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Laspisa D, Illa-Berenguer E, Bang S, Schmitz RJ, Parrott W, Wallace J. Mining the Utricularia gibba genome for insulator-like elements for genetic engineering. FRONTIERS IN PLANT SCIENCE 2023; 14:1279231. [PMID: 38023853 PMCID: PMC10663240 DOI: 10.3389/fpls.2023.1279231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Introduction Gene expression is often controlled via cis-regulatory elements (CREs) that modulate the production of transcripts. For multi-gene genetic engineering and synthetic biology, precise control of transcription is crucial, both to insulate the transgenes from unwanted native regulation and to prevent readthrough or cross-regulation of transgenes within a multi-gene cassette. To prevent this activity, insulator-like elements, more properly referred to as transcriptional blockers, could be inserted to separate the transgenes so that they are independently regulated. However, only a few validated insulator-like elements are available for plants, and they tend to be larger than ideal. Methods To identify additional potential insulator-like sequences, we conducted a genome-wide analysis of Utricularia gibba (humped bladderwort), one of the smallest known plant genomes, with genes that are naturally close together. The 10 best insulator-like candidates were evaluated in vivo for insulator-like activity. Results We identified a total of 4,656 intergenic regions with expression profiles suggesting insulator-like activity. Comparisons of these regions across 45 other plant species (representing Monocots, Asterids, and Rosids) show low levels of syntenic conservation of these regions. Genome-wide analysis of unmethylated regions (UMRs) indicates ~87% of the targeted regions are unmethylated; however, interpretation of this is complicated because U. gibba has remarkably low levels of methylation across the genome, so that large UMRs frequently extend over multiple genes and intergenic spaces. We also could not identify any conserved motifs among our selected intergenic regions or shared with existing insulator-like elements for plants. Despite this lack of conservation, however, testing of 10 selected intergenic regions for insulator-like activity found two elements on par with a previously published element (EXOB) while being significantly smaller. Discussion Given the small number of insulator-like elements currently available for plants, our results make a significant addition to available tools. The high hit rate (2 out of 10) also implies that more useful sequences are likely present in our selected intergenic regions; additional validation work will be required to identify which will be most useful for plant genetic engineering.
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Affiliation(s)
- Daniel Laspisa
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Sohyun Bang
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Jason Wallace
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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Kurbidaeva A, Purugganan M. Insulators in Plants: Progress and Open Questions. Genes (Basel) 2021; 12:genes12091422. [PMID: 34573404 PMCID: PMC8470105 DOI: 10.3390/genes12091422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
The genomes of higher eukaryotes are partitioned into topologically associated domains or TADs, and insulators (also known as boundary elements) are the key elements responsible for their formation and maintenance. Insulators were first identified and extensively studied in Drosophila as well as mammalian genomes, and have also been described in yeast and plants. In addition, many insulator proteins are known in Drosophila, and some have been investigated in mammals. However, much less is known about this important class of non-coding DNA elements in plant genomes. In this review, we take a detailed look at known plant insulators across different species and provide an overview of potential determinants of plant insulator functions, including cis-elements and boundary proteins. We also discuss methods previously used in attempts to identify plant insulators, provide a perspective on their importance for research and biotechnology, and discuss areas of potential future research.
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Zhao Y, Kim JY, Karan R, Jung JH, Pathak B, Williamson B, Kannan B, Wang D, Fan C, Yu W, Dong S, Srivastava V, Altpeter F. Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane. PLANT MOLECULAR BIOLOGY 2019; 100:247-263. [PMID: 30919152 DOI: 10.1007/s11103-019-00856-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/15/2019] [Indexed: 05/23/2023]
Abstract
A selectable marker free, highly expressed single copy locus flanked by insulators was created as landing pad for transgene stacking in sugarcane. These events displayed superior transgene expression compared to single-copy transgenic lines lacking insulators. Excision of the selectable marker gene from transgenic sugarcane lines was supported by FLPe/FRT site-specific recombination. Sugarcane, a tropical C4 grass in the genus Saccharum (Poaceae), accounts for nearly 80% of sugar produced worldwide and is also an important feedstock for biofuel production. Generating transgenic sugarcane with predictable and stable transgene expression is critical for crop improvement. In this study, we generated a highly expressed single copy locus as landing pad for transgene stacking. Transgenic sugarcane lines with stable integration of a single copy nptII expression cassette flanked by insulators supported higher transgene expression along with reduced line to line variation when compared to single copy events without insulators by NPTII ELISA analysis. Subsequently, the nptII selectable marker gene was efficiently excised from the sugarcane genome by the FLPe/FRT site-specific recombination system to create selectable marker free plants. This study provides valuable resources for future gene stacking using site-specific recombination or genome editing tools.
