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Khan MA, Herring G, Zhu JY, Oliva M, Fourie E, Johnston B, Zhang Z, Potter J, Pineda L, Pflueger J, Swain T, Pflueger C, Lloyd JPB, Secco D, Small I, Kidd BN, Lister R. CRISPRi-based circuits to control gene expression in plants. Nat Biotechnol 2024:10.1038/s41587-024-02236-w. [PMID: 38769424 DOI: 10.1038/s41587-024-02236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
The construction of synthetic gene circuits in plants has been limited by a lack of orthogonal and modular parts. Here, we implement a CRISPR (clustered regularly interspaced short palindromic repeats) interference (CRISPRi)-based reversible gene circuit platform in plants. We create a toolkit of engineered repressible promoters of different strengths and construct NOT and NOR gates in Arabidopsis thaliana protoplasts. We determine the optimal processing system to express single guide RNAs from RNA Pol II promoters to introduce NOR gate programmability for interfacing with host regulatory sequences. The performance of a NOR gate in stably transformed Arabidopsis plants demonstrates the system's programmability and reversibility in a complex multicellular organism. Furthermore, cross-species activity of CRISPRi-based logic gates is shown in Physcomitrium patens, Triticum aestivum and Brassica napus protoplasts. Layering multiple NOR gates together creates OR, NIMPLY and AND logic functions, highlighting the modularity of our system. Our CRISPRi circuits are orthogonal, compact, reversible, programmable and modular and provide a platform for sophisticated spatiotemporal control of gene expression in plants.
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Affiliation(s)
- Muhammad Adil Khan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Gabrielle Herring
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Yuan Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marina Oliva
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Elliott Fourie
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Benjamin Johnston
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Zhining Zhang
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jarred Potter
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Luke Pineda
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Tessa Swain
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Christian Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - David Secco
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Brendan N Kidd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland, Australia.
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
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2
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Moreno-Giménez E, Gandía M, Sáez Z, Manzanares P, Yenush L, Orzáez D, Marcos JF, Garrigues S. FungalBraid 2.0: expanding the synthetic biology toolbox for the biotechnological exploitation of filamentous fungi. Front Bioeng Biotechnol 2023; 11:1222812. [PMID: 37609115 PMCID: PMC10441238 DOI: 10.3389/fbioe.2023.1222812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/12/2023] [Indexed: 08/24/2023] Open
Abstract
Fungal synthetic biology is a rapidly expanding field that aims to optimize the biotechnological exploitation of fungi through the generation of standard, ready-to-use genetic elements, and universal syntax and rules for contributory use by the fungal research community. Recently, an increasing number of synthetic biology toolkits have been developed and applied to filamentous fungi, which highlights the relevance of these organisms in the biotechnology field. The FungalBraid (FB) modular cloning platform enables interchangeability of DNA parts with the GoldenBraid (GB) platform, which is designed for plants, and other systems that are compatible with the standard Golden Gate cloning and syntax, and uses binary pCAMBIA-derived vectors to allow Agrobacterium tumefaciens-mediated transformation of a wide range of fungal species. In this study, we have expanded the original FB catalog by adding 27 new DNA parts that were functionally validated in vivo. Among these are the resistance selection markers for the antibiotics phleomycin and terbinafine, as well as the uridine-auxotrophic marker pyr4. We also used a normalized luciferase reporter system to validate several promoters, such as PpkiA, P7760, Pef1α, and PafpB constitutive promoters, and PglaA, PamyB, and PxlnA inducible promoters. Additionally, the recently developed dCas9-regulated GB_SynP synthetic promoter collection for orthogonal CRISPR activation (CRISPRa) in plants has been adapted in fungi through the FB system. In general, the expansion of the FB catalog is of great interest to the scientific community since it increases the number of possible modular and interchangeable DNA assemblies, exponentially increasing the possibilities of studying, developing, and exploiting filamentous fungi.
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Affiliation(s)
- Elena Moreno-Giménez
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Mónica Gandía
- Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department. Faculty of Pharmacy. Universitat de València. Vicente Andrés Estellés s/n, Valencia, Spain
| | - Zara Sáez
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Paloma Manzanares
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universitat Politècnica de València (UPV), Valencia, Spain
| | - Jose F. Marcos
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
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3
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Kobercová E, Srba M, Fischer L. Sulfadiazine and phosphinothricin selection systems optimised for the transformation of tobacco BY-2 cells. PLANT CELL REPORTS 2023; 42:535-548. [PMID: 36609768 DOI: 10.1007/s00299-022-02975-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
We extended the applicability of the BY-2 cell line as a model by introducing two new selection systems. Our protocol provides guidelines for optimising Basta selection in other recalcitrant models. Tobacco BY-2 cell line is the most commonly used cytological model in plant research. It is uniform, can be simply treated by chemicals, synchronised and easily transformed. However, only a few selection systems are available that complicate advanced studies using multiple stacked transgenes and extensive gene editing. In our work, we adopted for BY-2 cell line two other selection systems: sulfadiazine and phosphinothricin (PPT, an active ingredient of Basta herbicide). We show that sulfadiazine can be used in a wide range of concentrations. It is suitable for co-transformation and subsequent double selection with kanamycin or hygromycin, which are standardly used for BY-2 transformation. We also have domesticated the sulfadiazine resistance for the user-friendly GoldenBraid cloning system. Compared to sulfadiazine, establishing selection on phosphinothricin was considerably more challenging. It did not work in any concentration of PPT with standardly cultured cells. Since the selection is based on blocking glutamine synthetase and consequent ammonium toxicity and deficiency of assimilated nitrogen, we tried to manipulate nitrogen availability. We found that the PPT selection reliably works only with nitrogen-starved cells with reduced nitrate reserves that are selected on a medium without ammonium nitrate. Both these adjustments prevent the release of large amounts of ammonium, which can toxify the entire culture in the case of standardly cultured cells. Since high nitrogen reserves can be a common feature of in vitro cultures grown on MS media, nitrogen starvation could be a key step in establishing phosphinothricin resistance in other plant models.
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Affiliation(s)
- Eliška Kobercová
- Department of Experimental Plant Biology, Charles University Faculty of Science, Viničná 5, Prague 2, Czech Republic
| | - Miroslav Srba
- Department of Experimental Plant Biology, Charles University Faculty of Science, Viničná 5, Prague 2, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Charles University Faculty of Science, Viničná 5, Prague 2, Czech Republic.
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4
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Salonia F, Ciacciulli A, Pappalardo HD, Poles L, Pindo M, Larger S, Caruso P, Caruso M, Licciardello C. A dual sgRNA-directed CRISPR/Cas9 construct for editing the fruit-specific β-cyclase 2 gene in pigmented citrus fruits. FRONTIERS IN PLANT SCIENCE 2022; 13:975917. [PMID: 36582639 PMCID: PMC9792771 DOI: 10.3389/fpls.2022.975917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
CRISPR/Cas9 genome editing is a modern biotechnological approach used to improve plant varieties, modifying only one or a few traits of a specific variety. However, this technology cannot be easily used to improve fruit quality traits in citrus, due to the lack of knowledge of key genes, long juvenile stage, and the difficulty regenerating whole plants of specific varieties. Here, we introduce a genome editing approach with the aim of producing citrus plantlets whose fruits contain both lycopene and anthocyanins. Our method employs a dual single guide RNA (sgRNA)-directed genome editing approach to knockout the fruit-specific β-cyclase 2 gene, responsible for the conversion of lycopene to beta-carotene. The gene is targeted by two sgRNAs simultaneously to create a large deletion, as well as to induce point mutations in both sgRNA targets. The EHA105 strain of Agrobacterium tumefaciens was used to transform five different anthocyanin-pigmented sweet oranges, belonging to the Tarocco and Sanguigno varietal groups, and 'Carrizo' citrange, a citrus rootstock as a model for citrus transformation. Among 58 plantlets sequenced in the target region, 86% of them were successfully edited. The most frequent mutations were deletions (from -1 to -74 nucleotides) and insertions (+1 nucleotide). Moreover, a novel event was identified in six plantlets, consisting of the inversion of the region between the two sgRNAs. For 20 plantlets in which a single mutation occurred, we excluded chimeric events. Plantlets did not show an altered phenotype in vegetative tissues. To the best of our knowledge, this work represents the first example of the use of a genome editing approach to potentially improve qualitative traits of citrus fruit.
