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Shi Y, Tan Q, Yang C, Li S, Li Y, He B, Xie H, Duan X, Chen L. Establishment of a Cleavage-Based Single-Plasmid Dual-Luciferase Surrogate Reporter for the Cleavage Efficiency Evaluation of CRISPR-Cas12a Systems and Its Primary Application. CRISPR J 2024; 7:156-167. [PMID: 38922054 DOI: 10.1089/crispr.2024.0038] [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: 06/27/2024] Open
Abstract
CRISPR-Cas technology is a widely utilized gene-editing tool that involves gRNA-guided sequence recognition and Cas nuclease-mediated cleavage. The design and evaluation of gRNA are essential for enhancing CRISPR/Cas editing efficiency. Various assays such as single-strand annealing, in vitro cleavage, and T7 endonuclease I (T7EI) are commonly used to assess gRNA-mediated Cas protein cleavage activity. In this study, a firefly luciferase and Renilla luciferase co-expressed and a cleavage-based single-plasmid dual-luciferase surrogate reporter was built to evaluate the gRNA-mediated Cas12a cleavage efficiency. The cleavage activities of CRISPR-Cas12a can be quantitatively determined by the recovery degree of firefly luciferase activity. The cleavage efficiency of CRISPR-Cas12a can be quantitatively measured by the recovery of firefly luciferase activity. By using this system, the cleavage efficiency of CRISPR-Cas12a on hepatitis B virus (HBV)/D expression plasmid was evaluated, revealing a negative correlation between gRNA cleavage efficiency and HBV gene expression measured using an enzyme-linked immunosorbent assay. This simple, efficient, and quantifiable system only requires the dual-luciferase vector and CRISPR-Cas12a vector, making it a valuable tool for selecting effective gRNAs for gene editing.
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Affiliation(s)
- Yaoqiang Shi
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Qi Tan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Chunhui Yang
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Shilin Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Yujia Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Baoren He
- The Joint Laboratory on Transfusion-Transmitted Diseases (TTDs) Between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Nanning, China
| | - He Xie
- The Hospital of Xidian Group, Xi'an, China
| | - Xiaoqiong Duan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Limin Chen
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
- The Joint Laboratory on Transfusion-Transmitted Diseases (TTDs) Between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Nanning, China
- The Hospital of Xidian Group, Xi'an, China
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2
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Bennis NX, Kostanjšek M, van den Broek M, Daran JMG. Improving CRISPR-Cas9 mediated genome integration in interspecific hybrid yeasts. N Biotechnol 2023; 76:49-62. [PMID: 37028644 DOI: 10.1016/j.nbt.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
Saccharomyces pastorianus is not a classical taxon, it is an interspecific hybrid resulting from the cross of Saccharomyces cerevisiae and Saccharomyces eubayanus. Exhibiting heterosis for phenotypic traits such as wort α-oligosaccharide consumption and fermentation at low temperature, it has been domesticated to become the main workhorse of the brewing industry. Although CRISPR-Cas9 has been shown to be functional in S. pastorianus, repair of CRISPR- induced double strand break is unpredictable and preferentially uses the homoeologous chromosome as template, preventing targeted introduction of the desired repair construct. Here, we demonstrate that lager hybrids can be edited with near 100% efficiency at carefully selected landing sites on the chimeric SeScCHRIII. The landing sites were systematically selected and evaluated for (i) absence of loss of heterozygosity upon CRISPR-editing, (ii) efficiency of the gRNA, and (iii) absence of effect on strain physiology. Successful examples of highly efficient single and double gene integration illustrated that genome editing can be applied in interspecies hybrids, paving the way to a new impulse to lager yeast strain development. DATA AVAILABILITY: Data underlying graphs and figures found in this manuscript are deposited at the 4TU research dat center (https://data.4tu.nl/info/en/) and available through the doi: 10.4121/21648329.
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Lackner M, Helmbrecht N, Pääbo S, Riesenberg S. Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic substitutions. Nucleic Acids Res 2023; 51:e26. [PMID: 36620901 PMCID: PMC10018342 DOI: 10.1093/nar/gkac1254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/18/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
CRISPR nucleases can introduce double-stranded DNA breaks in genomes at positions specified by guide RNAs. When repaired by the cell, this may result in the introduction of insertions and deletions or nucleotide substitutions provided by exogenous DNA donors. However, cellular repair can also result in unintended on-target effects, primarily larger deletions and loss of heterozygosity due to gene conversion. Here we present a strategy that allows easy and reliable detection of unintended on-target effects as well as the generation of control cells that carry wild-type alleles but have demonstratively undergone genome editing at the target site. Our 'sequence-ascertained favorable editing' (SAFE) donor approach relies on the use of DNA donor mixtures containing the desired nucleotide substitutions or the wild-type alleles together with combinations of additional 'diagnostic' substitutions unlikely to have any effects. Sequencing of the target sites then results in that two different sequences are seen when both chromosomes are edited with 'SAFE' donors containing different sets of substitutions, while a single sequence indicates unintended effects such as deletions or gene conversion. We analyzed more than 850 human embryonic stem cell clones edited with 'SAFE' donors and detect all copy number changes and almost all clones with gene conversion.
