therapeutic effects of stem cells have been confirmed in a wide range of disease models, their safety still remains an issue. Hence, scientists are concentrating on generating functionally improved stem cells by using programmable nucleases such as CRISPR. Therefore, in this chapter, we have summarized the applicable options of the CRISPR/Cas platforms by weighing their advantages and limitations in drug discovery and gene therapy.
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Affiliation(s)
- Delger Bayarsaikhan
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea
| | - Govigerel Bayarsaikhan
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea
| | - Bonghee Lee
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea.
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18
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Yu S, Price MA, Wang Y, Liu Y, Guo Y, Ni X, Rosser SJ, Bi C, Wang M. CRISPR-dCas9 Mediated Cytosine Deaminase Base Editing in Bacillus subtilis. ACS Synth Biol 2020; 9:1781-1789. [PMID: 32551562 DOI: 10.1021/acssynbio.0c00151] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Base editing technology based on clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) is a recent addition to the family of CRISPR technologies. Compared with the traditional CRISPR/Cas9 technology, it does not rely on DNA double strand break and homologous recombination, and can realize gene inactivation and point mutation more quickly and simply. Herein, we first developed a base editing method for genome editing in Bacillus subtilis utilizing CRISPR/dCas9 (a fully nuclease-deficient mutant of Cas9 from S. pyogenes) and activation-induced cytidine deaminase (AID). This method achieved three and four loci simultaneous editing with editing efficiency up to 100% and 50%, respectively. Our base editing system in B. subtilis has a 5 nt editing window, which is similar to previously reported base editing in other microorganisms. We demonstrated that the plasmid curing rate is almost 100%, which is advantageous for multiple rounds of genome engineering in B. subtilis. Finally, we applied multiplex genome editing to generate a B. subtilis 168 mutant strain with eight inactive extracellular protease genes in just two rounds of base editing and plasmid curing, suggesting that it is a powerful tool for gene manipulation in B. subtilis and industrial applications in the future.
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Affiliation(s)
- Sili Yu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Marcus A. Price
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Yu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yang Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Susan J. Rosser
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Changhao Bi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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