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Affiliation(s)
- Fabrizio Salonia
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Angelo Ciacciulli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Helena Domenica Pappalardo
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Lara Poles
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Trento with S. Michele all’ Adige, Trento, Italy
| | - Simone Larger
- Research and Innovation Centre, Trento with S. Michele all’ Adige, Trento, Italy
| | - Paola Caruso
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Marco Caruso
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
| | - Concetta Licciardello
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Acireale, Italy
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5
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Abstract
The continual demand for specialized molecular cloning techniques that suit a broad range of applications has driven the development of many different cloning strategies. One method that has gained significant traction is Golden Gate assembly, which achieves hierarchical assembly of DNA parts by utilizing Type IIS restriction enzymes to produce user-specified sticky ends on cut DNA fragments. This technique has been modularized and standardized, and includes different subfamilies of methods, the most widely adopted of which are the MoClo and Golden Braid standards. Moreover, specialized toolboxes tailored to specific applications or organisms are also available. Still, the quantity and range of assembly methods can constitute a barrier to adoption for new users, and even experienced scientists might find it difficult to discern which tools are best suited toward their goals. In this review, we provide a beginner-friendly guide to Golden Gate assembly, compare the different available standards, and detail the specific features and quirks of commonly used toolboxes. We also provide an update on the state-of-the-art in Golden Gate technology, discussing recent advances and challenges to inform existing users and promote standard practices.
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Affiliation(s)
- Jasmine
E. Bird
- School
of Computing, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Jon Marles-Wright
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom,
| | - Andrea Giachino
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom,School
of Science, Engineering & Environment, University of Salford, Salford, M5 4NT, United Kingdom
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6
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Gomide MDS, Leitão MDC, Coelho CM. Biocircuits in plants and eukaryotic algae. FRONTIERS IN PLANT SCIENCE 2022; 13:982959. [PMID: 36212277 PMCID: PMC9545776 DOI: 10.3389/fpls.2022.982959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As one of synthetic biology's foundations, biocircuits are a strategy of genetic parts assembling to recognize a signal and to produce a desirable output to interfere with a biological function. In this review, we revisited the progress in the biocircuits technology basis and its mandatory elements, such as the characterization and assembly of functional parts. Furthermore, for a successful implementation, the transcriptional control systems are a relevant point, and the computational tools help to predict the best combinations among the biological parts planned to be used to achieve the desirable phenotype. However, many challenges are involved in delivering and stabilizing the synthetic structures. Some research experiences, such as the golden crops, biosensors, and artificial photosynthetic structures, can indicate the positive and limiting aspects of the practice. Finally, we envision that the modulatory structural feature and the possibility of finer gene regulation through biocircuits can contribute to the complex design of synthetic chromosomes aiming to develop plants and algae with new or improved functions.
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Affiliation(s)
- Mayna da Silveira Gomide
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
- School of Medicine, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - Matheus de Castro Leitão
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
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7
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Moreno-Giménez E, Selma S, Calvache C, Orzáez D. GB_SynP: A Modular dCas9-Regulated Synthetic Promoter Collection for Fine-Tuned Recombinant Gene Expression in Plants. ACS Synth Biol 2022; 11:3037-3048. [PMID: 36044643 PMCID: PMC9486966 DOI: 10.1021/acssynbio.2c00238] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Indexed: 01/24/2023]
Abstract
Programmable transcriptional factors based on the CRISPR architecture are becoming commonly used in plants for endogenous gene regulation. In plants, a potent CRISPR tool for gene induction is the so-called dCasEV2.1 activation system, which has shown remarkable genome-wide specificity combined with a strong activation capacity. To explore the ability of dCasEV2.1 to act as a transactivator for orthogonal synthetic promoters, a collection of DNA parts was created (GB_SynP) for combinatorial synthetic promoter building. The collection includes (i) minimal promoter parts with the TATA box and 5'UTR regions, (ii) proximal parts containing single or multiple copies of the target sequence for the gRNA, thus functioning as regulatory cis boxes, and (iii) sequence-randomized distal parts that ensure the adequate length of the resulting promoter. A total of 35 promoters were assembled using the GB_SynP collection, showing in all cases minimal background and predictable activation levels depending on the proximal parts used. GB_SynP was also employed in a combinatorial expression analysis of an autoluminescence pathway in Nicotiana benthamiana, showing the value of this tool in extracting important biological information such as the determination of the limiting steps in an enzymatic pathway.
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Affiliation(s)
- Elena Moreno-Giménez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Sara Selma
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Camilo Calvache
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Diego Orzáez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
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8
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Hu G, Wang K, Huang B, Mila I, Frasse P, Maza E, Djari A, Hernould M, Zouine M, Li Z, Bouzayen M. The auxin-responsive transcription factor SlDOF9 regulates inflorescence and flower development in tomato. NATURE PLANTS 2022; 8:419-433. [PMID: 35422080 DOI: 10.1038/s41477-022-01121-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 03/03/2022] [Indexed: 05/04/2023]
Abstract
Understanding the mechanisms underlying differentiation of inflorescence and flower meristems is essential towards enlarging our knowledge of reproductive organ formation and to open new prospects for improving yield traits. Here, we show that SlDOF9 is a new modulator of floral differentiation in tomato. CRISPR/Cas9 knockout strategy uncovered the role of SlDOF9 in controlling inflorescence meristem and floral meristem differentiation via the regulation of cell division genes and inflorescence architecture regulator LIN. Tomato dof9-KO lines have more flowers in both determinate and indeterminate cultivars and produce more fruit upon vibration-assisted fertilization. SlDOF9 regulates inflorescence development through an auxin-dependent ARF5-DOF9 module that seems to operate, at least in part, differently in Arabidopsis and tomato. Our findings add a new actor to the complex mechanisms underlying reproductive organ differentiation in flowering plants and provide leads towards addressing the diversity of factors controlling the transition to reproductive organs.
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Affiliation(s)
- Guojian Hu
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Keke Wang
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Baowen Huang
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Isabelle Mila
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
| | - Pierre Frasse
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Elie Maza
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Anis Djari
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Michel Hernould
- Biologie du Fruit et Pathologie-UMR 1332, Université Bordeaux, INRAE, Villenave d'Ornon, France
| | - Mohamed Zouine
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Mondher Bouzayen
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France.
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France.
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China.
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9
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Garcia-Perez E, Diego-Martin B, Quijano-Rubio A, Moreno-Giménez E, Selma S, Orzaez D, Vazquez-Vilar M. A copper switch for inducing CRISPR/Cas9-based transcriptional activation tightly regulates gene expression in Nicotiana benthamiana. BMC Biotechnol 2022; 22:12. [PMID: 35331211 PMCID: PMC8943966 DOI: 10.1186/s12896-022-00741-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/11/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND CRISPR-based programmable transcriptional activators (PTAs) are used in plants for rewiring gene networks. Better tuning of their activity in a time and dose-dependent manner should allow precise control of gene expression. Here, we report the optimization of a Copper Inducible system called CI-switch for conditional gene activation in Nicotiana benthamiana. In the presence of copper, the copper-responsive factor CUP2 undergoes a conformational change and binds a DNA motif named copper-binding site (CBS). RESULTS In this study, we tested several activation domains fused to CUP2 and found that the non-viral Gal4 domain results in strong activation of a reporter gene equipped with a minimal promoter, offering advantages over previous designs. To connect copper regulation with downstream programmable elements, several copper-dependent configurations of the strong dCasEV2.1 PTA were assayed, aiming at maximizing activation range, while minimizing undesired background expression. The best configuration involved a dual copper regulation of the two protein components of the PTA, namely dCas9:EDLL and MS2:VPR, and a constitutive RNA pol III-driven expression of the third component, a guide RNA with anchoring sites for the MS2 RNA-binding domain. With these optimizations, the CI/dCasEV2.1 system resulted in copper-dependent activation rates of 2,600-fold and 245-fold for the endogenous N. benthamiana DFR and PAL2 genes, respectively, with negligible expression in the absence of the trigger. CONCLUSIONS The tight regulation of copper over CI/dCasEV2.1 makes this system ideal for the conditional production of plant-derived metabolites and recombinant proteins in the field.
