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Yang Y, Shao Y, Chaffin TA, Lee JH, Poindexter MR, Ahkami AH, Blumwald E, Stewart CN. Performance of abiotic stress-inducible synthetic promoters in genetically engineered hybrid poplar ( Populus tremula × Populus alba). Front Plant Sci 2022; 13:1011939. [PMID: 36330242 PMCID: PMC9623294 DOI: 10.3389/fpls.2022.1011939] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/28/2022] [Indexed: 05/27/2023]
Abstract
Abiotic stresses can cause significant damage to plants. For sustainable bioenergy crop production, it is critical to generate resistant crops to such stress. Engineering promoters to control the precise expression of stress resistance genes is a very effective way to address the problem. Here we developed stably transformed Populus tremula × Populus alba hybrid poplar (INRA 717-1B4) containing one-of-six synthetic drought stress-inducible promoters (SDs; SD9-1, SD9-2, SD9-3, SD13-1, SD18-1, and SD18-3) identified previously by transient transformation assays. We screened green fluorescent protein (GFP) induction in poplar under osmotic stress conditions. Of six transgenic lines containing synthetic promoter, three lines (SD18-1, 9-2, and 9-3) had significant GFP expression in both salt and osmotic stress treatments. Each synthetic promoter employed heptamerized repeats of specific and short cis-regulatory elements (7 repeats of 7-8 bases). To verify whether the repeats of longer sequences can improve osmotic stress responsiveness, a transgenic poplar containing the synthetic promoter of the heptamerized entire SD9 motif (20 bases, containing all partial SD9 motifs) was generated and measured for GFP induction under osmotic stress. The heptamerized entire SD9 motif did not result in higher GFP expression than the shorter promoters consisting of heptamerized SD9-1, 9-2, and 9-3 (partial SD9) motifs. This result indicates that shorter synthetic promoters (~50 bp) can be used for versatile control of gene expression in transgenic poplar. These synthetic promoters will be useful tools to engineer stress-resilient bioenergy tree crops in the future.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Yuanhua Shao
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Timothy A. Chaffin
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Jun Hyung Lee
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Magen R. Poindexter
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - C. Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Plant Sciences, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
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Yang Y, Lee JH, Poindexter MR, Shao Y, Liu W, Lenaghan SC, Ahkami AH, Blumwald E, Stewart CN. Rational design and testing of abiotic stress-inducible synthetic promoters from poplar cis-regulatory elements. Plant Biotechnol J 2021; 19:1354-1369. [PMID: 33471413 PMCID: PMC8313130 DOI: 10.1111/pbi.13550] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/31/2020] [Accepted: 01/09/2021] [Indexed: 05/27/2023]
Abstract
Abiotic stress resistance traits may be especially crucial for sustainable production of bioenergy tree crops. Here, we show the performance of a set of rationally designed osmotic-related and salt stress-inducible synthetic promoters for use in hybrid poplar. De novo motif-detecting algorithms yielded 30 water-deficit (SD) and 34 salt stress (SS) candidate DNA motifs from relevant poplar transcriptomes. We selected three conserved water-deficit stress motifs (SD18, SD13 and SD9) found in 16 co-expressed gene promoters, and we discovered a well-conserved motif for salt response (SS16). We characterized several native poplar stress-inducible promoters to enable comparisons with our synthetic promoters. Fifteen synthetic promoters were designed using various SD and SS subdomains, in which heptameric repeats of five-to-eight subdomain bases were fused to a common core promoter downstream, which, in turn, drove a green fluorescent protein (GFP) gene for reporter assays. These 15 synthetic promoters were screened by transient expression assays in poplar leaf mesophyll protoplasts and agroinfiltrated Nicotiana benthamiana leaves under osmotic stress conditions. Twelve synthetic promoters were induced in transient expression assays with a GFP readout. Of these, five promoters (SD18-1, SD9-2, SS16-1, SS16-2 and SS16-3) endowed higher inducibility under osmotic stress conditions than native promoters. These five synthetic promoters were stably transformed into Arabidopsis thaliana to study inducibility in whole plants. Herein, SD18-1 and SD9-2 were induced by water-deficit stress, whereas SS16-1, SS16-2 and SS16-3 were induced by salt stress. The synthetic biology design pipeline resulted in five synthetic promoters that outperformed endogenous promoters in transgenic plants.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Jun Hyung Lee
