1
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Gorjifard S, Jores T, Tonnies J, Mueth NA, Bubb K, Wrightsman T, Buckler ES, Fields S, Cuperus JT, Queitsch C. Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability. Nat Commun 2024; 15:5868. [PMID: 38997252 PMCID: PMC11245536 DOI: 10.1038/s41467-024-50174-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
The 3' end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plants Arabidopsis thaliana and Zea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conduct in silico evolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.
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Affiliation(s)
- Sayeh Gorjifard
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- Graduate Program in Biology, University of Washington, Seattle, WA, 98195, USA
| | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Kerry Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
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2
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Yaschenko AE, Alonso JM, Stepanova AN. Arabidopsis as a model for translational research. THE PLANT CELL 2024:koae065. [PMID: 38411602 DOI: 10.1093/plcell/koae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage lab and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.
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Affiliation(s)
- Anna E Yaschenko
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
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3
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Gorjifard S, Jores T, Tonnies J, Mueth NA, Bubb K, Wrightsman T, Buckler ES, Fields S, Cuperus JT, Queitsch C. Arabidopsis and Maize Terminator Strength is Determined by GC Content, Polyadenylation Motifs and Cleavage Probability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.16.545379. [PMID: 37398426 PMCID: PMC10312805 DOI: 10.1101/2023.06.16.545379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The 3' end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plants Arabidopsis thaliana and Zea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conduct in silico evolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.
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Affiliation(s)
- Sayeh Gorjifard
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Graduate Program in Biology, University of Washington, Seattle, WA 98195
| | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Kerry Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Department of Medicine, University of Washington, Seattle, WA 98195
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
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4
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Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai CJ, Tuskan GA, Ranney TG, Yang X, Liu W. Plant Promoters and Terminators for High-Precision Bioengineering. BIODESIGN RESEARCH 2023; 5:0013. [PMID: 37849460 PMCID: PMC10328392 DOI: 10.34133/bdr.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 10/19/2023] Open
Abstract
High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.
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Affiliation(s)
- Emily G. Brooks
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Estefania Elorriaga
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James R. Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Jui Tsai
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Thomas G. Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Xiaohan Yang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
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5
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Improvement of recombinant miraculin production in transgenic tomato by crossbreeding-based genetic background modification. Transgenic Res 2022; 31:567-578. [PMID: 35974134 DOI: 10.1007/s11248-022-00320-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/02/2022] [Indexed: 10/15/2022]
Abstract
An important optimization step in plant-based recombinant protein production systems is the selection of an appropriate cultivar after a potential host has been determined. Previously, we have shown that transgenic tomatoes of the variety 'Micro-Tom' accumulate incredibly high levels of miraculin (MIR) due to the introduction of MIR gene controlled by a CaMV35S promoter and a heat-shock protein terminator. However, 'Micro-Tom' is unsuitable for commercial production of MIR as it is a dwarf cultivar characterized by small-sized fruit and poor yield. Here, we used the crossbreeding approach to transfer the high MIR accumulation trait of transgenic 'Micro-Tom' tomatoes to 'Natsunokoma' and 'Aichi First', two commercial cultivars producing medium and large fruit sizes, respectively. Fruits of the resultant crossbred lines were larger (~ 95 times), but their miraculin accumulation levels (~ 1,062 μg/g fresh mass) were comparable to the donor cultivar, indicating that the high miraculin accumulation trait was preserved regardless of fruit size or cultivar. Further, the transferred trait resulted in a 3-4 fold increase in overall miraculin production than that of the previously reported line 5B. These findings demonstrate the effectiveness of crossbreeding in improving MIR production in tomatoes and could pave the way for a more efficient production of recombinant proteins in other plants.