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Affiliation(s)
| | | | | | | | - Sara Selma
- Instituto Biología Molecular de Plantas, CSIC-UPV, Valencia, Spain
| | - Diego Orzaez
- Instituto Biología Molecular de Plantas, CSIC-UPV, Valencia, Spain
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10
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Calvache C, Vazquez‐Vilar M, Selma S, Uranga M, Fernández‐del‐Carmen A, Daròs J, Orzáez D. Strong and tunable anti-CRISPR/Cas activities in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:399-408. [PMID: 34632687 PMCID: PMC8753356 DOI: 10.1111/pbi.13723] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/01/2021] [Accepted: 09/24/2021] [Indexed: 05/12/2023]
Abstract
CRISPR/Cas has revolutionized genome engineering in plants. However, the use of anti-CRISPR proteins as tools to prevent CRISPR/Cas-mediated gene editing and gene activation in plants has not been explored yet. This study describes the characterization of two anti-CRISPR proteins, AcrIIA4 and AcrVA1, in Nicotiana benthamiana. Our results demonstrate that AcrIIA4 prevents site-directed mutagenesis in leaves when transiently co-expressed with CRISPR/Cas9. In a similar way, AcrVA1 is able to prevent CRISPR/Cas12a-mediated gene editing. Moreover, using a N. benthamiana line constitutively expressing Cas9, we show that the viral delivery of AcrIIA4 using Tobacco etch virus is able to completely abolish the high editing levels obtained when the guide RNA is delivered with a virus, in this case Potato virus X. We also show that AcrIIA4 and AcrVA1 repress CRISPR/dCas-based transcriptional activation of reporter genes. In the case of AcrIIA4, this repression occurs in a highly efficient, dose-dependent manner. Furthermore, the fusion of an auxin degron to AcrIIA4 results in auxin-regulated activation of a downstream reporter gene. The strong anti-Cas activity of AcrIIA4 and AcrVA1 reported here opens new possibilities for customized control of gene editing and gene expression in plants.
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Affiliation(s)
- Camilo Calvache
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC)Universitat Politècnica de ValènciaValenciaSpain
| | - Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC)Universitat Politècnica de ValènciaValenciaSpain
| | - Sara Selma
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC)Universitat Politècnica de ValènciaValenciaSpain
| | - Mireia Uranga
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC)Universitat Politècnica de ValènciaValenciaSpain
| | - Asun Fernández‐del‐Carmen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC)Universitat Politècnica de ValènciaValenciaSpain
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC)Universitat Politècnica de ValènciaValenciaSpain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones Científicas (CSIC)Universitat Politècnica de ValènciaValenciaSpain
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11
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Cao HX, Vu GTH, Gailing O. From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees. Int J Mol Sci 2022; 23:966. [PMID: 35055150 PMCID: PMC8780650 DOI: 10.3390/ijms23020966] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.
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Affiliation(s)
- Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Giang Thi Ha Vu
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
- Center for Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Gottingen, Germany
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12
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Boccia M, Grzech D, Lopes AA, O’Connor SE, Caputi L. Directed Biosynthesis of New to Nature Alkaloids in a Heterologous Nicotiana benthamiana Expression Host. FRONTIERS IN PLANT SCIENCE 2022; 13:919443. [PMID: 35812900 PMCID: PMC9257203 DOI: 10.3389/fpls.2022.919443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 05/17/2023]
Abstract
Plants produce a wide variety of pharmacologically active molecules classified as natural products. Derivatization of these natural products can modulate or improve the bioactivity of the parent compound. Unfortunately, chemical derivatization of natural products is often difficult or impractical. Here we use the newly discovered biosynthetic genes for two monoterpene indole alkaloids, alstonine and stemmadenine acetate, to generate analogs of these compounds. We reconstitute these biosynthetic genes in the heterologous host Nicotiana benthamiana along with an unnatural starting substrate to produce the corresponding new-to-nature alkaloid product.
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Affiliation(s)
- Marianna Boccia
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Adriana A. Lopes
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, Brazil
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- *Correspondence: Sarah E. O’Connor,
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- Lorenzo Caputi,
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13
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Vazquez-Vilar M, Juarez P, Bernabé-Orts JM, Orzaez D. Design of Multiplexing CRISPR/Cas9 Constructs for Plant Genome Engineering Using the GoldenBraid DNA Assembly Standard. Methods Mol Biol 2022; 2379:27-44. [PMID: 35188654 DOI: 10.1007/978-1-0716-1791-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Due to the huge potential of CRISPR/Cas9 for synthetic biology and genome engineering, many plant researchers are adopting this technology in their laboratories. CRISPR/Cas9 allows multiplexing of guide RNAs (gRNAs), therefore targeting several loci in the genome simultaneously. However, making DNA constructs for this purpose is not always straightforward for first-time users. Here we show how to make multiplex CRISPR/Cas9 constructs using the GoldenBraid (GB) DNA assembly system. As an example, we create a polycistronic gRNA construct that guides a dead version of Cas9 to three different positions of the nopaline synthase promoter, leading to transcriptional repression. After a description of the reagents, the protocol describes step-by-step the considerations for DNA target selection and the molecular cloning process of the final T-DNA construct as well as its testing by transient expression in Nicotiana benthamiana leaves along with a reporter construct for luciferase expression.
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Affiliation(s)
- M Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - P Juarez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - J M Bernabé-Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - D Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain.
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14
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González B, Vazquez-Vilar M, Sánchez-Vicente J, Orzáez D. Optimization of Vectors and Targeting Strategies Including GoldenBraid and Genome Editing Tools: GoldenBraid Assembly of Multiplex CRISPR /Cas12a Guide RNAs for Gene Editing in Nicotiana benthamiana. Methods Mol Biol 2022; 2480:193-214. [PMID: 35616865 DOI: 10.1007/978-1-0716-2241-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
New breeding techniques, especially CRISPR/Cas, could facilitate the expansion and diversification of molecular farming crops by speeding up the introduction of new traits that improve their value as biofactories. One of the main advantages of CRISPR/Cas is its ability to target multiple loci simultaneously, a key feature known as multiplexing. This characteristic is especially relevant for polyploid species, as it is the case of Nicotiana benthamiana and other species of the same genus widely used in molecular farming. Here, we describe in detail the making of a multiplex DNA construct for genome editing in N. benthamiana using the GoldenBraid modular cloning platform. In this case, the procedure is adapted for the requirements of LbCas12a (Lachnospiraceae bacterium Cas12a), a nuclease whose cloning strategy differs from that of the more often used SpCas9 (Streptococcus pyogenes Cas9) enzyme. LbCas12a-mediated edition has several advantages, as its high editing efficiency, described for different plant species, and its T/A-rich PAM sequence, which expands the range of genomic loci that can be targeted by site-specific nucleases. The protocol also includes recommendations for the selection of protospacer sequences and indications for the analysis of editing results.
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15
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González-Grandío E, Demirer GS, Ma W, Brady S, Landry MP. A Ratiometric Dual Color Luciferase Reporter for Fast Characterization of Transcriptional Regulatory Elements in Plants. ACS Synth Biol 2021; 10:2763-2766. [PMID: 34520169 PMCID: PMC10503406 DOI: 10.1021/acssynbio.1c00248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plant synthetic biology requires precise characterization of genetic elements to construct complex genetic circuits that can improve plant traits or confer them with new characteristics. Transcriptional reporter assays are essential to quantify the effect of gene expression regulator elements. Additionally, transcriptional reporter systems are a key tool in understanding control of gene expression in biology. In this work, we construct and characterize a dual color luciferase ratiometric reporter system that possesses several advantages over currently used reporters. It is ratiometric, thus reducing variability and increasing consistency between experiments; it is fast, as both reporters can be measured at the same time in a single reaction, and it is less expensive to perform than current dual luciferase reporter assays. We have validated our system quantifying the transcriptional capability of a panel of promoters and terminators commonly used in synthetic biology with a broad range of expression magnitudes, and in a biologically relevant system, nitrate response.