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Affiliation(s)
| | - Nelly Helmbrecht
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Sachsen 04103, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Sachsen 04103, Germany
- Okinawa Institute of Science and Technology, Onna-son, Okinawa 904-0495, Japan
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CRISPR-Cas9 Editing Induces Loss of Heterozygosity in the Pathogenic Yeast Candida parapsilosis. mSphere 2022; 7:e0039322. [PMID: 36416551 PMCID: PMC9769790 DOI: 10.1128/msphere.00393-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Genetic manipulation is often used to study gene function. However, unplanned genome changes (including single nucleotide polymorphisms [SNPs], aneuploidy, and loss of heterozygosity [LOH]) can affect the phenotypic traits of the engineered strains. Here, we compared the effect of classical deletion methods (replacing target alleles with selectable markers by homologous recombination) with CRISPR-Cas9 editing in the diploid human-pathogenic yeast Candida parapsilosis. We sequenced the genomes of 9 isolates that were modified using classic recombination methods and 12 that were edited using CRISPR-Cas9. As a control, the genomes of eight isolates that were transformed with a Cas9-expressing plasmid in the absence of a guide RNA were also sequenced. Following gene manipulation using classic homologous recombination, only one strain exhibited extensive LOH near the targeted gene (8.9 kb), whereas another contained multiple LOH events not associated with the intended modification. In contrast, large regions of LOH (up to >1,100 kb) were observed in most CRISPR-Cas9-edited strains. LOH most commonly occurred adjacent to the Cas9 cut site and extended to the telomere in four isolates. In two isolates, we observed LOH on chromosomes that were not targeted by CRISPR-Cas9. Among the CRISPR-edited isolates, two exhibited cysteine and methionine auxotrophy caused by LOH at a heterozygous site in MET10, approximately 11 and 157 kb downstream from the Cas9 target site, respectively. C. parapsilosis isolates have relatively low levels of heterozygosity. However, our results show that mutation complementation to confirm observed phenotypes is required when using CRISPR-Cas9. IMPORTANCE CRISPR-Cas9 has greatly streamlined gene editing and is now the gold standard and first choice for genetic engineering. However, we show that in diploid species, extra care should be taken in confirming the cause of any phenotypic changes observed. We show that the Cas9-induced double-strand break is often associated with loss of heterozygosity in the asexual diploid human fungal pathogen Candida parapsilosis. This can result in deleterious heterozygous variants (e.g., stop gain in one allele) becoming homozygous, resulting in unplanned phenotypic changes. Our results stress the importance of mutation complementation even when using CRISPR-Cas9.
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Bouchaut B, Hollmann F, Asveld L. Differences in barriers for controlled learning about safety between biotechnology and chemistry. Nat Commun 2022; 13:4103. [PMID: 35835765 PMCID: PMC9283460 DOI: 10.1038/s41467-022-31870-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/07/2022] [Indexed: 12/18/2022] Open
Abstract
In contrast to chemical industry, biotechnology is still not competitive for the production of chemicals, materials, and biofuels. Here, the authors discuss the underlying reasons and propose to address the problem through regulatory changes and risk management.
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Affiliation(s)
- Britte Bouchaut
- Section of Biotechnology and Society, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands.
| | - Frank Hollmann
- Section of Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Lotte Asveld
- Section of Biotechnology and Society, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
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Wang WY, Cai HQ, Qu SY, Lin WH, Liang CC, Liu H, Xie ZX, Yuan YJ. Genomic Variation-Mediating Fluconazole Resistance in Yeast. Biomolecules 2022; 12:biom12060845. [PMID: 35740970 PMCID: PMC9221393 DOI: 10.3390/biom12060845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
Fungal infections pose a serious and growing threat to public health. These infections can be treated with antifungal drugs by killing hazardous fungi in the body. However, the resistance can develop over time when fungi are exposed to antifungal drugs by generating genomic variations, including mutation, aneuploidy, and loss of heterozygosity. The variations could reduce the binding affinity of a drug to its target or block the pathway through which drugs exert their activity. Here, we review genomic variation-mediating fluconazole resistance in the yeast Candida, with the hope of highlighting the functional consequences of genomic variations for the antifungal resistance.