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6
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Imran M, Liu T, Wang Z, Wang M, Liu S, Gao X, Wang A, Liu S, Tian Z, Zhang M. Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:948751. [PMID: 35958213 PMCID: PMC9361848 DOI: 10.3389/fpls.2022.948751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs, that are vital for gene expression regulation in eukaryotes. Whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent, non-overlapping mature miRNAs, we named them nested miRNAs. However, the extent of nested miR159 structural evolutionary conservation and its promoter characterization remains unknown. In this study, the sequence alignment and phylogenetic analysis reveal that the MIR159 family is ancient, and its nested miR159 structures are evolutionary conserved in different plant species. The overexpression of ath-MIR159a, including the 1.2 kb downstream region, has no effect on rescuing the mir159ab phenotype. The promoter truncation results revealed that the 1.0 kb promoter of ath-MIR159a is sufficient for rescuing the mir159ab phenotype. The cis-regulatory elements in the ath-miR159a promoters indicated functions related to different phytohormones, abiotic stresses, and transcriptional activation. While the MybSt1 motif-containing region is not responsible for activating the regulation of the miR159a promoter. The qRT-PCR results showed that overexpression of ath-MIR159a led to high expression levels of miR159a.1-5 and miR159a.1-3 and complemented the growth defect of mir159ab via downregulation of MYB33 and MYB65. Furthermore, continuously higher expression of the miR159a.2 duplex in transgenic lines with the curly leaf phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that it is possible for a miRNA precursor to encode several regulatory small RNAs in plants. Taken together, our study demonstrates that the nested miR159 structure is evolutionary conserved and miRNA-mediated gene regulation is more complex than previously thought.
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Affiliation(s)
- Muhammad Imran
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Tengfei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
| | - Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xinyan Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Anning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Songfeng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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7
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de Felippes FF, Shand K, Waterhouse PM. Identification of a Transferrable Terminator Element That Inhibits Small RNA Production and Improves Transgene Expression Levels. FRONTIERS IN PLANT SCIENCE 2022; 13:877793. [PMID: 35651775 PMCID: PMC9149433 DOI: 10.3389/fpls.2022.877793] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/27/2022] [Indexed: 06/06/2023]
Abstract
The role of terminators is more commonly associated with the polyadenylation and 3' end formation of new transcripts. Recent evidence, however, suggests that this regulatory region can have a dramatic impact on gene expression. Nonetheless, little is known about the molecular mechanisms leading to the improvements associated with terminator usage in plants and the different elements in a plant terminator. Here, we identified an element in the Arabidopsis HSP18.2 terminator (tHSP) to be essential for the high level of expression seen for transgenes under the regulation of this terminator. Our molecular analyses suggest that this newly identified sequence acts to improve transcription termination, leading to fewer read-through events and decreased amounts of small RNAs originating from the transgene. Besides protecting against silencing, the tHSP-derived sequence positively impacts splicing efficiency, helping to promote gene expression. Moreover, we show that this sequence can be used to generate chimeric terminators with enhanced efficiency, resulting in stronger transgene expression and significantly expanding the availability of efficient terminators that can be part of good expression systems. Thus, our data make an important contribution toward a better understanding of plant terminators, with the identification of a new element that has a direct impact on gene expression, and at the same time, creates new possibilities to modulate gene expression via the manipulation of 3' regulatory regions.
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Affiliation(s)
- Felipe Fenselau de Felippes
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council (ARC) Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kylie Shand
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Peter M. Waterhouse
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Research Council (ARC) Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology, Brisbane, QLD, Australia
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8
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Hung YH, Slotkin RK. The initiation of RNA interference (RNAi) in plants. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102014. [PMID: 33657510 DOI: 10.1016/j.pbi.2021.102014] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/19/2021] [Accepted: 01/24/2021] [Indexed: 05/15/2023]
Abstract
When an mRNA enters into the RNA degradation pathway called RNA interference (RNAi), it is cleaved into small interfering RNAs (siRNAs) that then target complementary mRNAs for destruction. The consequence of entry into RNAi is mRNA degradation, post-transcriptional silencing and in some cases transcriptional silencing. RNAi functions as a defense against transposable element and virus activity, and in plants, RNAi additionally plays a role in development by regulating some genes. However, it is unknown how specific transcripts are selected for RNAi, and how most genic mRNAs steer clear. This Current Opinion article explores the key question of how RNAs are selected for entry into RNAi, and proposes models that enable the cell to distinguish between transcripts to translate versus destroy.
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Affiliation(s)
- Yu-Hung Hung
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA; Division of Biological Sciences, University of Missouri-Columbia, 65211, USA.