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Affiliation(s)
- Eduardo González-Grandío
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
| | - Gozde S Demirer
- University of California Davis, Department of Plant Biology and Genome Center, Davis, California 95616, United States
| | - Wenhe Ma
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
| | - Siobhan Brady
- University of California Davis, Department of Plant Biology and Genome Center, Davis, California 95616, United States
| | - Markita P Landry
- University of California Berkeley, Chemical and Biomolecular Engineering, Berkeley, California 94720, United States
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16
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Náprstková A, Malínská K, Záveská Drábková L, Billey E, Náprstková D, Sýkorová E, Bousquet-Antonelli C, Honys D. Characterization of ALBA Family Expression and Localization in Arabidopsis thaliana Generative Organs. Int J Mol Sci 2021; 22:1652. [PMID: 33562109 PMCID: PMC7914821 DOI: 10.3390/ijms22041652] [Citation(s) in RCA: 4] [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: 01/17/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
ALBA DNA/RNA-binding proteins form an ancient family, which in eukaryotes diversified into two Rpp25-like and Rpp20-like subfamilies. In most studied model organisms, their function remains unclear, but they are usually associated with RNA metabolism, mRNA translatability and stress response. In plants, the enriched number of ALBA family members remains poorly understood. Here, we studied ALBA dynamics during reproductive development in Arabidopsis at the levels of gene expression and protein localization, both under standard conditions and following heat stress. In generative tissues, ALBA proteins showed the strongest signal in mature pollen where they localized predominantly in cytoplasmic foci, particularly in regions surrounding the vegetative nucleus and sperm cells. Finally, we demonstrated the involvement of two Rpp25-like subfamily members ALBA4 and ALBA6 in RNA metabolism in mature pollen supported by their co-localization with poly(A)-binding protein 3 (PABP3). Collectively, we demonstrated the engagement of ALBA proteins in male reproductive development and the heat stress response, highlighting the involvement of ALBA4 and ALBA6 in RNA metabolism, storage and/or translational control in pollen upon heat stress. Such dynamic re-localization of ALBA proteins in a controlled, developmentally and environmentally regulated manner, likely reflects not only their redundancy but also their possible functional diversification in plants.
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Affiliation(s)
- Alena Náprstková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Kateřina Malínská
- Imaging Facility, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic;
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Elodie Billey
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; (E.B.); (C.B.-A.)
- LGDP-UMR5096, Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Dagmar Náprstková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
| | - Eva Sýkorová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská, 612 00 Brno, Czech Republic;
| | - Cécile Bousquet-Antonelli
- CNRS LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; (E.B.); (C.B.-A.)
- LGDP-UMR5096, Université de Perpignan via Domitia, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (A.N.); (L.Z.D.); (D.N.)
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17
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Vazquez-Vilar M, Garcia-Carpintero V, Selma S, Bernabé-Orts JM, Sanchez-Vicente J, Salazar-Sarasua B, Ressa A, de Paola C, Ajenjo M, Quintela JC, Fernández-del-Carmen A, Granell A, Orzáez D. The GB4.0 Platform, an All-In-One Tool for CRISPR/Cas-Based Multiplex Genome Engineering in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:689937. [PMID: 34276739 PMCID: PMC8284049 DOI: 10.3389/fpls.2021.689937] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/31/2021] [Indexed: 05/22/2023]
Abstract
CRISPR/Cas ability to target several loci simultaneously (multiplexing) is a game-changer in plant breeding. Multiplexing not only accelerates trait pyramiding but also can unveil traits hidden by functional redundancy. Furthermore, multiplexing enhances dCas-based programmable gene expression and enables cascade-like gene regulation. However, the design and assembly of multiplex constructs comprising tandemly arrayed guide RNAs (gRNAs) requires scarless cloning and is still troublesome due to the presence of repetitive sequences, thus hampering a more widespread use. Here we present a comprehensive extension of the software-assisted cloning platform GoldenBraid (GB), in which, on top of its multigene cloning software, we integrate new tools for the Type IIS-based easy and rapid assembly of up to six tandemly-arrayed gRNAs with both Cas9 and Cas12a, using the gRNA-tRNA-spaced and the crRNA unspaced approaches, respectively. As stress tests for the new tools, we assembled and used for Agrobacterium-mediated stable transformation a 17 Cas9-gRNAs construct targeting a subset of the Squamosa-Promoter Binding Protein-Like (SPL) gene family in Nicotiana tabacum. The 14 selected genes are targets of miR156, thus potentially playing an important role in juvenile-to-adult and vegetative-to-reproductive phase transitions. With the 17 gRNAs construct we generated a collection of Cas9-free SPL edited T1 plants harboring up to 9 biallelic mutations and showing leaf juvenility and more branching. The functionality of GB-assembled dCas9 and dCas12a-based CRISPR/Cas activators and repressors using single and multiplexing gRNAs was validated using a Luciferase reporter with the Solanum lycopersicum Mtb promoter or the Agrobacterium tumefaciens nopaline synthase promoter in transient expression in Nicotiana benthamiana. With the incorporation of the new web-based tools and the accompanying collection of DNA parts, the GB4.0 genome edition turns an all-in-one open platform for plant genome engineering.
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Affiliation(s)
- Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Víctor Garcia-Carpintero
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Sara Selma
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Joan M. Bernabé-Orts
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Javier Sanchez-Vicente
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Blanca Salazar-Sarasua
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Arianna Ressa
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Carmine de Paola
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - María Ajenjo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | | | - Asun Fernández-del-Carmen
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
- *Correspondence: Diego Orzáez
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18
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Cai YM, Kallam K, Tidd H, Gendarini G, Salzman A, Patron NJ. Rational design of minimal synthetic promoters for plants. Nucleic Acids Res 2020; 48:11845-11856. [PMID: 32856047 DOI: 10.1101/2020.05.14.095406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/03/2020] [Accepted: 08/04/2020] [Indexed: 05/20/2023] Open
Abstract
Promoters serve a critical role in establishing baseline transcriptional capacity through the recruitment of proteins, including transcription factors. Previously, a paucity of data for cis-regulatory elements in plants meant that it was challenging to determine which sequence elements in plant promoter sequences contributed to transcriptional function. In this study, we have identified functional elements in the promoters of plant genes and plant pathogens that utilize plant transcriptional machinery for gene expression. We have established a quantitative experimental system to investigate transcriptional function, investigating how identity, density and position contribute to regulatory function. We then identified permissive architectures for minimal synthetic plant promoters enabling the computational design of a suite of synthetic promoters of different strengths. These have been used to regulate the relative expression of output genes in simple genetic devices.
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Affiliation(s)
- Yao-Min Cai
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Henry Tidd
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Giovanni Gendarini
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Amanda Salzman
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Nicola J Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
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19
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Cai YM, Kallam K, Tidd H, Gendarini G, Salzman A, Patron N. Rational design of minimal synthetic promoters for plants. Nucleic Acids Res 2020; 48:11845-11856. [PMID: 32856047 PMCID: PMC7708054 DOI: 10.1093/nar/gkaa682] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/03/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
Promoters serve a critical role in establishing baseline transcriptional capacity through the recruitment of proteins, including transcription factors. Previously, a paucity of data for cis-regulatory elements in plants meant that it was challenging to determine which sequence elements in plant promoter sequences contributed to transcriptional function. In this study, we have identified functional elements in the promoters of plant genes and plant pathogens that utilize plant transcriptional machinery for gene expression. We have established a quantitative experimental system to investigate transcriptional function, investigating how identity, density and position contribute to regulatory function. We then identified permissive architectures for minimal synthetic plant promoters enabling the computational design of a suite of synthetic promoters of different strengths. These have been used to regulate the relative expression of output genes in simple genetic devices.
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Affiliation(s)
- Yao-Min Cai
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Henry Tidd
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Giovanni Gendarini
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Amanda Salzman
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
| | - Nicola J Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norfolk NR4 7UZ, UK
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20
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Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host. Non-model bacteria offer unique and versatile metabolisms for synthetic biology. In this Perspective, the authors explore the limited availability of well-characterised biological parts in these species and argue that bacteriophages represent a diverse trove of orthogonal parts.
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21
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McCarthy DM, Medford JI. Quantitative and Predictive Genetic Parts for Plant Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2020; 11:512526. [PMID: 33123175 PMCID: PMC7573182 DOI: 10.3389/fpls.2020.512526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Plant synthetic biology aims to harness the natural abilities of plants and to turn them to new purposes. A primary goal of plant synthetic biology is to produce predictable and programmable genetic circuits from simple regulatory elements and well-characterized genetic components. The number of available DNA parts for plants is increasing, and the methods for rapid quantitative characterization are being developed, but the field of plant synthetic biology is still in its early stages. We here describe methods used to describe the quantitative properties of genetic components needed for plant synthetic biology. Once the quantitative properties and transfer function of a variety of genetic parts are known, computers can select the optimal components to assemble into functional devices, such as toggle switches and positive feedback circuits. However, while the variety of circuits and traits that can be put into plants are limitless, doing synthetic biology in plants poses unique challenges. Plants are composed of differentiated cells and tissues, each representing potentially unique regulatory or developmental contexts to introduced synthetic genetic circuits. Further, plants have evolved to be highly sensitive to environmental influences, such as light or temperature, any of which can affect the quantitative function of individual parts or whole circuits. Measuring the function of plant components within the context of a plant cell and, ideally, in a living plant, will be essential to using these components in gene circuits with predictable function. Mathematical modeling will be needed to account for the variety of contexts a genetic part will experience in different plant tissues or environments. With such understanding in hand, it may be possible to redesign plant traits to serve human and environmental needs.