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Antony JS, Hinz JM, Wyrick JJ. Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:924914. [PMID: 35706506 PMCID: PMC9190257 DOI: 10.3389/fbioe.2022.924914] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/26/2022] Open
Abstract
The versatility of clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) genome editing makes it a popular tool for many research and biotechnology applications. Recent advancements in genome editing in eukaryotic organisms, like fungi, allow for precise manipulation of genetic information and fine-tuned control of gene expression. Here, we provide an overview of CRISPR genome editing technologies in yeast, with a particular focus on Saccharomyces cerevisiae. We describe the tools and methods that have been previously developed for genome editing in Saccharomyces cerevisiae and discuss tips and experimental tricks for promoting efficient, marker-free genome editing in this model organism. These include sgRNA design and expression, multiplexing genome editing, optimizing Cas9 expression, allele-specific editing in diploid cells, and understanding the impact of chromatin on genome editing. Finally, we summarize recent studies describing the potential pitfalls of using CRISPR genome targeting in yeast, including the induction of background mutations.
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Affiliation(s)
- Jacob S. Antony
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John M. Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
- *Correspondence: John J. Wyrick,
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Simkin D, Papakis V, Bustos BI, Ambrosi CM, Ryan SJ, Baru V, Williams LA, Dempsey GT, McManus OB, Landers JE, Lubbe SJ, George AL, Kiskinis E. Homozygous might be hemizygous: CRISPR/Cas9 editing in iPSCs results in detrimental on-target defects that escape standard quality controls. Stem Cell Reports 2022; 17:993-1008. [PMID: 35276091 PMCID: PMC9023783 DOI: 10.1016/j.stemcr.2022.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
The ability to precisely edit the genome of human induced pluripotent stem cell (iPSC) lines using CRISPR/Cas9 has enabled the development of cellular models that can address genotype to phenotype relationships. While genome editing is becoming an essential tool in iPSC-based disease modeling studies, there is no established quality control workflow for edited cells. Moreover, large on-target deletions and insertions that occur through DNA repair mechanisms have recently been uncovered in CRISPR/Cas9-edited loci. Yet the frequency of these events in human iPSCs remains unclear, as they can be difficult to detect. We examined 27 iPSC clones generated after targeting 9 loci and found that 33% had acquired large, on-target genomic defects, including insertions and loss of heterozygosity. Critically, all defects had escaped standard PCR and Sanger sequencing analysis. We describe a cost-efficient quality control strategy that successfully identified all edited clones with detrimental on-target events and could facilitate the integrity of iPSC-based studies.
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Affiliation(s)
- Dina Simkin
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Vasileios Papakis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bernabe I Bustos
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | | | | | | | | | | | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Steven J Lubbe
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA; Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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9
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A Saccharomyces eubayanus haploid resource for research studies. Sci Rep 2022; 12:5976. [PMID: 35396494 PMCID: PMC8993842 DOI: 10.1038/s41598-022-10048-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/01/2022] [Indexed: 12/16/2022] Open
Abstract
Since its identification, Saccharomyces eubayanus has been recognized as the missing parent of the lager hybrid, S. pastorianus. This wild yeast has never been isolated from fermentation environments, thus representing an interesting candidate for evolutionary, ecological and genetic studies. However, it is imperative to develop additional molecular genetics tools to ease manipulation and thus facilitate future studies. With this in mind, we generated a collection of stable haploid strains representative of three main lineages described in S. eubayanus (PB-1, PB-2 and PB-3), by deleting the HO gene using CRISPR-Cas9 and tetrad micromanipulation. Phenotypic characterization under different conditions demonstrated that the haploid derivates were extremely similar to their parental strains. Genomic analysis in three strains highlighted a likely low frequency of off-targets, and sequencing of a single tetrad evidenced no structural variants in any of the haploid spores. Finally, we demonstrate the utilization of the haploid set by challenging the strains under mass-mating conditions. In this way, we found that S. eubayanus under liquid conditions has a preference to remain in a haploid state, unlike S. cerevisiae that mates rapidly. This haploid resource is a novel set of strains for future yeast molecular genetics studies.