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9
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Ono A, Hiwasa-Tanase K, Nonaka S, Ezura H. The accumulation of recombinant miraculin is independent of fruit size in tomato. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:161-165. [PMID: 34177337 PMCID: PMC8215467 DOI: 10.5511/plantbiotechnology.20.0904a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/04/2020] [Indexed: 06/13/2023]
Abstract
The taste-modifying protein miraculin (MIR) has received increasing interest as a new low-calorie sweetener. In our previous study using the tomato variety 'Micro-Tom,' it was shown that in transgenic tomatoes in which MIR was expressed by using the cauliflower mosaic virus 35S promoter (p35S) and a heat shock protein terminator (tHSP) cassette (p35S-MIR-tHSP), higher levels of miraculin accumulated than when MIR was driven by the nopaline synthase terminator (tNOS) cassette (p35S-MIR-tNOS). 'Micro-Tom' is a dwarf tomato used for research and shows a low yield. To achieve high productivity of MIR, it is essential to improve the MIR accumulation potential by using high-yielding cultivars. In this study, we evaluate whether the high MIR accumulation trait mediated by the tHSP appears even when fruit size increases. A line in which the p35S-MIR-tHSP cassette was introduced into a high-yielding variety was bred by backcrossing. The line homozygous for MIR showed higher accumulation of MIR than the heterozygous line. Despite large differences in fruit size, the MIR level in the backcross line was similar to that in the p35S-MIR-tHSP line (background 'Micro-Tom'). It was approximately 3.1 times and 4.0 times higher than those in miracle fruits and the p35S-MIR-tNOS tomato line 5B ('Moneymaker' background, which exhibits the highest miraculin productivity achieved thus far), respectively. These results demonstrate that the high MIR accumulation trait mediated by the tHSP appears even when fruit size is increased.
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Affiliation(s)
- Azusa Ono
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kyoko Hiwasa-Tanase
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Satoko Nonaka
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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10
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F de Felippes F, McHale M, Doran RL, Roden S, Eamens AL, Finnegan EJ, Waterhouse PM. The key role of terminators on the expression and post-transcriptional gene silencing of transgenes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:96-112. [PMID: 32603508 DOI: 10.1111/tpj.14907] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/08/2020] [Accepted: 06/17/2020] [Indexed: 05/18/2023]
Abstract
Transgenes have become essential to modern biology, being an important tool in functional genomic studies and also in the development of biotechnological products. One of the major challenges in the generation of transgenic lines concerns the expression of transgenes, which, compared to endogenes, are particularly susceptible to silencing mediated by small RNAs (sRNAs). Several reasons have been put forward to explain why transgenes often trigger the production of sRNAs, such as the high level of expression induced by commonly used strong constitutive promoters, the lack of introns, and features resembling viral and other exogenous sequences. However, the relative contributions of the different genomic elements with respect to protecting genes from the silencing machinery and their molecular mechanisms remain unclear. Here, we present the results of a mutagenesis screen conceived to identify features involved in the protection of endogenes against becoming a template for the production of sRNAs. Interestingly, all of the recovered mutants had alterations in genes with proposed function in transcription termination, suggesting a central role of terminators in this process. Indeed, using a GFP reporter system, we show that, among different genetic elements tested, the terminator sequence had the greatest effect on transgene-derived sRNA accumulation and that a well-defined poly(A) site might be especially important. Finally, we describe an unexpected mechanism, where transgenes containing certain intron/terminator combinations lead to an increase in the production of sRNAs, which appears to interfere with splicing.