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Affiliation(s)
- Yang Zhao
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Jae Y Kim
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Ratna Karan
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Je H Jung
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
- Smart Farm Research Center, Institute of Natural Products, Korea Institute of Science and Technology (KIST), Gangwon-do, 25451, Republic of Korea
| | - Bhuvan Pathak
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Bruce Williamson
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Baskaran Kannan
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Duoduo Wang
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Chunyang Fan
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Wenjin Yu
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Shujie Dong
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Vibha Srivastava
- Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Fredy Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Florida - IFAS, Gainesville, FL, 32611, USA.
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Oliver KR, McComb JA, Greene WK. Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol 2014; 5:1886-901. [PMID: 24065734 PMCID: PMC3814199 DOI: 10.1093/gbe/evt141] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin's "abominable mystery": the spectacular success of the angiosperms.
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Affiliation(s)
- Keith R Oliver
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
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Petolino JF, Davies JP. Designed transcriptional regulators for trait development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 201-202:128-36. [PMID: 23352411 DOI: 10.1016/j.plantsci.2012.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 12/05/2012] [Accepted: 12/07/2012] [Indexed: 05/21/2023]
Abstract
Development is largely controlled by proteins that regulate gene expression at the level of transcription. These regulatory proteins, the genes that control them, and the genes that they control, are organized in a hierarchical structure of complex interactions. Altering the expression of genes encoding regulatory proteins controlling critical nodes in this hierarchy has potential for dramatic phenotypic modification. Constitutive over-expression of genes encoding regulatory proteins in transgenic plants has resulted in agronomically interesting phenotypes along with developmental abnormalities. For trait development, the magnitude and timing of expression of genes encoding key regulatory proteins will need to be precisely controlled and targeted to specific cells and tissues at certain developmental timepoints. Such control is made possible by designed transcriptional regulators which are fusions of engineered DNA binding proteins and activator or repressor domains. Expression of genes encoding such designed transcriptional regulators enable the selective modulation of endogenous gene expression. Genes encoding proteins controlling regulatory networks are prime targets for up- or down-regulation via such designed transcriptional regulators.
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MESH Headings
- Adaptation, Physiological
- Crops, Agricultural/genetics
- Crops, Agricultural/metabolism
- Crops, Agricultural/physiology
- DNA, Plant/genetics
- DNA, Plant/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Droughts
- Gene Expression Regulation, Plant
- Genes, Plant
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Plants, Genetically Modified/physiology
- Protein Interaction Mapping
- Protein Structure, Tertiary
- Regulatory Elements, Transcriptional
- Regulatory Sequences, Nucleic Acid
- Temperature
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptional Activation
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Chénais B, Caruso A, Hiard S, Casse N. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene 2012; 509:7-15. [PMID: 22921893 DOI: 10.1016/j.gene.2012.07.042] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 07/16/2012] [Accepted: 07/25/2012] [Indexed: 11/25/2022]
Abstract
Transposable elements (TEs) are present in roughly all genomes. These mobile DNA sequences are able to invade genomes and their impact on genome evolution is substantial. The mobility of TEs can induce the appearance of deleterious mutations, gene disruption and chromosome rearrangements, but transposition activity also has positive aspects and the mutational activities of TEs contribute to the genetic diversity of organisms. This short review aims to give a brief overview of the impact TEs may have on animal and plant genome structure and expression, and the relationship between TEs and the stress response of organisms, including insecticide resistance.
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Affiliation(s)
- Benoît Chénais
- Université du Maine, EA2160 Mer Molécules Santé, UFR Sciences et Techniques, Avenue Olivier Messiaen, F-72085 Le Mans, France.
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Faizal A, Geelen D. Agroinfiltration of intact leaves as a method for the transient and stable transformation of saponin producing Maesa lanceolata. PLANT CELL REPORTS 2012; 31:1517-1526. [PMID: 22534683 DOI: 10.1007/s00299-012-1266-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/05/2012] [Accepted: 04/10/2012] [Indexed: 05/31/2023]
Abstract
UNLABELLED A method has been developed to genetically transform the medicinal plant Maesa lanceolata. Initially, we tested conditions for transient expression of GFP-bearing constructs in agroinfiltrated leaves. Leaf tissues of M. lanceolata were infiltrated with Agrobacterium tumefaciens carrying a nuclear-targeted GFP construct to allow the quantification of the transformation efficiency. The number of transfected cells was depended on the bacterial density, bacterial strains, the co-cultivation time, and presence of acetosyringone. The transient transformation assay generated the highest ratio of transfected cells over non-transfected cells upon 5 days post-infiltration using A. tumefaciens strain LBA4404 at an OD₆₀₀ = 1.0 in the presence of 100 μM acetosyringone and in the absence of a viral suppressor construct. In a second series of experiments we set up a stable transformation protocol that resulted in the regeneration of kanamycin-resistant plants expressing nuclear GFP. This transformation protocol will be used to introduce overexpression and RNAi constructs into M. lanceolata plants that may interfere with triterpenoid saponin biosynthesis. KEY MESSAGE We have developed a transformation protocol for saponin producing Maesa lanceolata. Using the protocol reported here, now we are able to generate the tools for the modification of saponin production.
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Affiliation(s)
- Ahmad Faizal
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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