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Fernandez‐Moreno J, Yaschenko AE, Neubauer M, Marchi AJ, Zhao C, Ascencio‐Ibanez JT, Alonso JM, Stepanova AN. A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1942-1956. [PMID: 38379432 PMCID: PMC11182585 DOI: 10.1111/pbi.14313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Advancement of DNA-synthesis technologies has greatly facilitated the development of synthetic biology tools. However, high-complexity DNA sequences containing tandems of short repeats are still notoriously difficult to produce synthetically, with commercial DNA synthesis companies usually rejecting orders that exceed specific sequence complexity thresholds. To overcome this limitation, we developed a simple, single-tube reaction method that enables the generation of DNA sequences containing multiple repetitive elements. Our strategy involves commercial synthesis and PCR amplification of padded sequences that contain the repeats of interest, along with random intervening sequence stuffers that include type IIS restriction enzyme sites. GoldenBraid molecular cloning technology is then employed to remove the stuffers, rejoin the repeats together in a predefined order, and subclone the tandem(s) in a vector using a single-tube digestion-ligation reaction. In our hands, this new approach is much simpler, more versatile and efficient than previously developed solutions to this problem. As a proof of concept, two different phytohormone-responsive, synthetic, repetitive proximal promoters were generated and tested in planta in the context of transcriptional reporters. Analysis of transgenic lines carrying the synthetic ethylene-responsive promoter 10x2EBS-S10 fused to the GUS reporter gene uncovered several developmentally regulated ethylene response maxima, indicating the utility of this reporter for monitoring the involvement of ethylene in a variety of physiologically relevant processes. These encouraging results suggest that this reporter system can be leveraged to investigate the ethylene response to biotic and abiotic factors with high spatial and temporal resolution.
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Affiliation(s)
| | - Anna E. Yaschenko
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Matthew Neubauer
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Alex J. Marchi
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Chengsong Zhao
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - José T. Ascencio‐Ibanez
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Jose M. Alonso
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Anna N. Stepanova
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
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Wong S, Jimenez S, Slavcev RA. Construction and characterization of a novel miniaturized filamentous phagemid for targeted mammalian gene transfer. Microb Cell Fact 2023; 22:124. [PMID: 37430278 DOI: 10.1186/s12934-023-02135-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/24/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND As simplistic proteinaceous carriers of genetic material, phages offer great potential as targeted vectors for mammalian transgene delivery. The filamentous phage M13 is a single-stranded DNA phage with attractive characteristics for gene delivery, including a theoretically unlimited DNA carrying capacity, amenability to tropism modification via phage display, and a well-characterized genome that is easy to genetically modify. The bacterial backbone in gene transfer plasmids consists of elements only necessary for amplification in prokaryotes, and, as such, are superfluous in the mammalian cell. These problematic elements include antibiotic resistance genes, which can disseminate antibiotic resistance, and CpG motifs, which are inflammatory in animals and can lead to transgene silencing. RESULTS Here, we examined how M13-based phagemids could be improved for transgene delivery by removing the bacterial backbone. A transgene cassette was flanked by isolated initiation and termination elements from the phage origin of replication. Phage proteins provided in trans by a helper would replicate only the cassette, without any bacterial backbone. The rescue efficiency of "miniphagemids" from these split origins was equal to, if not greater than, isogenic "full phagemids" arising from intact origins. The type of cassette encoded by the miniphagemid as well as the choice of host strain constrained the efficiency of phagemid rescue. CONCLUSIONS The use of two separated domains of the f1 ori improves upon a single wildtype origin while still resulting in high titres of miniphagemid gene transfer vectors. Highly pure lysates of miniaturized phagemids could be rapidly obtained in a straightforward procedure without additional downstream processing.
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Affiliation(s)
- Shirley Wong
- School of Pharmacy, University of Waterloo, Waterloo, Canada.
| | - Salma Jimenez
- School of Pharmacy, University of Waterloo, Waterloo, Canada
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Qin G, Wu S, Zhang L, Li Y, Liu C, Yu J, Deng L, Xiao G, Zhang Z. An Efficient Modular Gateway Recombinase-Based Gene Stacking System for Generating Multi-Trait Transgenic Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040488. [PMID: 35214820 PMCID: PMC8879548 DOI: 10.3390/plants11040488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 05/14/2023]
Abstract
Transgenic technology can transfer favorable traits regardless of reproductive isolation and is an important method in plant synthetic biology and genetic improvement. Complex metabolic pathway modification and pyramiding breeding strategies often require the introduction of multiple genes at once, but the current vector assembly systems for constructing multigene expression cassettes are not completely satisfactory. In this study, a new in vitro gene stacking system, GuanNan Stacking (GNS), was developed. Through the introduction of Type IIS restriction enzyme-mediated Golden Gate cloning, GNS allows the modular, standardized assembly of target gene expression cassettes. Because of the introduction of Gateway recombination, GNS facilitates the cloning of superlarge transgene expression cassettes, allows multiple expression cassettes to be efficiently assembled in a binary vector simultaneously, and is compatible with the Cre enzyme-mediated marker deletion mechanism. The linked dual positive-negative marker selection strategy ensures the efficient acquisition of target recombinant plasmids without prokaryotic selection markers in the T-DNA region. The host-independent negative selection marker combined with the TAC backbone ensures the cloning and transfer of large T-DNAs (>100 kb). Using the GNS system, we constructed a binary vector containing five foreign gene expression cassettes and obtained transgenic rice carrying the target traits, proving that the method developed in this research is a powerful tool for plant metabolic engineering and compound trait transgenic breeding.
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Affiliation(s)
- Guannan Qin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suting Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
| | - Liying Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
| | - Yanyao Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunmei Liu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianghui Yu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
| | - Lihua Deng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (G.Q.); (Y.L.); (C.L.); (J.Y.); (L.D.)
| | - Guoying Xiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Correspondence: (G.X.); (Z.Z.)
| | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (L.Z.)
- Correspondence: (G.X.); (Z.Z.)
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