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Affiliation(s)
- Felipe F de Felippes
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD, 4000, Australia
| | - Marcus McHale
- Plant Systems Biology Laboratory, Áras de Brún, National University of Ireland Galway (NUIG), Research Road, Galway, H91TK33, Ireland
| | - Rachel L Doran
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD, 4000, Australia
| | - Sally Roden
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD, 4000, Australia
| | - Andrew L Eamens
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - E Jean Finnegan
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD, 4000, Australia
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11
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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12
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de Felippes FF, Waterhouse PM. The Whys and Wherefores of Transitivity in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:579376. [PMID: 32983223 PMCID: PMC7488869 DOI: 10.3389/fpls.2020.579376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/14/2020] [Indexed: 05/05/2023]
Abstract
Transitivity in plants is a mechanism that produces secondary small interfering RNAs (siRNAs) from a transcript targeted by primary small RNAs (sRNAs). It expands the silencing signal to additional sequences of the transcript. The process requires RNA-dependent RNA polymerases (RDRs), which convert single-stranded RNA targets into a double-stranded (ds) RNA, the precursor of siRNAs and is critical for effective and amplified responses to virus infection. It is also important for the production of endogenous secondary siRNAs, such as phased siRNAs (phasiRNAs), which regulate several genes involved in development and adaptation. Transitivity on endogenous transcripts is very specific, utilizing special primary sRNAs, such as miRNAs with unique features, and particular ARGONAUTEs. In contrast, transitivity on transgene and virus (exogenous) transcripts is more generic. This dichotomy of responses implies the existence of a mechanism that differentiates self from non-self targets. In this work, we examine the possible mechanistic process behind the dichotomy and the intriguing counter-intuitive directionality of transitive sequence-spread in plants.
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13
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Nakanishi K, Morikane S, Hosokawa N, Kajihara Y, Kurohane K, Niwa Y, Kobayashi H, Imai Y. Plant-derived secretory component forms secretory IgA with shiga toxin 1-specific dimeric IgA produced by mouse cells and whole plants. PLANT CELL REPORTS 2019; 38:161-172. [PMID: 30506369 DOI: 10.1007/s00299-018-2358-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
A key module, secretory component (SC), was efficiently expressed in Arabidopsis thaliana. The plant-based SC and immunoglobulin A of animal or plant origin formed secretory IgA that maintains antigen-binding activity. Plant expression systems are suitable for scalable and cost-effective production of biologics. Secretory immunoglobulin A (SIgA) will be useful as a therapeutic antibody against mucosal pathogens. SIgA is equipped with a secretory component (SC), which assists the performance of SIgA on the mucosal surface. Here we produced SC using a plant expression system and formed SIgA with dimeric IgAs produced by mouse cells as well as by whole plants. To increase the expression level, an endoplasmic reticulum retention signal peptide, KDEL (Lys-Asp-Glu-Leu), was added to mouse SC (SC-KDEL). The SC-KDEL cDNA was inserted into a binary vector with a translational enhancer and an efficient terminator. The SC-KDEL transgenic Arabidopsis thaliana produced SC-KDEL at the level of 2.7% of total leaf proteins. In vitro reaction of the plant-derived SC-KDEL with mouse dimeric monoclonal IgAs resulted in the formation of SIgA. When reacted with Shiga toxin 1 (Stx1)-specific ones, the antigen-binding activity was maintained. When an A. thaliana plant expressing SC-KDEL was crossed with one expressing dimeric IgA specific for Stx1, the plant-based SIgA exhibited antigen-binding activity. Leaf extracts of the crossbred transgenic plants neutralized Stx1 cytotoxicity against Stx1-sensitive cells. These results suggest that transgenic plants expressing SC-KDEL will provide a versatile means of SIgA production.
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Affiliation(s)
- Katsuhiro Nakanishi
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Shota Morikane
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Nao Hosokawa
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Yuka Kajihara
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Kohta Kurohane
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Yasuo Niwa
- Laboratory of Plant Molecular Improvement, Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Hirokazu Kobayashi
- Laboratory of Plant Molecular Improvement, Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Yasuyuki Imai
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka City, Shizuoka, 422-8526, Japan.
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Tran NHT, Oguchi T, Matsunaga E, Kawaoka A, Watanabe KN, Kikuchi A. Transcriptional enhancement of a bacterial choline oxidase A gene by an HSP terminator improves the glycine betaine production and salinity stress tolerance of Eucalyptus camaldulensis trees. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:215-224. [PMID: 31819726 PMCID: PMC6879367 DOI: 10.5511/plantbiotechnology.18.0510b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
Novel transgenic Eucalyptus camaldulensis trees expressing the bacterial choline oxidase A (codA) gene by the Cauliflower mosaic virus (CaMV) 35S promoter and the Arabidopsis thaliana heat shock protein (HSP) terminator was developed. To evaluate the codA transcription level and the metabolic products and abiotic stress tolerance of the transgenic trees, a six-month semi-confined screen house cultivation trial was conducted under a moderate-stringency salt-stress condition. The transcription level of the CaMV 35S promoter driven-codA was more than fourfold higher, and the content of glycine betaine, the metabolic product of codA, was twofold higher, with the HSP terminator than with the nopaline synthase (NOS) terminator. Moreover, the screen house cultivation revealed that the growth of transgenic trees under the salt stress condition was alleviated in correlation with the glycine betaine concentration. These results suggest that the enhancement of codA transcription by the HSP terminator increased the abiotic stress tolerance of Eucalyptus plantation trees.