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22
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Application of the Safe-By-Design Concept in Crop Breeding Innovation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17176420. [PMID: 32899303 PMCID: PMC7504444 DOI: 10.3390/ijerph17176420] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022]
Abstract
The present paper proposes the application of the safe-by-design concept to crop breeding innovation with the aim to accommodate safety considerations for new agricultural food and feed products. Safe-by-design can be implemented in all stages of the innovation cycle of agricultural products, from the early stages of research and development towards the post-market stage. Our proposed application of safe-by-design can be part of “responsible research and innovation” concepts, because they share features such as risk prevention strategies and a participatory approach. Early awareness of potential safety issues can guide the development of agricultural products towards safe options, both at the process and product level, and thus may help to reduce extensive pre-market assessment studies that might otherwise be needed further downstream for regulatory product approval. Here, it is discussed how the proposed safe-by-design approach can be introduced into the development of safe food crops using emerging technologies, such as gene editing and synthetic biology, and how this may help to safeguard the safety of our food and feed supply in the light of the ongoing global innovations in agricultural crop breeding.
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23
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Kundert P, Sarrion-Perdigones A, Gonzalez Y, Katoh-Kurasawa M, Hirose S, Lehmann P, Venken KJT, Shaulsky G. A GoldenBraid cloning system for synthetic biology in social amoebae. Nucleic Acids Res 2020; 48:4139-4146. [PMID: 32232356 PMCID: PMC7192589 DOI: 10.1093/nar/gkaa185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023] Open
Abstract
GoldenBraid is a rapid, modular, and robust cloning system used to assemble and combine genetic elements. Dictyostelium amoebae represent an intriguing synthetic biological chassis with tractable applications in development, chemotaxis, bacteria–host interactions, and allorecognition. We present GoldenBraid as a synthetic biological framework for Dictyostelium, including a library of 250 DNA parts and assemblies and a proof-of-concept strain that illustrates cAMP-chemotaxis with four fluorescent reporters coded by one plasmid.
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Affiliation(s)
- Peter Kundert
- Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, TX, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shigenori Hirose
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Peter Lehmann
- Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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24
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Patron NJ. Beyond natural: synthetic expansions of botanical form and function. THE NEW PHYTOLOGIST 2020; 227:295-310. [PMID: 32239523 PMCID: PMC7383487 DOI: 10.1111/nph.16562] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/03/2020] [Indexed: 05/05/2023]
Abstract
Powered by developments that enabled genome-scale investigations, systems biology emerged as a field aiming to understand how phenotypes emerge from network functions. These advances fuelled a new engineering discipline focussed on synthetic reconstructions of complex biological systems with the goal of predictable rational design and control. Initially, progress in the nascent field of synthetic biology was slow due to the ad hoc nature of molecular biology methods such as cloning. The application of engineering principles such as standardisation, together with several key technical advances, enabled a revolution in the speed and accuracy of genetic manipulation. Combined with mathematical and statistical modelling, this has improved the predictability of engineering biological systems of which nonlinearity and stochasticity are intrinsic features leading to remarkable achievements in biotechnology as well as novel insights into biological function. In the past decade, there has been slow but steady progress in establishing foundations for synthetic biology in plant systems. Recently, this has enabled model-informed rational design to be successfully applied to the engineering of plant gene regulation and metabolism. Synthetic biology is now poised to transform the potential of plant biotechnology. However, reaching full potential will require conscious adjustments to the skillsets and mind sets of plant scientists.
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Affiliation(s)
- Nicola J. Patron
- Engineering BiologyEarlham InstituteNorwich Research Park, NorwichNorfolkNR4 7UZUK
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25
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Ochoa-Fernandez R, Abel NB, Wieland FG, Schlegel J, Koch LA, Miller JB, Engesser R, Giuriani G, Brandl SM, Timmer J, Weber W, Ott T, Simon R, Zurbriggen MD. Optogenetic control of gene expression in plants in the presence of ambient white light. Nat Methods 2020; 17:717-725. [PMID: 32601426 DOI: 10.1038/s41592-020-0868-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/24/2020] [Accepted: 05/18/2020] [Indexed: 12/22/2022]
Abstract
Optogenetics is the genetic approach for controlling cellular processes with light. It provides spatiotemporal, quantitative and reversible control over biological signaling and metabolic processes, overcoming limitations of chemically inducible systems. However, optogenetics lags in plant research because ambient light required for growth leads to undesired system activation. We solved this issue by developing plant usable light-switch elements (PULSE), an optogenetic tool for reversibly controlling gene expression in plants under ambient light. PULSE combines a blue-light-regulated repressor with a red-light-inducible switch. Gene expression is only activated under red light and remains inactive under white light or in darkness. Supported by a quantitative mathematical model, we characterized PULSE in protoplasts and achieved high induction rates, and we combined it with CRISPR-Cas9-based technologies to target synthetic signaling and developmental pathways. We applied PULSE to control immune responses in plant leaves and generated Arabidopsis transgenic plants. PULSE opens broad experimental avenues in plant research and biotechnology.
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Affiliation(s)
- Rocio Ochoa-Fernandez
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany.,iGRAD Plant Graduate School, University of Düsseldorf, Düsseldorf, Germany
| | - Nikolaj B Abel
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | | | - Jenia Schlegel
- iGRAD Plant Graduate School, University of Düsseldorf, Düsseldorf, Germany.,Institute of Developmental Genetics, University of Düsseldorf, Düsseldorf, Germany
| | - Leonie-Alexa Koch
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany
| | - J Benjamin Miller
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Raphael Engesser
- Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany
| | - Giovanni Giuriani
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany.,Univeersity of Glasgow, Glasgow, Scotland, UK
| | - Simon M Brandl
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jens Timmer
- Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Thomas Ott
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Rüdiger Simon
- iGRAD Plant Graduate School, University of Düsseldorf, Düsseldorf, Germany.,Institute of Developmental Genetics, University of Düsseldorf, Düsseldorf, Germany.,CEPLAS-Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany. .,iGRAD Plant Graduate School, University of Düsseldorf, Düsseldorf, Germany. .,CEPLAS-Cluster of Excellence on Plant Sciences, Düsseldorf, Germany.
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26
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Sarrion-Perdigones A, Gonzalez Y, Venken KJT. Rapid and Efficient Synthetic Assembly of Multiplex Luciferase Reporter Plasmids for the Simultaneous Monitoring of Up to Six Cellular Signaling Pathways. ACTA ACUST UNITED AC 2020; 131:e121. [PMID: 32539183 DOI: 10.1002/cpmb.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-throughput cell-based screening assays are valuable tools in the discovery of chemical probes and therapeutic agents. Such assays are designed to examine the effects of small compounds on targets, pathways, or phenotypes participating in normal and disease processes. While most cell-based assays measure single quantities, multiplexed assays seek to address these limitations by obtaining multiple simultaneous measurements. The signals from such measurements should be independently detectable and cover large dynamic ranges. Luciferases are good candidates for generation of such signals. They are genetically encoded, versatile, and cost-effective, and their output signals can be sensitively detected. We recently developed a multiplex luciferase assay that allows monitoring the activity of five experimental pathways against one control simultaneously. We used synthetic assembly cloning to assemble all six luciferase reporter units into a single vector over eight stitching rounds. Because all six reporters are on a single piece of DNA, a single vector ensures stoichiometric ratios of each transcriptional unit in each transfected cell, resulting in lower experimental variation. Our proof-of-concept multiplex hextuple luciferase assay was designed to simultaneously monitor the p53, TGF-β, NF-κβ, c-Myc, and MAPK/JNK signaling pathways. The same synthetic assembly cloning pipeline allows the stitching of numerous other cellular pathway luciferase reporters. Here we present an improved three-step synthetic assembly protocol to quickly and efficiently generate multiplex hextuple luciferase reporter plasmids for other signaling pathways of interest. This improved assembly protocol provides the opportunity to analyze any five desired pathways at once much more quickly. Protocols are provided on how to prepare DNA components and destination vector plasmids, design synthetic DNA, perform assembly cloning of new transcriptional reporter elements, implement multipartite synthetic assembly cloning of single-pathway luciferase reporters, and carry out one-step assembly of final multiplex hextuple luciferase vectors. We present protocols on how to perform multiplex hextuple luciferase in an accompanying Current Protocols in Molecular Biology article. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of DNA parts and destination vectors for synthetic assembly cloning Basic Protocol 2: DNA synthesis and assembly cloning of a typical transcriptional reporter element Alternate Protocol: DNA synthesis and assembly cloning of a challenging transcriptional reporter element Basic Protocol 3: Multipartite synthetic assembly cloning of individual pathway luciferase reporters Basic Protocol 4: One step assembly into final multiplex hextuple luciferase vectors Support Protocol: Generation of home-made chemocompetent E. coli DH10B-T1R cells.