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Magen R. Poindexter
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Yuanhua Shao
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Wusheng Liu
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Department of Horticultural ScienceNorth Carolina State UniversityRaleighNCUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL)Pacific Northwest National Laboratory (PNNL)RichlandWAUSA
| | | | - Charles Neal Stewart
- Center for Agricultural Synthetic BiologyUniversity of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
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Rigoulot SB, Schimel TM, Lee JH, Sears RG, Brabazon H, Layton JS, Li L, Meier KA, Poindexter MR, Schmid MJ, Seaberry EM, Brabazon JW, Madajian JA, Finander MJ, DiBenedetto J, Occhialini A, Lenaghan SC, Stewart CN. Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants. Plant Biotechnol J 2021; 19:830-843. [PMID: 33179383 PMCID: PMC8051605 DOI: 10.1111/pbi.13510] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/31/2020] [Indexed: 05/24/2023]
Abstract
Reverse genetics approaches have revolutionized plant biology and agriculture. Phenomics has the prospect of bridging plant phenotypes with genes, including transgenes, to transform agricultural fields. Genetically encoded fluorescent proteins (FPs) have revolutionized plant biology paradigms in gene expression, protein trafficking and plant physiology. While the first instance of plant canopy imaging of green fluorescent protein (GFP) was performed over 25 years ago, modern phenomics has largely ignored fluorescence as a transgene expression device despite the burgeoning FP colour palette available to plant biologists. Here, we show a new platform for stand-off imaging of plant canopies expressing a wide variety of FP genes. The platform-the fluorescence-inducing laser projector (FILP)-uses an ultra-low-noise camera to image a scene illuminated by compact diode lasers of various colours, coupled with emission filters to resolve individual FPs, to phenotype transgenic plants expressing FP genes. Each of the 20 FPs screened in plants were imaged at >3 m using FILP in a laboratory-based laser range. We also show that pairs of co-expressed fluorescence proteins can be imaged in canopies. The FILP system enabled a rapid synthetic promoter screen: starting from 2000 synthetic promoters transfected into protoplasts to FILP-imaged agroinfiltrated Nicotiana benthamiana plants in a matter of weeks, which was useful to characterize a water stress-inducible synthetic promoter. FILP canopy imaging was also accomplished for stably transformed GFP potato and in a split-GFP assay, which illustrates the flexibility of the instrument for analysing fluorescence signals in plant canopies.
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Affiliation(s)
- Stephen B. Rigoulot
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Tayler M. Schimel
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of MechanicalAerospace and Biomedical EngineeringUniversity of TennesseeKnoxvilleTNUSA
| | - Jun Hyung Lee
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Robert G. Sears
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Holly Brabazon
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Brabazon AppsKnoxvilleTNUSA
| | - Jessica S. Layton
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Li Li
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Kerry A. Meier
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Magen R. Poindexter
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Manuel J. Schmid
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Erin M. Seaberry
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | | | - Jonathan A. Madajian
- Mission Support and Test Services Special Technology LaboratorySanta BarbaraCAUSA
| | | | - John DiBenedetto
- Mission Support and Test Services Special Technology LaboratorySanta BarbaraCAUSA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - C. Neal Stewart
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
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Lee JH, Mazarei M, Pfotenhauer AC, Dorrough AB, Poindexter MR, Hewezi T, Lenaghan SC, Graham DE, Stewart CN. Epigenetic Footprints of CRISPR/Cas9-Mediated Genome Editing in Plants. Front Plant Sci 2020; 10:1720. [PMID: 32117329 PMCID: PMC7026911 DOI: 10.3389/fpls.2019.01720] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/06/2019] [Indexed: 05/19/2023]
Abstract