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Affiliation(s)
- Ngoc-Ha Thi Tran
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8752, Japan
| | - Taichi Oguchi
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8752, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8752, Japan
| | - Etsuko Matsunaga
- Agri-Biotechnology Research Laboratory, Nippon Paper Industries Co., Ltd., 5-21-1 Oji, Kita Ward, Tokyo 114-0002, Japan
| | - Akiyoshi Kawaoka
- Agri-Biotechnology Research Laboratory, Nippon Paper Industries Co., Ltd., 5-21-1 Oji, Kita Ward, Tokyo 114-0002, Japan
| | - Kazuo N. Watanabe
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8752, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8752, Japan
| | - Akira Kikuchi
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8752, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8752, Japan
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15
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Shinozaki Y, Ezura K, Hu J, Okabe Y, Bénard C, Prodhomme D, Gibon Y, Sun TP, Ezura H, Ariizumi T. Identification and functional study of a mild allele of SlDELLA gene conferring the potential for improved yield in tomato. Sci Rep 2018; 8:12043. [PMID: 30104574 PMCID: PMC6089951 DOI: 10.1038/s41598-018-30502-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022] Open
Abstract
Parthenocarpy, or pollination-independent fruit set, is an attractive trait for fruit production and can be induced by increased responses to the phytohormone gibberellin (GA), which regulates diverse aspects of plant development. GA signaling in plants is negatively regulated by DELLA proteins. A loss-of-function mutant of tomato DELLA (SlDELLA), procera (pro) thus exhibits enhanced GA-response phenotypes including parthenocarpy, although the pro mutation also confers some disadvantages for practical breeding. This study identified a new milder hypomorphic allele of SlDELLA, procera-2 (pro-2), which showed weaker GA-response phenotypes than pro. The pro-2 mutant contains a single nucleotide substitution, corresponding to a single amino acid substitution in the SAW subdomain of the SlDELLA. Accumulation of the mutated SlDELLA transcripts in wild-type (WT) resulted in parthenocarpy, while introduction of intact SlDELLA into pro-2 rescued mutant phenotypes. Yeast two-hybrid assays revealed that SlDELLA interacted with three tomato homologues of GID1 GA receptors with increasing affinity upon GA treatment, while their interactions were reduced by the pro and pro-2 mutations. Both pro and pro-2 mutants produced higher fruit yields under high temperature conditions, which were resulted from higher fruit set efficiency, demonstrating the potential for genetic parthenocarpy to improve yield under adverse environmental conditions.