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Affiliation(s)
- Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas.,McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, Texas
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27
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Plant terpenoid metabolism co-opts a component of the cell wall biosynthesis machinery. Nat Chem Biol 2020; 16:740-748. [PMID: 32424305 DOI: 10.1038/s41589-020-0541-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 04/03/2020] [Indexed: 01/06/2023]
Abstract
Glycosylation is one of the most prevalent molecular modifications in nature. Single or multiple sugars can decorate a wide range of acceptors from proteins to lipids, cell wall glycans and small molecules, dramatically affecting their activity. Here, we discovered that by 'hijacking' an enzyme of the cellulose synthesis machinery involved in cell wall assembly, plants evolved cellulose synthase-like enzymes (Csls) and acquired the capacity to glucuronidate specialized metabolites, that is, triterpenoid saponins. Apparently, endoplasmic reticulum-membrane localization of Csls and of other pathway proteins was part of evolving a new glycosyltransferase function, as plant metabolite glycosyltransferases typically act in the cytosol. Discovery of glucuronic acid transferases across several plant orders uncovered the long-pursued enzymatic reaction in the production of a low-calorie sweetener from licorice roots. Our work opens the way for engineering potent saponins through microbial fermentation and plant-based systems.
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28
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Leydon AR, Gala HP, Guiziou S, Nemhauser JL. Engineering Synthetic Signaling in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:767-788. [PMID: 32092279 DOI: 10.1146/annurev-arplant-081519-035852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Synthetic signaling is a branch of synthetic biology that aims to understand native genetic regulatory mechanisms and to use these insights to engineer interventions and devices that achieve specified design parameters. Applying synthetic signaling approaches to plants offers the promise of mitigating the worst effects of climate change and providing a means to engineer crops for entirely novel environments, such as those in space travel. The ability to engineer new traits using synthetic signaling methods will require standardized libraries of biological parts and methods to assemble them; the decoupling of complex processes into simpler subsystems; and mathematical models that can accelerate the design-build-test-learn cycle. The field of plant synthetic signaling is relatively new, but it is poised for rapid advancement. Translation from the laboratory to the field is likely to be slowed, however, by the lack of constructive dialogue between researchers and other stakeholders.
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Affiliation(s)
- Alexander R Leydon
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Hardik P Gala
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Sarah Guiziou
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Jennifer L Nemhauser
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
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29
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Bernabé-Orts JM, Quijano-Rubio A, Vazquez-Vilar M, Mancheño-Bonillo J, Moles-Casas V, Selma S, Gianoglio S, Granell A, Orzaez D. A memory switch for plant synthetic biology based on the phage ϕC31 integration system. Nucleic Acids Res 2020; 48:3379-3394. [PMID: 32083668 PMCID: PMC7102980 DOI: 10.1093/nar/gkaa104] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023] Open
Abstract
Synthetic biology has advanced from the setup of basic genetic devices to the design of increasingly complex gene circuits to provide organisms with new functions. While many bacterial, fungal and mammalian unicellular chassis have been extensively engineered, this progress has been delayed in plants due to the lack of reliable DNA parts and devices that enable precise control over these new synthetic functions. In particular, memory switches based on DNA site-specific recombination have been the tool of choice to build long-term and stable synthetic memory in other organisms, because they enable a shift between two alternative states registering the information at the DNA level. Here we report a memory switch for whole plants based on the bacteriophage ϕC31 site-specific integrase. The switch was built as a modular device made of standard DNA parts, designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally operated by action of the ϕC31 integrase (Int), and its recombination directionality factor (RDF). The kinetics, memory, and reversibility of the switch were extensively characterized in Nicotiana benthamiana plants.
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Affiliation(s)
- Joan Miquel Bernabé-Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Alfredo Quijano-Rubio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Javier Mancheño-Bonillo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Victor Moles-Casas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Sara Selma
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Silvia Gianoglio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
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30
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Fernandez MA, Belda-Palazon B, Julian J, Coego A, Lozano-Juste J, Iñigo S, Rodriguez L, Bueso E, Goossens A, Rodriguez PL. RBR-Type E3 Ligases and the Ubiquitin-Conjugating Enzyme UBC26 Regulate Abscisic Acid Receptor Levels and Signaling. PLANT PHYSIOLOGY 2020; 182:1723-1742. [PMID: 31699847 PMCID: PMC7140949 DOI: 10.1104/pp.19.00898] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/21/2019] [Indexed: 05/06/2023]
Abstract
The turnover of abscisic acid (ABA) signaling core components modulates the plant's response to ABA and is regulated by ubiquitination. We show that Arabidopsis (Arabidopsis thaliana) RING Finger ABA-Related1 (RFA1) and RFA4 E3 ubiquitin ligases, members of the RING between RING fingers (RBR)-type RSL1/RFA family, are key regulators of ABA receptor stability in root and leaf tissues, targeting ABA receptors for degradation in different subcellular locations. RFA1 is localized both in the nucleus and cytosol, whereas RFA4 shows specific nuclear localization and promotes nuclear degradation of ABA receptors. Therefore, members of the RSL1/RFA family interact with ABA receptors at plasma membrane, cytosol, and nucleus, targeting them for degradation via the endosomal/vacuolar RSL1-dependent pathway or 26S proteasome. Additionally, we provide insight into the physiological function of the relatively unexplored plant RBR-type E3 ligases, and through mutagenesis and biochemical assays we identified cysteine-361 in RFA4 as the putative active site cysteine, which is a distinctive feature of RBR-type E3 ligases. Endogenous levels of PYR1 and PYL4 ABA receptors were higher in the rfa1 rfa4 double mutant than in wild-type plants. UBC26 was identified as the cognate nuclear E2 enzyme that interacts with the RFA4 E3 ligase and forms UBC26-RFA4-receptor complexes in nuclear speckles. Loss-of-function ubc26 alleles and the rfa1 rfa4 double mutant showed enhanced sensitivity to ABA and accumulation of ABA receptors compared with the wild type. Together, our results reveal a sophisticated mechanism by which ABA receptors are targeted by ubiquitin at different subcellular locations, in which the complexity of the ABA receptor family is mirrored in the partner RBR-type E3 ligases.
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Affiliation(s)
- Maria Angeles Fernandez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Borja Belda-Palazon
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Jose Julian
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Alberto Coego
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Sabrina Iñigo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lesia Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Eduardo Bueso
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
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31
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Yan P, Zeng Y, Shen W, Tuo D, Li X, Zhou P. Nimble Cloning: A Simple, Versatile, and Efficient System for Standardized Molecular Cloning. Front Bioeng Biotechnol 2020; 7:460. [PMID: 32010678 PMCID: PMC6974442 DOI: 10.3389/fbioe.2019.00460] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Molecular cloning is one of the most fundamental technologies in molecular biology, and has been critical for driving biotechnological advances. In this study, we have developed a novel method for standardized molecular cloning. The cloning technique known as "Nimble Cloning" uses the restriction enzyme, SfiI, in combination with the T5 exonuclease, to linearize the vector and generate 3'-overhangs simultaneously. Both PCR products and plasmids can be used for the cloning reaction in the Nimble Cloning system. The cloning system is highly efficient, suitable for gene expression in both prokaryotic and eukaryotic expression systems, and enables the reuse of DNA fragments or plasmid entry clones. Nimble Cloning is applicable for the cloning of single or multiple fragments, as well as multi-site cloning. Due also to its simplicity and versatility, the cloning method has great potential for the modular assembly of DNA constructs.