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10
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Efficient breeding of industrial brewing yeast strains using CRISPR/Cas9-aided mating-type switching. Appl Microbiol Biotechnol 2021; 105:8359-8376. [PMID: 34643787 PMCID: PMC8557189 DOI: 10.1007/s00253-021-11626-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/01/2022]
Abstract
Yeast breeding is a powerful tool for developing and improving brewing yeast in a number of industry-relevant respects. However, breeding of industrial brewing yeast can be challenging, as strains are typically sterile and have large complex genomes. To facilitate breeding, we used the CRISPR/Cas9 system to generate double-stranded breaks in the MAT locus, generating transformants with a single specified mating type. The single mating type remained stable even after loss of the Cas9 plasmid, despite the strains being homothallic, and these strains could be readily mated with other brewing yeast transformants of opposite mating type. As a proof of concept, we applied this technology to generate yeast hybrids with an aim to increase β-lyase activity for fermentation of beer with enhanced hop flavour. First, a genetic and phenotypic pre-screening of 38 strains was carried out in order to identify potential parent strains with high β-lyase activity. Mating-competent transformants of eight parent strains were generated, and these were used to generate over 60 hybrids that were screened for β-lyase activity. Selected phenolic off-flavour positive (POF +) hybrids were further sporulated to generate meiotic segregants with high β-lyase activity, efficient wort fermentation, and lack of POF, all traits that are desirable in strains for the fermentation of modern hop-forward beers. Our study demonstrates the power of combining the CRISPR/Cas9 system with classic yeast breeding to facilitate development and diversification of brewing yeast. KEY POINTS: • CRISPR/Cas9-based mating-type switching was applied to industrial yeast strains. • Transformed strains could be readily mated to form intraspecific hybrids. • Hybrids exhibited heterosis for a number of brewing-relevant traits.
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Bouchaut B, Asveld L. Responsible Learning About Risks Arising from Emerging Biotechnologies. SCIENCE AND ENGINEERING ETHICS 2021; 27:22. [PMID: 33779839 PMCID: PMC8007500 DOI: 10.1007/s11948-021-00300-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/18/2021] [Indexed: 05/08/2023]
Abstract
Genetic engineering techniques (e.g., CRISPR-Cas) have led to an increase in biotechnological developments, possibly leading to uncertain risks. The European Union aims to anticipate these by embedding the Precautionary Principle in its regulation for risk management. This principle revolves around taking preventive action in the face of uncertainty and provides guidelines to take precautionary measures when dealing with important values such as health or environmental safety. However, when dealing with 'new' technologies, it can be hard for risk managers to estimate the societal or environmental consequences of a biotechnology that might arise once introduced or embedded in society due to that these sometimes do not comply with the established norms within risk assessment. When there is insufficient knowledge, stakeholders active in early developmental stages (e.g., researchers) could provide necessary knowledge by conducting research specifically devoted to what these unknown risks could entail. In theory, the Safe-by-Design (SbD) approach could enable such a controlled learning environment to gradually identify what these uncertain risks are, to which we refer as responsible learning. In this paper, we argue that three conditions need to be present to enable such an environment: (1) regulatory flexibility, (2) co-responsibility between researchers and regulators, and (3) openness towards all stakeholders. If one of these conditions would not be present, the SbD approach cannot be implemented to its fullest potential, thereby limiting an environment for responsible learning and possibly leaving current policy behind to anticipate uncertain risks.
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Affiliation(s)
- Britte Bouchaut
- Department of Biotechnology, Section of Biotechnology and Society, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| | - Lotte Asveld
- Department of Biotechnology, Section of Biotechnology and Society, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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Rainha J, Rodrigues JL, Rodrigues LR. CRISPR-Cas9: A Powerful Tool to Efficiently Engineer Saccharomyces cerevisiae. Life (Basel) 2020; 11:13. [PMID: 33375364 PMCID: PMC7823794 DOI: 10.3390/life11010013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/27/2022] Open
Abstract
Saccharomyces cerevisiae has been for a long time a common model for fundamental biological studies and a popular biotechnological engineering platform to produce chemicals, fuels, and pharmaceuticals due to its peculiar characteristics. Both lines of research require an effective editing of the native genetic elements or the inclusion of heterologous pathways into the yeast genome. Although S. cerevisiae is a well-known host with several molecular biology tools available, a more precise tool is still needed. The clustered, regularly interspaced, short palindromic repeats-associated Cas9 (CRISPR-Cas9) system is a current, widespread genome editing tool. The implementation of a reprogrammable, precise, and specific method, such as CRISPR-Cas9, to edit the S. cerevisiae genome has revolutionized laboratory practices. Herein, we describe and discuss some applications of the CRISPR-Cas9 system in S. cerevisiae from simple gene knockouts to more complex processes such as artificial heterologous pathway integration, transcriptional regulation, or tolerance engineering.