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Affiliation(s)
- Yoshihito Shinozaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Research Fellow of Japan Society for Promotion of Science (JSPS), Kojimachi, Tokyo, 102-0083, Japan
| | - Kentaro Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Research Fellow of Japan Society for Promotion of Science (JSPS), Kojimachi, Tokyo, 102-0083, Japan
| | - Jianhong Hu
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Yoshihiro Okabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Camille Bénard
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ, Bordeaux, Villenave d'Ornon, F-33883, France
| | - Duyen Prodhomme
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ, Bordeaux, Villenave d'Ornon, F-33883, France
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ, Bordeaux, Villenave d'Ornon, F-33883, France
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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16
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Castiglia D, Leone S, Tamburino R, Sannino L, Fonderico J, Melchiorre C, Carpentieri A, Grillo S, Picone D, Scotti N. High-level production of single chain monellin mutants with enhanced sweetness and stability in tobacco chloroplasts. PLANTA 2018; 248:465-476. [PMID: 29777363 DOI: 10.1007/s00425-018-2920-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
MAIN CONCLUSION Plastid-based MNEI protein mutants retain the structure, stability and sweetness of their bacterial counterparts, confirming the attractiveness of the plastid transformation technology for high-yield production of recombinant proteins. The prevalence of obesity and diabetes has dramatically increased the industrial demand for the development and use of alternatives to sugar and traditional sweeteners. Sweet proteins, such as MNEI, a single chain derivative of monellin, are the most promising candidates for industrial applications. In this work, we describe the use of tobacco chloroplasts as a stable plant expression platform to produce three MNEI protein mutants with improved taste profile and stability. All plant-based proteins were correctly expressed in tobacco chloroplasts, purified and subjected to in-depth chemical and sensory analyses. Recombinant MNEI mutants showed a protein yield ranging from 5% to more than 50% of total soluble proteins, which, to date, represents the highest accumulation level of MNEI mutants in plants. Comparative analyses demonstrated the high similarity, in terms of structure, stability and function, of the proteins produced in plant chloroplasts and bacteria. The high yield and the extreme sweetness perceived for the plant-derived proteins prove that plastid transformation technology is a safe, stable and cost-effective production platform for low-calorie sweeteners, with an estimated production of up to 25-30 mg of pure protein/plant.
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Affiliation(s)
- Daniela Castiglia
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Portici, NA, Italy
| | - Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Portici, NA, Italy
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Portici, NA, Italy
| | - Jole Fonderico
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Chiara Melchiorre
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Andrea Carpentieri
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Stefania Grillo
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Portici, NA, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Portici, NA, Italy.
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17
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Yamamoto T, Hoshikawa K, Ezura K, Okazawa R, Fujita S, Takaoka M, Mason HS, Ezura H, Miura K. Improvement of the transient expression system for production of recombinant proteins in plants. Sci Rep 2018; 8:4755. [PMID: 29555968 PMCID: PMC5859073 DOI: 10.1038/s41598-018-23024-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/30/2018] [Indexed: 01/24/2023] Open
Abstract
An efficient and high yielding expression system is required to produce recombinant proteins. Furthermore, the transient expression system can be used to identify the localization of proteins in plant cells. In this study, we demonstrated that combination of a geminiviral replication and a double terminator dramatically enhanced the transient protein expression level in plants. The GFP protein was expressed transiently in lettuce, Nicotiana benthamiana, tomatoes, eggplants, hot peppers, melons, and orchids with agroinfiltration. Compared to a single terminator, a double terminator enhanced the expression level. A heat shock protein terminator combined with an extensin terminator resulted in the highest protein expression. Transiently expressed GFP was confirmed by immunoblot analysis with anti-GFP antibodies. Quantitative analysis revealed that the geminiviral vector with a double terminator resulted in the expression of at least 3.7 mg/g fresh weight of GFP in Nicotiana benthamiana, approximately 2-fold that of the geminiviral vector with a single terminator. These results indicated that combination of the geminiviral replication and a double terminator is a useful tool for transient expression of the gene of interest in plant cells.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Ken Hoshikawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kentaro Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Risa Okazawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Satoshi Fujita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Miyo Takaoka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Hugh S Mason
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute at Arizona State University, Tempe, AZ, 85287, USA
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
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18