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Affiliation(s)
- Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yanjing Zeng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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32
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Diego-Martin B, González B, Vazquez-Vilar M, Selma S, Mateos-Fernández R, Gianoglio S, Fernández-del-Carmen A, Orzáez D. Pilot Production of SARS-CoV-2 Related Proteins in Plants: A Proof of Concept for Rapid Repurposing of Indoor Farms Into Biomanufacturing Facilities. FRONTIERS IN PLANT SCIENCE 2020; 11:612781. [PMID: 33424908 PMCID: PMC7785703 DOI: 10.3389/fpls.2020.612781] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/02/2020] [Indexed: 05/21/2023]
Abstract
The current CoVid-19 crisis is revealing the strengths and the weaknesses of the world's capacity to respond to a global health crisis. A critical weakness has resulted from the excessive centralization of the current biomanufacturing capacities, a matter of great concern, if not a source of nationalistic tensions. On the positive side, scientific data and information have been shared at an unprecedented speed fuelled by the preprint phenomena, and this has considerably strengthened our ability to develop new technology-based solutions. In this work, we explore how, in a context of rapid exchange of scientific information, plant biofactories can serve as a rapid and easily adaptable solution for local manufacturing of bioreagents, more specifically recombinant antibodies. For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. For the design of the antibodies, we took advantage, among other data sources, of the DNA sequence information made rapidly available by other groups in preprint publications. mAbs were engineered as single-chain fragments fused to a human gamma Fc and transiently expressed using a viral vector. In parallel, we also produced the recombinant SARS-CoV-2 N protein and the receptor binding domain (RBD) of the Spike protein in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies, we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Our results indicate that gram amounts of anti-SARS-CoV-2 antibodies could be easily produced in little more than 6 weeks in repurposed greenhouses with little infrastructure requirements using N. benthamiana as production platform. Similar procedures could be easily deployed to produce diagnostic reagents and, eventually, could be adapted for rapid therapeutic responses.
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33
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Examining multiple cellular pathways at once using multiplex hextuple luciferase assaying. Nat Commun 2019; 10:5710. [PMID: 31836712 PMCID: PMC6911020 DOI: 10.1038/s41467-019-13651-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/14/2019] [Indexed: 01/24/2023] Open
Abstract
Sensitive simultaneous assessment of multiple signaling pathways within the same cells requires orthogonal reporters that can assay over large dynamic ranges. Luciferases are such genetically encoded candidates due to their sensitivity, versatility, and cost-effectiveness. We expand luciferase multiplexing in post-lysis endpoint luciferase assays from two to six. Light emissions are distinguished by a combination of distinct substrates and emission spectra deconvolution. All six luciferase reporter units are stitched together into one plasmid facilitating delivery of all reporter units through a process we termed solotransfection, minimizing experimental errors. We engineer a multiplex hextuple luciferase assay to probe pathway fluxes through five transcriptional response elements against a control constitutive promoter. We can monitor effects of siRNA, ligand, and chemical compound treatments on their target pathways along with the four other probed cellular pathways. We demonstrate the effectiveness and adaptiveness of multiplex luciferase assaying, and its broad application across different research fields. Multiplexed detection of luciferase-based sensors in the same sample is challenging and limited by the substrates’ emission spectra. Here the authors establish a system based on three different luciferases and sequential detection to achieve measurements of up to six parameters within the same experiment.
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34
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Bernabé‐Orts JM, Casas‐Rodrigo I, Minguet EG, Landolfi V, Garcia‐Carpintero V, Gianoglio S, Vázquez‐Vilar M, Granell A, Orzaez D. Assessment of Cas12a-mediated gene editing efficiency in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1971-1984. [PMID: 30950179 PMCID: PMC6737022 DOI: 10.1111/pbi.13113] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/19/2019] [Accepted: 03/20/2019] [Indexed: 05/17/2023]
Abstract
The CRISPR/Cas12a editing system opens new possibilities for plant genome engineering. To obtain a comparative assessment of RNA-guided endonuclease (RGEN) types in plants, we adapted the CRISPR/Cas12a system to the GoldenBraid (GB) modular cloning platform and compared the efficiency of Acidaminococcus (As) and Lachnospiraceae (Lb) Cas12a variants with the previously described GB-assembled Streptococcus pyogenes Cas9 (SpCas9) constructs in eight Nicotiana benthamiana loci using transient expression. All three nucleases showed drastic target-dependent differences in efficiency, with LbCas12 producing higher mutagenesis rates in five of the eight loci assayed, as estimated with the T7E1 endonuclease assay. Attempts to engineer crRNA direct repeat (DR) had little effect improving on-target efficiency for AsCas12a and resulted deleterious in the case of LbCas12a. To complete the assessment of Cas12a activity, we carried out genome editing experiments in three different model plants, namely N. benthamiana, Solanum lycopersicum and Arabidopsis thaliana. For the latter, we also resequenced Cas12a-free segregating T2 lines to assess possible off-target effects. Our results showed that the mutagenesis footprint of Cas12a is enriched in deletions of -10 to -2 nucleotides and included in some instances complex rearrangements in the surroundings of the target sites. We found no evidence of off-target mutations neither in related sequences nor somewhere else in the genome. Collectively, this study shows that LbCas12a is a viable alternative to SpCas9 for plant genome engineering.
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Affiliation(s)
- Joan Miquel Bernabé‐Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Iván Casas‐Rodrigo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
- Present address:
Department of Biosystems Science and EngineeringEidgenössische Technische Hochschule (ETH) ZurichBaselSwitzerland
| | - Eugenio G. Minguet
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Viola Landolfi
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoGrugliascoItaly
| | - Victor Garcia‐Carpintero
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - Silvia Gianoglio
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoGrugliascoItaly
| | - Marta Vázquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
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Selma S, Bernabé‐Orts JM, Vazquez‐Vilar M, Diego‐Martin B, Ajenjo M, Garcia‐Carpintero V, Granell A, Orzaez D. Strong gene activation in plants with genome-wide specificity using a new orthogonal CRISPR/Cas9-based programmable transcriptional activator. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1703-1705. [PMID: 31034138 PMCID: PMC6686126 DOI: 10.1111/pbi.13138] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 05/03/2023]
Affiliation(s)
- Sara Selma
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Joan Miquel Bernabé‐Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Borja Diego‐Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Maria Ajenjo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Victor Garcia‐Carpintero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
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Palaci J, Virdi V, Depicker A. Transformation strategies for stable expression of complex hetero-multimeric proteins like secretory immunoglobulin A in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1760-1769. [PMID: 30801876 PMCID: PMC6686127 DOI: 10.1111/pbi.13098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
Plant expression systems have proven to be exceptional in producing high-value complex polymeric proteins such as secretory IgAs (SIgAs). However, polymeric protein production requires the expression of multiple genes, which can be transformed as single or multiple T-DNA units to generate stable transgenic plant lines. Here, we evaluated four strategies to stably transform multiple genes and to obtain high expression of all components. Using the in-seed expression of a simplified secretory IgA (sSIgA) as a reference molecule, we conclude that it is better to spread the genes over two T-DNAs than to contain them in a single T-DNA, because of the presence of homologous recombination events and gene silencing. These T-DNAs can be cotransformed to obtain transgenic plants in one transformation step. However, if time permits, more transformants with high production levels of the polymeric protein can be obtained either by sequential transformation or by in-parallel transformation followed by crossing of transformants independently selected for excellent expression of the genes in each T-DNA.