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Affiliation(s)
| | | | - Lígia R. Rodrigues
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (J.R.); (J.L.R.)
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13
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Prat F, Toutain J, Boutin J, Amintas S, Cullot G, Lalanne M, Lamrissi-Garcia I, Moranvillier I, Richard E, Blouin JM, Dabernat S, Moreau-Gaudry F, Bedel A. Mutation-Specific Guide RNA for Compound Heterozygous Porphyria On-target Scarless Correction by CRISPR/Cas9 in Stem Cells. Stem Cell Reports 2020; 15:677-693. [PMID: 32795423 PMCID: PMC7486222 DOI: 10.1016/j.stemcr.2020.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 01/31/2023] Open
Abstract
CRISPR/Cas9 is a promising technology for gene correction. However, the edition is often biallelic, and uncontrolled small insertions and deletions (indels) concomitant to precise correction are created. Mutation-specific guide RNAs were recently tested to correct dominant inherited diseases, sparing the wild-type allele. We tested an original approach to correct compound heterozygous recessive mutations. We compared editing efficiency and genotoxicity by biallelic guide RNA versus mutant allele-specific guide RNA in iPSCs derived from a congenital erythropoietic porphyria patient carrying compound heterozygous mutations resulting in UROS gene invalidation. We obtained UROS function rescue and metabolic correction with both guides with the potential of use for porphyria clinical intervention. However, unlike the biallelic one, the mutant allele-specific guide was free of on-target collateral damage. We recommend this design to avoid genotoxicity and to obtain on-target scarless gene correction for recessive disease with frequent cases of compound heterozygous mutations.
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Affiliation(s)
- Florence Prat
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | - Jérôme Toutain
- Medical Genetic Laboratory, CHU Bordeaux, Bordeaux 33000, France
| | - Julian Boutin
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | - Samuel Amintas
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Laboratory of Tumor Biology, CHU Bordeaux, Pessac 33604, France
| | - Grégoire Cullot
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | - Magalie Lalanne
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | - Isabelle Lamrissi-Garcia
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France
| | | | - Emmanuel Richard
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France
| | - Jean-Marc Blouin
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France
| | - Sandrine Dabernat
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France
| | - François Moreau-Gaudry
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France
| | - Aurélie Bedel
- Univ Bordeaux, Bordeaux 33000, France; INSERM U1035, Biotherapy of Genetic Diseases, Inflammatory Disorders and Cancers, Bordeaux 33000, France; Biochemistry Laboratory, CHU Bordeaux, Bordeaux 33000, France; Laboratory of Excellence, GR-Ex, Imagine Institute, Paris 75015, France.
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Slattery SS, Wang H, Giguere DJ, Kocsis C, Urquhart BL, Karas BJ, Edgell DR. Plasmid-based complementation of large deletions in Phaeodactylum tricornutum biosynthetic genes generated by Cas9 editing. Sci Rep 2020; 10:13879. [PMID: 32807825 PMCID: PMC7431573 DOI: 10.1038/s41598-020-70769-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
The model diatom Phaeodactylum tricornutum is an attractive candidate for synthetic biology applications. Development of auxotrophic strains of P. tricornutum would provide alternative selective markers to commonly used antibiotic resistance genes. Here, using CRISPR/Cas9, we show successful editing of genes in the uracil, histidine, and tryptophan biosynthetic pathways. Nanopore long-read sequencing indicates that editing events are characterized by the occurrence of large deletions of up to ~ 2.7 kb centered on the editing site. The uracil and histidine-requiring phenotypes can be complemented by plasmid-based copies of the intact genes after curing of the Cas9-editing plasmid. Growth of uracil auxotrophs on media supplemented with 5-fluoroorotic acid and uracil results in loss of the complementing plasmid, providing a facile method for plasmid curing with potential applications in strain engineering and CRISPR editing. Metabolomic characterization of uracil auxotrophs revealed changes in cellular orotate concentrations consistent with partial or complete loss of orotate phosphoribosyltransferase activity. Our results expand the range of P. tricornutum auxotrophic strains and demonstrate that auxotrophic complementation markers provide a viable alternative to traditionally used antibiotic selection markers. Plasmid-based auxotrophic markers should expand the range of genome engineering applications and provide a means for biocontainment of engineered P. tricornutum strains.
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Affiliation(s)
- Samuel S Slattery
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Helen Wang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Daniel J Giguere
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Csanad Kocsis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Bradley L Urquhart
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada.