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Takayama M, Matsukura C, Ariizumi T, Ezura H. Activating glutamate decarboxylase activity by removing the autoinhibitory domain leads to hyper γ-aminobutyric acid (GABA) accumulation in tomato fruit. PLANT CELL REPORTS 2017; 36:103-116. [PMID: 27704232 DOI: 10.1007/s00299-016-2061-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/26/2016] [Indexed: 05/05/2023]
Abstract
The C-terminal extension region of SlGAD3 is likely involved in autoinhibition, and removing this domain increases GABA levels in tomato fruits. γ-Aminobutyric acid (GABA) is a ubiquitous non-protein amino acid with several health-promoting benefits. In many plants including tomato, GABA is synthesized via decarboxylation of glutamate in a reaction catalyzed by glutamate decarboxylase (GAD), which generally contains a C-terminal autoinhibitory domain. We previously generated transgenic tomato plants in which tomato GAD3 (SlGAD3) was expressed using the 35S promoter/NOS terminator expression cassette (35S-SlGAD3-NOS), yielding a four- to fivefold increase in GABA levels in red-ripe fruits compared to the control. In this study, to further increase GABA accumulation in tomato fruits, we expressed SlGAD3 with (SlGAD3 OX ) or without (SlGAD3ΔC OX ) a putative autoinhibitory domain in tomato using the fruit ripening-specific E8 promoter and the Arabidopsis heat shock protein 18.2 (HSP) terminator. Although the GABA levels in SlGAD3 OX fruits were equivalent to those in 35S-SlGAD3-NOS fruits, GABA levels in SlGAD3ΔC OX fruits increased by 11- to 18-fold compared to control plants, indicating that removing the autoinhibitory domain increases GABA biosynthesis activity. Furthermore, the increased GABA levels were accompanied by a drastic reduction in glutamate and aspartate levels, indicating that enhanced GABA biosynthesis affects amino acid metabolism in ripe-fruits. Moreover, SlGAD3ΔC OX fruits exhibited an orange-ripe phenotype, which was associated with reduced levels of both carotenoid and mRNA transcripts of ethylene-responsive carotenogenic genes, suggesting that over activation of GAD influences ethylene sensitivity. Our strategy utilizing the E8 promoter and HSP terminator expression cassette, together with SlGAD3 C-terminal deletion, would facilitate the production of tomato fruits with increased GABA levels.
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Affiliation(s)
- Mariko Takayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Chiaki Matsukura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan.
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19
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Hiwasa-Tanase K, Ezura H. Molecular Breeding to Create Optimized Crops: From Genetic Manipulation to Potential Applications in Plant Factories. FRONTIERS IN PLANT SCIENCE 2016; 7:539. [PMID: 27200016 PMCID: PMC4842755 DOI: 10.3389/fpls.2016.00539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
Crop cultivation in controlled environment plant factories offers great potential to stabilize the yield and quality of agricultural products. However, many crops are currently unsuited to these environments, particularly closed cultivation systems, due to space limitations, low light intensity, high implementation costs, and high energy requirements. A major barrier to closed system cultivation is the high running cost, which necessitates the use of high-margin crops for economic viability. High-value crops include those with enhanced nutritional value or containing additional functional components for pharmaceutical production or with the aim of providing health benefits. In addition, it is important to develop cultivars equipped with growth parameters that are suitable for closed cultivation. Small plant size is of particular importance due to the limited cultivation space. Other advantageous traits are short production cycle, the ability to grow under low light, and high nutriculture availability. Cost-effectiveness is improved from the use of cultivars that are specifically optimized for closed system cultivation. This review describes the features of closed cultivation systems and the potential application of molecular breeding to create crops that are optimized for cost-effectiveness and productivity in closed cultivation systems.
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20
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Takayama M, Koike S, Kusano M, Matsukura C, Saito K, Ariizumi T, Ezura H. Tomato Glutamate Decarboxylase Genes SlGAD2 and SlGAD3 Play Key Roles in Regulating γ-Aminobutyric Acid Levels in Tomato (Solanum lycopersicum). PLANT & CELL PHYSIOLOGY 2015; 56:1533-45. [PMID: 26009591 DOI: 10.1093/pcp/pcv075] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 05/19/2015] [Indexed: 05/21/2023]
Abstract
Tomato (Solanum lycopersicum) can accumulate relatively high levels of γ-aminobutyric acid (GABA) during fruit development. However, the molecular mechanism underlying GABA accumulation and its physiological function in tomato fruits remain elusive. We previously identified three tomato genes (SlGAD1, SlGAD2 and SlGAD3) encoding glutamate decarboxylase (GAD), likely the key enzyme for GABA biosynthesis in tomato fruits. In this study, we generated transgenic tomato plants in which each SlGAD was suppressed and those in which all three SlGADs were simultaneously suppressed. A significant decrease in GABA levels, i.e. 50-81% compared with wild-type (WT) levels, was observed in mature green (MG) fruits of the SlGAD2-suppressed lines, while a more drastic reduction (up to <10% of WT levels) was observed in the SlGAD3- and triple SlGAD-suppressed lines. These findings suggest that both SlGAD2 and SlGAD3 expression are crucial for GABA biosynthesis in tomato fruits. The importance of SlGAD3 expression was also confirmed by generating transgenic tomato plants that over-expressed SlGAD3. The MG and red fruits of the over-expressing transgenic lines contained higher levels of GABA (2.7- to 5.2-fold) than those of the WT. We also determined that strong down-regulation of the SlGADs had little effect on overall plant growth, fruit development or primary fruit metabolism under normal growth conditions.