CRISPR/Cas9 has been widely applied to various plant species accelerating the pace of plant genome editing and precision breeding in crops. Unintended effects beyond off-target nucleotide mutations are still somewhat unexplored. We investigated the degree and patterns of epigenetic changes after gene editing. We examined changes in DNA methylation in genome-edited promoters of naturally hypermethylated genes (AT1G72350 and AT1G09970) and hypomethylated genes (AT3G17320 and AT5G28770) from Arabidopsis. Transgenic plants were developed via Agrobacterium-mediated floral dip transformation. Homozygous edited lines were selected from segregated T2 plants by an in vitro digestion assay using ribonucleoprotein complex. Bisulfite sequencing comparisons were made between paired groups of edited and non-edited plants to identify changes in DNA methylation of the targeted loci. We found that directed mutagenesis via CRISPR/Cas9 resulted in no unintended morphological or epigenetic alterations. Phenotypes of wild-type, transgenic empty vector, and transgenic edited plants were similar. Epigenetic profiles revealed that methylation patterns of promoter regions flanking target sequences were identical among wild-type, transgenic empty vector, and transgenic edited plants. There was no effect of mutation type on epigenetic status. We also evaluated off-target mutagenesis effects in the edited plants. Potential off-target sites containing up to 4-bp mismatch of each target were sequenced. No off-target mutations were detected in candidate sites. Our results showed that CRISPR/Cas9 did not leave an epigenetic footprint on either the immediate gene-edited DNA and flanking DNA or introduce off-target mutations.
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Affiliation(s)
- Jun Hyung Lee
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Alexander C. Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Food Science, University of Tennessee, Knoxville, TN, United States
| | - Aubrey B. Dorrough
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Magen R. Poindexter
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Department of Food Science, University of Tennessee, Knoxville, TN, United States
| | - David E. Graham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
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Persad R, Reuter DN, Dice LT, Nguyen MA, Rigoulot SB, Layton JS, Schmid MJ, Poindexter MR, Occhialini A, Stewart CN, Lenaghan SC. The Q-System as a Synthetic Transcriptional Regulator in Plants. Front Plant Sci 2020; 11:245. [PMID: 32218793 PMCID: PMC7078239 DOI: 10.3389/fpls.2020.00245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/17/2020] [Indexed: 05/07/2023]
Abstract
A primary focus of the rapidly growing field of plant synthetic biology is to develop technologies to precisely regulate gene expression and engineer complex genetic circuits into plant chassis. At present, there are few orthogonal tools available for effectively controlling gene expression in plants, with most researchers instead using a limited set of viral elements or truncated native promoters. A powerful repressible-and engineerable-binary system that has been repurposed in a variety of eukaryotic systems is the Q-system from Neurospora crassa. Here, we demonstrate the functionality of the Q-system in plants through transient expression in soybean (Glycine max) protoplasts and agroinfiltration in Nicotiana benthamiana leaves. Further, using functional variants of the QF transcriptional activator, it was possible to modulate the expression of reporter genes and to fully suppress the system through expression of the QS repressor. As a potential application for plant-based biosensors (phytosensors), we demonstrated the ability of the Q-system to amplify the signal from a weak promoter, enabling remote detection of a fluorescent reporter that was previously undetectable. In addition, we demonstrated that it was possible to coordinate the expression of multiple genes through the expression of a single QF activator. Based on the results from this study, the Q-system represents a powerful orthogonal tool for precise control of gene expression in plants, with envisioned applications in metabolic engineering, phytosensors, and biotic and abiotic stress tolerance.
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Affiliation(s)
- Ramona Persad
- Department of Food Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - D. Nikki Reuter
- Department of Food Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lezlee T. Dice
- Department of Food Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mary-Anne Nguyen
- Department of Food Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Stephen B. Rigoulot
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jessica S. Layton
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Manuel J. Schmid
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Magen R. Poindexter
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Alessandro Occhialini
- Department of Food Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - C. Neal Stewart
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Scott C. Lenaghan
- Department of Food Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- *Correspondence: Scott C. Lenaghan,
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