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15
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Varela C, Bartel C, Onetto C, Borneman A. Targeted gene deletion in Brettanomyces bruxellensis with an expression-free CRISPR-Cas9 system. Appl Microbiol Biotechnol 2020; 104:7105-7115. [DOI: 10.1007/s00253-020-10750-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
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16
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Boonekamp FJ, Dashko S, Duiker D, Gehrmann T, van den Broek M, den Ridder M, Pabst M, Robert V, Abeel T, Postma ED, Daran JM, Daran-Lapujade P. Design and Experimental Evaluation of a Minimal, Innocuous Watermarking Strategy to Distinguish Near-Identical DNA and RNA Sequences. ACS Synth Biol 2020; 9:1361-1375. [PMID: 32413257 PMCID: PMC7309318 DOI: 10.1021/acssynbio.0c00045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The construction of powerful cell factories requires intensive and extensive remodelling of microbial genomes. Considering the rapidly increasing number of these synthetic biology endeavors, there is an increasing need for DNA watermarking strategies that enable the discrimination between synthetic and native gene copies. While it is well documented that codon usage can affect translation, and most likely mRNA stability in eukaryotes, remarkably few quantitative studies explore the impact of watermarking on transcription, protein expression, and physiology in the popular model and industrial yeast Saccharomyces cerevisiae. The present study, using S. cerevisiae as eukaryotic paradigm, designed, implemented, and experimentally validated a systematic strategy to watermark DNA with minimal alteration of yeast physiology. The 13 genes encoding proteins involved in the major pathway for sugar utilization (i.e., glycolysis and alcoholic fermentation) were simultaneously watermarked in a yeast strain using the previously published pathway swapping strategy. Carefully swapping codons of these naturally codon optimized, highly expressed genes, did not affect yeast physiology and did not alter transcript abundance, protein abundance, and protein activity besides a mild effect on Gpm1. The markerQuant bioinformatics method could reliably discriminate native from watermarked genes and transcripts. Furthermore, presence of watermarks enabled selective CRISPR/Cas genome editing, specifically targeting the native gene copy while leaving the synthetic, watermarked variant intact. This study offers a validated strategy to simply watermark genes in S. cerevisiae.
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Affiliation(s)
- Francine J. Boonekamp
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Sofia Dashko
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Donna Duiker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Thies Gehrmann
- Westerdijk Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Vincent Robert
- Westerdijk Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Thomas Abeel
- Intelligent Systems − Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628XE Delft, The Netherlands
| | - Eline D. Postma
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
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17
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Yu J, Xiang X, Huang J, Liang X, Pan X, Dong Z, Petersen TS, Qu K, Yang L, Zhao X, Li S, Zheng T, Xu Z, Liu C, Han P, Xu F, Yang H, Liu X, Zhang X, Bolund L, Luo Y, Lin L. Haplotyping by CRISPR-mediated DNA circularization (CRISPR-hapC) broadens allele-specific gene editing. Nucleic Acids Res 2020; 48:e25. [PMID: 31943080 PMCID: PMC7049710 DOI: 10.1093/nar/gkz1233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/19/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022] Open
Abstract
Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising the disease-causing allele and the distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISPR-hapC) for haplotyping. Based on the generation (with a pair of CRISPRs) of extrachromosomal circular DNA in cells, the CRISPR-hapC can map haplotypes from a few hundred bases to over 200 Mb. To streamline and demonstrate the applicability of the CRISPR-hapC and asPAM CRISPR for allele-specific gene editing, we reanalyzed the 1000 human pan-genome and generated a high frequency asPAM SNP and CRISPR database (www.crispratlas.com/knockout) for four CRISPR systems (SaCas9, SpCas9, xCas9 and Cas12a). Using the huntingtin (HTT) CAG expansion and transthyretin (TTR) exon 2 mutation as examples, we showed that the asPAM CRISPRs can specifically discriminate active and dead PAMs for all 23 loci tested. Combination of the CRISPR-hapC and asPAM CRISPRs further demonstrated the capability for achieving highly accurate and haplotype-specific deletion of the HTT CAG expansion allele and TTR exon 2 mutation in human cells. Taken together, our study provides a new approach and an important resource for genome research and allele-specific (haplotype-specific) gene therapy.