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Affiliation(s)
- Jorge Palaci
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- VIB Center for Plant Systems BiologyGentBelgium
| | - Vikram Virdi
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- VIB Center for Plant Systems BiologyGentBelgium
- Department of Biochemistry and MicrobiologyGhent UniversityGentBelgium
- VIB Center for Medical BiotechnologyGentBelgium
| | - Ann Depicker
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGentBelgium
- VIB Center for Plant Systems BiologyGentBelgium
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Liu S, Xiao H, Zhang F, Lu Z, Zhang Y, Deng A, Li Z, Yang C, Wen T. A seamless and iterative DNA assembly method named PS-Brick and its assisted metabolic engineering for threonine and 1-propanol production. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:180. [PMID: 31338122 PMCID: PMC6628500 DOI: 10.1186/s13068-019-1520-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND DNA assembly is an essential technique enabling metabolic engineering and synthetic biology. Combining novel DNA assembly technologies with rational metabolic engineering can facilitate the construction of microbial cell factories. Amino acids and derived biochemicals are important products in industrial biotechnology with wide application and huge markets. DNA assembly scenarios encountered in metabolic engineering for the construction of amino acid and related compound producers, such as design-build-test-learn cycles, construction of precise genetic circuits and repetitive DNA molecules, usually require for iterative, scarless and repetitive sequence assembly methods, respectively. RESULTS Restriction endonuclease (RE)-assisted strategies constitute one of the major categories of DNA assembly. Here, we developed a Type IIP and IIS RE-assisted method named PS-Brick that comprehensively takes advantage of the properties of PCR fragments and REs for iterative, seamless and repetitive sequence assembly. One round of PS-Brick reaction using purified plasmids and PCR fragments was accomplished within several hours, and transformation of the resultant reaction product from this PS-Brick assembly reaction exhibited high efficiency (104-105 CFUs/µg DNA) and high accuracy (~ 90%). An application of metabolic engineering to threonine production, including the release of feedback regulation, elimination of metabolic bottlenecks, intensification of threonine export and inactivation of threonine catabolism, was stepwise resolved in E. coli by rounds of "design-build-test-learn" cycles through the iterative PS-Brick paradigm, and 45.71 g/L threonine was obtained through fed-batch fermentation. In addition to the value of the iterative character of PS-Brick for sequential strain engineering, seamless cloning enabled precise in-frame fusion for codon saturation mutagenesis and bicistronic design, and the repetitive sequence cloning ability of PS-Brick enabled construction of tandem CRISPR sgRNA arrays for genome editing. Moreover, the heterologous pathway deriving 1-propanol pathway from threonine, composed of Lactococcus lactis kivD and Saccharomyces cerevisiae ADH2, was assembled by one cycle of PS-Brick, resulting in 1.35 g/L 1-propanol in fed-batch fermentation. CONCLUSIONS To the best of our knowledge, the PS-Brick framework is the first RE-assisted DNA assembly method using the strengths of both Type IIP and IIS REs. In this study, PS-Brick was demonstrated to be an efficient DNA assembly method for pathway construction and genome editing and was successfully applied in design-build-test-learn (DBTL) cycles of metabolic engineering for the production of threonine and threonine-derived 1-propanol. The PS-Brick presents a valuable addition to the current toolbox of synthetic biology and metabolic engineering.
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Affiliation(s)
- Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Haihan Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230039 China
| | - Zheng Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhongcai Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Cui Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
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Chiasson D, Giménez-Oya V, Bircheneder M, Bachmaier S, Studtrucker T, Ryan J, Sollweck K, Leonhardt H, Boshart M, Dietrich P, Parniske M. A unified multi-kingdom Golden Gate cloning platform. Sci Rep 2019; 9:10131. [PMID: 31300661 PMCID: PMC6626145 DOI: 10.1038/s41598-019-46171-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/19/2019] [Indexed: 12/21/2022] Open
Abstract
Assembling composite DNA modules from custom DNA parts has become routine due to recent technological breakthroughs such as Golden Gate modular cloning. Using Golden Gate, one can efficiently assemble custom transcription units and piece units together to generate higher-order assemblies. Although Golden Gate cloning systems have been developed to assemble DNA plasmids required for experimental work in model species, they are not typically applicable to organisms from other kingdoms. Consequently, a typical molecular biology laboratory working across kingdoms must use multiple cloning strategies to assemble DNA constructs for experimental assays. To simplify the DNA assembly process, we developed a multi-kingdom (MK) Golden Gate assembly platform for experimental work in species from the kingdoms Fungi, Eubacteria, Protista, Plantae, and Animalia. Plasmid backbone and part overhangs are consistent across the platform, saving both time and resources in the laboratory. We demonstrate the functionality of the system by performing a variety of experiments across kingdoms including genome editing, fluorescence microscopy, and protein interaction assays. The versatile MK system therefore streamlines the assembly of modular DNA constructs for biological assays across a range of model organisms.
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Affiliation(s)
- David Chiasson
- Faculty of Biology, Genetics, LMU Munich, D-82152, Martinsried, Germany. .,Department of Biology, Saint Mary's University, B3H 3C3, Halifax, Canada.
| | | | | | - Sabine Bachmaier
- Faculty of Biology, Genetics, LMU Munich, D-82152, Martinsried, Germany
| | - Tanja Studtrucker
- Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | - Joel Ryan
- Faculty of Biology and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, Großhaderner Str. 2, D-82152, Martinsried, Germany
| | | | - Heinrich Leonhardt
- Faculty of Biology and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, Großhaderner Str. 2, D-82152, Martinsried, Germany
| | - Michael Boshart
- Faculty of Biology, Genetics, LMU Munich, D-82152, Martinsried, Germany
| | - Petra Dietrich
- Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | - Martin Parniske
- Faculty of Biology, Genetics, LMU Munich, D-82152, Martinsried, Germany.
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Gantner J, Ordon J, Ilse T, Kretschmer C, Gruetzner R, Löfke C, Dagdas Y, Bürstenbinder K, Marillonnet S, Stuttmann J. Peripheral infrastructure vectors and an extended set of plant parts for the Modular Cloning system. PLoS One 2018; 13:e0197185. [PMID: 29847550 PMCID: PMC5976141 DOI: 10.1371/journal.pone.0197185] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/27/2018] [Indexed: 11/21/2022] Open
Abstract
Standardized DNA assembly strategies facilitate the generation of multigene constructs from collections of building blocks in plant synthetic biology. A common syntax for hierarchical DNA assembly following the Golden Gate principle employing Type IIs restriction endonucleases was recently developed, and underlies the Modular Cloning and GoldenBraid systems. In these systems, transcriptional units and/or multigene constructs are assembled from libraries of standardized building blocks, also referred to as phytobricks, in several hierarchical levels and by iterative Golden Gate reactions. Here, a toolkit containing further modules for the novel DNA assembly standards was developed. Intended for use with Modular Cloning, most modules are also compatible with GoldenBraid. Firstly, a collection of approximately 80 additional phytobricks is provided, comprising e.g. modules for inducible expression systems, promoters or epitope tags. Furthermore, DNA modules were developed for connecting Modular Cloning and Gateway cloning, either for toggling between systems or for standardized Gateway destination vector assembly. Finally, first instances of a "peripheral infrastructure" around Modular Cloning are presented: While available toolkits are designed for the assembly of plant transformation constructs, vectors were created to also use coding sequence-containing phytobricks directly in yeast two hybrid interaction or bacterial infection assays. The presented material will further enhance versatility of hierarchical DNA assembly strategies.
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Affiliation(s)
- Johannes Gantner
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Jana Ordon
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Theresa Ilse
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Carola Kretschmer
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Ramona Gruetzner
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Christian Löfke
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Johannes Stuttmann
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
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Andreou AI, Nakayama N. Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly. PLoS One 2018; 13:e0189892. [PMID: 29293531 PMCID: PMC5749717 DOI: 10.1371/journal.pone.0189892] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/04/2017] [Indexed: 11/26/2022] Open
Abstract
Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.
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Affiliation(s)
- Andreas I. Andreou
- SynthSys Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Naomi Nakayama
- SynthSys Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Science at Extreme Condition, University of Edinburgh, Edinburgh, United Kingdom
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Pasin F, Bedoya LC, Bernabé-Orts JM, Gallo A, Simón-Mateo C, Orzaez D, García JA. Multiple T-DNA Delivery to Plants Using Novel Mini Binary Vectors with Compatible Replication Origins. ACS Synth Biol 2017; 6:1962-1968. [PMID: 28657330 DOI: 10.1021/acssynbio.6b00354] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Improved plants are necessary to meet human needs. Agrobacterium-mediated transformation is the most common method used to rewire plant capabilities. For plant gene delivery, DNA constructs are assembled into binary T-DNA vectors that rely on broad host range origins for bacterial replication. Here we present pLX vectors, a set of mini binary T-DNA plasmids suitable for Type IIS restriction endonuclease- and overlap-based assembly methods. pLX vectors include replicons from compatible broad host range plasmids. Simultaneous usage of pBBR1- and RK2-based pLX vectors in a two-plasmid/one-Agrobacterium strain strategy allowed multigene delivery to plants. Adoption of pLX vectors will facilitate routine plant transformations and targeted mutagenesis, as well as complex part and circuit characterization.
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Affiliation(s)
- Fabio Pasin
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Leonor C. Bedoya
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Joan Miquel Bernabé-Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Camino de Vera s/n, 46022 Valencia, Spain
| | - Araíz Gallo
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Carmen Simón-Mateo
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Camino de Vera s/n, 46022 Valencia, Spain
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