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Affiliation(s)
- Mariko Takayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Satoshi Koike
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Miyako Kusano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Chiaki Matsukura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan Graduate School of Pharmaceutical Sciences, Chiba University, Chiba-shi, Chiba 260-0856, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Kurokawa N, Hirai T, Takayama M, Hiwasa-Tanase K, Ezura H. An E8 promoter-HSP terminator cassette promotes the high-level accumulation of recombinant protein predominantly in transgenic tomato fruits: a case study of miraculin. PLANT CELL REPORTS 2013; 32:529-36. [PMID: 23306632 DOI: 10.1007/s00299-013-1384-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 12/21/2012] [Accepted: 01/02/2013] [Indexed: 05/24/2023]
Abstract
The E8 promoter-HSP terminator expression cassette is a powerful tool for increasing the accumulation of recombinant protein in a ripening tomato fruit. Strong, tissue-specific transgene expression is a desirable feature in transgenic plants to allow the production of variable recombinant proteins. The expression vector is a key tool to control the expression level and site of transgene and recombinant protein expression in transgenic plants. The combination of the E8 promoter, a fruit-ripening specific promoter, and a heat shock protein (HSP) terminator, derived from heat shock protein 18.2 of Arabidopsis thaliana, produces the strong and fruit-specific accumulation of recombinant miraculin in transgenic tomato. Miraculin gene expression was driven by an E8 promoter and HSP terminator cassette (E8-MIR-HSP) in transgenic tomato plants, and the miraculin concentration was the highest in the ripening fruits, representing 30-630 μg miraculin of the gram fresh weight. The highest level of miraculin concentration among the transgenic tomato plant lines containing the E8-MIR-HSP cassette was approximately four times higher than those observed in a previous study using a constitutive 35S promoter and NOS terminator cassette (Hiwasa-Tanase et al. in Plant Cell Rep 30:113-124, 2011). These results demonstrate that the combination of the E8 promoter and HSP terminator cassette is a useful tool to increase markedly the accumulation of recombinant proteins in a ripening fruit-specific manner.
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Affiliation(s)
- Natsuko Kurokawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
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22
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Hiwasa-Tanase K, Hirai T, Kato K, Duhita N, Ezura H. From miracle fruit to transgenic tomato: mass production of the taste-modifying protein miraculin in transgenic plants. PLANT CELL REPORTS 2012; 31:513-25. [PMID: 22160133 DOI: 10.1007/s00299-011-1197-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/22/2011] [Accepted: 11/22/2011] [Indexed: 05/05/2023]
Abstract
The utility of plants as biofactories has progressed in recent years. Some recombinant plant-derived pharmaceutical products have already reached the marketplace. However, with the exception of drugs and vaccines, a strong effort has not yet been made to bring recombinant products to market, as cost-effectiveness is critically important for commercialization. Sweet-tasting proteins and taste-modifying proteins have a great deal of potential in industry as substitutes for sugars and as artificial sweeteners. The taste-modifying protein, miraculin, functions to change the perception of a sour taste to a sweet one. This taste-modifying function can potentially be used not only as a low-calorie sweetener but also as a new seasoning that could be the basis of a new dietary lifestyle. However, miraculin is far from inexpensive, and its potential as a marketable product has not yet been fully developed. For the last several years, biotechnological production of this taste-modifying protein has progressed extensively. In this review, the characteristics of miraculin and recent advances in its production using transgenic plants are summarized, focusing on such topics as the suitability of plant species as expression hosts, the cultivation method for transgenic plants, the method of purifying miraculin and future advances required to achieve industrial use.
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Affiliation(s)
- Kyoko Hiwasa-Tanase
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
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