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Affiliation(s)
- Jiaying Yu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Xi Xiang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Xue Liang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Zhanying Dong
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | | | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Ling Yang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoying Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Siyuan Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Tianyu Zheng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Zhe Xu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Chengxun Liu
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Fengping Xu
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
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18
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Abstract
Fungal pathogens represent a major human threat affecting more than a billion people worldwide. Invasive infections are on the rise, which is of considerable concern because they are accompanied by an escalation of antifungal resistance. Deciphering the mechanisms underlying virulence traits and drug resistance strongly relies on genetic manipulation techniques such as generating mutant strains carrying specific mutations, or gene deletions. However, these processes have often been time-consuming and cumbersome in fungi due to a number of complications, depending on the species (e.g., diploid genomes, lack of a sexual cycle, low efficiency of transformation and/or homologous recombination, lack of cloning vectors, nonconventional codon usage, and paucity of dominant selectable markers). These issues are increasingly being addressed by applying clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 mediated genetic manipulation to medically relevant fungi. Here, we summarize the state of the art of CRISPR-Cas9 applications in four major human fungal pathogen lineages: Candida spp., Cryptococcus neoformans, Aspergillus fumigatus, and Mucorales. We highlight the different ways in which CRISPR has been customized to address the critical issues in different species, including different strategies to deliver the CRISPR-Cas9 elements, their transient or permanent expression, use of codon-optimized CAS9, and methods of marker recycling and scarless editing. Some approaches facilitate a more efficient use of homology-directed repair in fungi in which nonhomologous end joining is more commonly used to repair double-strand breaks (DSBs). Moreover, we highlight the most promising future perspectives, including gene drives, programmable base editors, and nonediting applications, some of which are currently available only in model fungi but may be adapted for future applications in pathogenic species. Finally, this review discusses how the further evolution of CRISPR technology will allow mycologists to tackle the multifaceted issue of fungal pathogenesis.
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Affiliation(s)
- Florent Morio
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- Département de Parasitologie et Mycologie Médicale, Université de Nantes, Nantes Université, EA1155 –IICiMed, Nantes, France
| | - Lisa Lombardi
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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19
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Functional expression of a bacterial α-ketoglutarate dehydrogenase in the cytosol of Saccharomyces cerevisiae. Metab Eng 2019; 56:190-197. [DOI: 10.1016/j.ymben.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/23/2022]
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20
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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21
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James TY, Michelotti LA, Glasco AD, Clemons RA, Powers RA, James ES, Simmons DR, Bai F, Ge S. Adaptation by Loss of Heterozygosity in Saccharomyces cerevisiae Clones Under Divergent Selection. Genetics 2019; 213:665-683. [PMID: 31371407 PMCID: PMC6781901 DOI: 10.1534/genetics.119.302411] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/29/2019] [Indexed: 01/14/2023] Open
Abstract
Loss of heterozygosity (LOH) is observed during vegetative growth and reproduction of diploid genotypes through mitotic crossovers, aneuploidy caused by nondisjunction, and gene conversion. We aimed to test the role that LOH plays during adaptation of two highly heterozygous Saccharomyces cerevisiae genotypes to multiple environments over a short time span in the laboratory. We hypothesized that adaptation would be observed through parallel LOH events across replicate populations. Using genome resequencing of 70 clones, we found that LOH was widespread with 5.2 LOH events per clone after ∼500 generations. The most common mode of LOH was gene conversion (51%) followed by crossing over consistent with either break-induced replication or double Holliday junction resolution. There was no evidence that LOH involved nondisjunction of whole chromosomes. We observed parallel LOH in both an environment-specific and environment-independent manner. LOH largely involved recombining existing variation between the parental genotypes, but also was observed after de novo, presumably beneficial, mutations occurred in the presence of canavanine, a toxic analog of arginine. One highly parallel LOH event involved the ENA salt efflux pump locus on chromosome IV, which showed repeated LOH to the allele from the European parent, an allele originally derived by introgression from S. paradoxus Using CRISPR-engineered LOH we showed that the fitness advantage provided by this single LOH event was 27%. Overall, we found extensive evidence that LOH could be adaptive and is likely to be a greater source of initial variation than de novo mutation for rapid evolution of diploid genotypes.
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Affiliation(s)
- Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Alexander D Glasco
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Rebecca A Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Robert A Powers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Ellen S James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - D Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Fengyan Bai
- Institute of Microbiology, Chinese Academy of Sciences, State Key Laboratory of Mycology, Chaoyang District, Beijing 100101, China
| | - Shuhua Ge
- Technology Development and Transfer Center, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100029, China
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22
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Rode NO, Estoup A, Bourguet D, Courtier-Orgogozo V, Débarre F. Population management using gene drive: molecular design, models of spread dynamics and assessment of ecological risks. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01165-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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23
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Gorter de Vries AR, Voskamp MA, van Aalst ACA, Kristensen LH, Jansen L, van den Broek M, Salazar AN, Brouwers N, Abeel T, Pronk JT, Daran JMG. Laboratory Evolution of a Saccharomyces cerevisiae × S. eubayanus Hybrid Under Simulated Lager-Brewing Conditions. Front Genet 2019; 10:242. [PMID: 31001314 PMCID: PMC6455053 DOI: 10.3389/fgene.2019.00242] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/04/2019] [Indexed: 11/23/2022] Open
Abstract
Saccharomyces pastorianus lager-brewing yeasts are domesticated hybrids of S. cerevisiae x S. eubayanus that display extensive inter-strain chromosome copy number variation and chromosomal recombinations. It is unclear to what extent such genome rearrangements are intrinsic to the domestication of hybrid brewing yeasts and whether they contribute to their industrial performance. Here, an allodiploid laboratory hybrid of S. cerevisiae and S. eubayanus was evolved for up to 418 generations on wort under simulated lager-brewing conditions in six independent sequential batch bioreactors. Characterization of 55 single-cell isolates from the evolved cultures showed large phenotypic diversity and whole-genome sequencing revealed a large array of mutations. Frequent loss of heterozygosity involved diverse, strain-specific chromosomal translocations, which differed from those observed in domesticated, aneuploid S. pastorianus brewing strains. In contrast to the extensive aneuploidy of domesticated S. pastorianus strains, the evolved isolates only showed limited (segmental) aneuploidy. Specific mutations could be linked to calcium-dependent flocculation, loss of maltotriose utilization and loss of mitochondrial activity, three industrially relevant traits that also occur in domesticated S. pastorianus strains. This study indicates that fast acquisition of extensive aneuploidy is not required for genetic adaptation of S. cerevisiae × S. eubayanus hybrids to brewing environments. In addition, this work demonstrates that, consistent with the diversity of brewing strains for maltotriose utilization, domestication under brewing conditions can result in loss of this industrially relevant trait. These observations have important implications for the design of strategies to improve industrial performance of novel laboratory-made hybrids.
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Affiliation(s)
- Arthur R. Gorter de Vries
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
| | - Maaike A. Voskamp
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
| | - Aafke C. A. van Aalst
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
| | - Line H. Kristensen
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
| | - Liset Jansen
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
| | - Marcel van den Broek
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
| | - Alex N. Salazar
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - Nick Brouwers
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, MA, United States
| | - Jack T. Pronk
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
| | - Jean-Marc G. Daran
- Industrial Microbiology, Department of Biotechnology Delft, Delft University of Technology, Delft, Netherlands
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24
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Oberhofer G, Ivy T, Hay BA. Cleave and Rescue, a novel selfish genetic element and general strategy for gene drive. Proc Natl Acad Sci U S A 2019; 116:6250-6259. [PMID: 30760597 PMCID: PMC6442612 DOI: 10.1073/pnas.1816928116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
There is great interest in being able to spread beneficial traits throughout wild populations in ways that are self-sustaining. Here, we describe a chromosomal selfish genetic element, CleaveR [Cleave and Rescue (ClvR)], able to achieve this goal. ClvR comprises two linked chromosomal components. One, germline-expressed Cas9 and guide RNAs (gRNAs)-the Cleaver-cleaves and thereby disrupts endogenous copies of a gene whose product is essential. The other, a recoded version of the essential gene resistant to cleavage and gene conversion with cleaved copies-the Rescue-provides essential gene function. ClvR enhances its transmission, and that of linked genes, by creating conditions in which progeny lacking ClvR die because they have no functional copies of the essential gene. In contrast, those who inherit ClvR survive, resulting in an increase in ClvR frequency. ClvR is predicted to spread to fixation under diverse conditions. To test these predictions, we generated a ClvR element in Drosophila melanogasterClvRtko is located on chromosome 3 and uses Cas9 and four gRNAs to disrupt melanogaster technical knockout (tko), an X-linked essential gene. Rescue activity is provided by tko from Drosophila virilisClvRtko results in germline and maternal carryover-dependent inactivation of melanogaster tko (>99% per generation); lethality caused by this loss is rescued by the virilis transgene; ClvRtko activities are robust to genetic diversity in strains from five continents; and uncleavable but functional melanogaster tko alleles were not observed. Finally, ClvRtko spreads to transgene fixation. The simplicity of ClvR suggests it may be useful for altering populations in diverse species.
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Affiliation(s)
- Georg Oberhofer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Tobin Ivy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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